diff options
| author | Mark H Weaver <mhw@netris.org> | 2017-08-06 00:23:20 -0400 |
|---|---|---|
| committer | Mark H Weaver <mhw@netris.org> | 2017-08-06 00:23:20 -0400 |
| commit | f167595ba1a4e0e419adc17de6af275bedf32822 (patch) | |
| tree | 6a582fbda8ad9d72962359add99e5ae219dd030d /gnu | |
| parent | e3df6938acc2ba2d2f7333d911b8bdc3697f0f75 (diff) | |
| parent | 01a61d7040b1794f36547b107abce6e967d59f21 (diff) | |
| download | guix-f167595ba1a4e0e419adc17de6af275bedf32822.tar guix-f167595ba1a4e0e419adc17de6af275bedf32822.tar.gz | |
Merge branch 'master' into core-updates
Diffstat (limited to 'gnu')
45 files changed, 2289 insertions, 381 deletions
diff --git a/gnu/bootloader/grub.scm b/gnu/bootloader/grub.scm index 3a3456ca46..ef62fe059b 100644 --- a/gnu/bootloader/grub.scm +++ b/gnu/bootloader/grub.scm @@ -55,6 +55,7 @@ grub-bootloader grub-efi-bootloader + grub-mkrescue-bootloader grub-configuration)) @@ -410,6 +411,11 @@ submenu \"GNU system, old configurations...\" {~%") (name 'grub-efi) (package grub-efi))) +(define* grub-mkrescue-bootloader + (bootloader + (inherit grub-efi-bootloader) + (package grub-hybrid))) + ;;; ;;; Compatibility macros. diff --git a/gnu/build/activation.scm b/gnu/build/activation.scm index 299c0728cb..9c58370ec3 100644 --- a/gnu/build/activation.scm +++ b/gnu/build/activation.scm @@ -313,6 +313,7 @@ they already exist." (false-if-exception (delete-file file))) (format #t "populating /etc from ~a...~%" etc) + (mkdir-p "/etc") ;; Create the /etc/ssl -> /run/current-system/profile/etc/ssl symlink. This ;; symlink, to a target outside of the store, probably doesn't belong in the diff --git a/gnu/build/file-systems.scm b/gnu/build/file-systems.scm index b6930497d6..203fbdfffb 100644 --- a/gnu/build/file-systems.scm +++ b/gnu/build/file-systems.scm @@ -373,15 +373,16 @@ not valid header was found." (define (disk-partitions) "Return the list of device names corresponding to valid disk partitions." - (define (last-character str) - (string-ref str (- (string-length str) 1))) - (define (partition? name major minor) - ;; Select device names that end in a digit, like libblkid's 'probe_all' - ;; function does. Checking for "/sys/dev/block/MAJOR:MINOR/partition" - ;; doesn't work for partitions coming from mapped devices. - (and (char-set-contains? char-set:digit (last-character name)) - (> major 2))) ;ignore RAM disks and floppy disks + ;; grub-mkrescue does some funny things for EFI support which + ;; makes it a lot more difficult than one would expect to support + ;; booting an ISO-9660 image from an USB flash drive. + ;; For example there's a buggy (too small) hidden partition in it + ;; which Linux mounts and then proceeds to fail while trying to + ;; fall off the edge. + ;; In any case, partition tables are supposed to be optional so + ;; here we allow checking entire disks for file systems, too. + (> major 2)) ;ignore RAM disks and floppy disks (call-with-input-file "/proc/partitions" (lambda (port) diff --git a/gnu/local.mk b/gnu/local.mk index 3f27a5f973..acdadd6294 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -582,7 +582,6 @@ dist_patch_DATA = \ %D%/packages/patches/eudev-rules-directory.patch \ %D%/packages/patches/evilwm-lost-focus-bug.patch \ %D%/packages/patches/exim-CVE-2017-1000369.patch \ - %D%/packages/patches/fabric-tests.patch \ %D%/packages/patches/fastcap-mulGlobal.patch \ %D%/packages/patches/fastcap-mulSetup.patch \ %D%/packages/patches/fasthenry-spAllocate.patch \ @@ -620,6 +619,7 @@ dist_patch_DATA = \ %D%/packages/patches/gcr-disable-failing-tests.patch \ %D%/packages/patches/gcr-fix-collection-tests-to-work-with-gpg-21.patch \ %D%/packages/patches/gdk-pixbuf-list-dir.patch \ + %D%/packages/patches/gd-CVE-2017-7890.patch \ %D%/packages/patches/gd-fix-gd2-read-test.patch \ %D%/packages/patches/gd-fix-tests-on-i686.patch \ %D%/packages/patches/gd-freetype-test-failure.patch \ @@ -637,6 +637,11 @@ dist_patch_DATA = \ %D%/packages/patches/ghostscript-runpath.patch \ %D%/packages/patches/glib-networking-ssl-cert-file.patch \ %D%/packages/patches/glib-tests-timer.patch \ + %D%/packages/patches/glibc-CVE-2015-5180.patch \ + %D%/packages/patches/glibc-CVE-2015-7547.patch \ + %D%/packages/patches/glibc-CVE-2016-3075.patch \ + %D%/packages/patches/glibc-CVE-2016-3706.patch \ + %D%/packages/patches/glibc-CVE-2016-4429.patch \ %D%/packages/patches/glibc-CVE-2017-1000366-pt1.patch \ %D%/packages/patches/glibc-CVE-2017-1000366-pt2.patch \ %D%/packages/patches/glibc-CVE-2017-1000366-pt3.patch \ diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index 02d9baf493..e8a1cb552c 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -1718,7 +1718,7 @@ throughput (in the same interval).") (define-public thefuck (package (name "thefuck") - (version "3.18") + (version "3.19") (source (origin (method url-fetch) (uri (string-append "https://github.com/nvbn/thefuck/archive/" @@ -1726,7 +1726,7 @@ throughput (in the same interval).") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1xsvkqh89rgxq5w03mnlcfkn9y39nfwhb2pjabjspcc2mi2mq5y6")) + "191zbvkyc02h0wwd46xwj4zzg7jhlr8xv0ji6knqkgjnk0nvqq01")) (patches (search-patches "thefuck-test-environ.patch")))) (build-system python-build-system) (arguments @@ -2105,28 +2105,22 @@ Intel DRM Driver.") (define-public fabric (package (name "fabric") - (version "1.13.1") + (version "1.13.2") (source (origin (method url-fetch) (uri (pypi-uri "Fabric" version)) (sha256 (base32 - "1z17hw0yiqp1blq217zxkg2jzkv8qd79saqhscgsw14mwlcqpwd0")) - (patches (search-patches "fabric-tests.patch")))) + "0k944dxr41whw7ib6380q9x15wyskx7fqni656icdn8rzshn9bwq")))) (build-system python-build-system) (arguments - `(#:python ,python-2)) ;Python 2 only + `(#:python ,python-2)) ; Python 2 only (native-inputs - `(("python2-fudge" ,python2-fudge) ; Requires < 1.0 - ("python2-jinja2" ,python2-jinja2) ; Requires < 3.0 - ("python2-nose" ,python2-nose))) ; Requires < 2.0 + `(("python2-fudge" ,python2-fudge) + ("python2-jinja2" ,python2-jinja2) + ("python2-nose" ,python2-nose))) (propagated-inputs - ;; Required upgrading python-paramiko 1.17.4 to fix an incompatibility - ;; between python-paramiko and newer python-pycrypto. Without this, the - ;; `fab` command fails with "ValueError: CTR mode needs counter - ;; parameter, not IV". See: - ;; https://github.com/paramiko/paramiko/pull/714#issuecomment-281191548. `(("python2-paramiko" ,python2-paramiko))) (home-page "http://fabfile.org") (synopsis "Simple Pythonic remote execution and deployment tool") diff --git a/gnu/packages/base.scm b/gnu/packages/base.scm index 725d91b976..1ccff1fcf5 100644 --- a/gnu/packages/base.scm +++ b/gnu/packages/base.scm @@ -790,6 +790,7 @@ GLIBC/HURD for a Hurd host" "glibc-versioned-locpath.patch" "glibc-o-largefile.patch" "glibc-vectorized-strcspn-guards.patch" + "glibc-CVE-2015-5180.patch" "glibc-CVE-2017-1000366-pt1.patch" "glibc-CVE-2017-1000366-pt2.patch" "glibc-CVE-2017-1000366-pt3.patch")))))) @@ -809,6 +810,10 @@ GLIBC/HURD for a Hurd host" "glibc-versioned-locpath.patch" "glibc-o-largefile.patch" "glibc-vectorized-strcspn-guards.patch" + "glibc-CVE-2015-5180.patch" + "glibc-CVE-2016-3075.patch" + "glibc-CVE-2016-3706.patch" + "glibc-CVE-2016-4429.patch" "glibc-CVE-2017-1000366-pt1.patch" "glibc-CVE-2017-1000366-pt2.patch" "glibc-CVE-2017-1000366-pt3.patch")))))) @@ -826,6 +831,11 @@ GLIBC/HURD for a Hurd host" "0j49682pm2nh4qbdw35bas82p1pgfnz4d2l7iwfyzvrvj0318wzb")) (patches (search-patches "glibc-ldd-x86_64.patch" "glibc-vectorized-strcspn-guards.patch" + "glibc-CVE-2015-5180.patch" + "glibc-CVE-2015-7547.patch" + "glibc-CVE-2016-3075.patch" + "glibc-CVE-2016-3706.patch" + "glibc-CVE-2016-4429.patch" "glibc-CVE-2017-1000366-pt1.patch" "glibc-CVE-2017-1000366-pt2.patch" "glibc-CVE-2017-1000366-pt3.patch")))) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2b4b400c19..84f070f0fd 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -48,6 +48,7 @@ #:use-module (gnu packages boost) #:use-module (gnu packages compression) #:use-module (gnu packages cpio) + #:use-module (gnu packages cran) #:use-module (gnu packages curl) #:use-module (gnu packages documentation) #:use-module (gnu packages databases) @@ -1636,7 +1637,7 @@ databases.") (build-system python-build-system) (arguments `(#:python ,python-2)) ; only Python 2 is supported (inputs - `(("htseq" ,htseq) + `(("htseq" ,python2-htseq) ("python-pybedtools" ,python2-pybedtools) ("python-cython" ,python2-cython) ("python-scikit-learn" ,python2-scikit-learn) @@ -2981,22 +2982,22 @@ HMMs).") (define-public htseq (package (name "htseq") - (version "0.6.1") + (version "0.9.1") (source (origin (method url-fetch) - (uri (string-append - "https://pypi.python.org/packages/source/H/HTSeq/HTSeq-" - version ".tar.gz")) + (uri (pypi-uri "HTSeq" version)) (sha256 (base32 - "1i85ppf2j2lj12m0x690qq5nn17xxk23pbbx2c83r8ayb5wngzwv")))) + "11flgb1381xdhk43bzbfm3vhnszkpqg6jk76rpa5xd1zbrvvlnxg")))) (build-system python-build-system) - (arguments `(#:python ,python-2)) ; only Python 2 is supported + (native-inputs + `(("python-cython" ,python-cython))) ;; Numpy needs to be propagated when htseq is used as a Python library. (propagated-inputs - `(("python-numpy" ,python2-numpy))) + `(("python-numpy" ,python-numpy))) (inputs - `(("python-pysam" ,python2-pysam))) + `(("python-pysam" ,python-pysam) + ("python-matplotlib" ,python-matplotlib))) (home-page "http://www-huber.embl.de/users/anders/HTSeq/") (synopsis "Analysing high-throughput sequencing data with Python") (description @@ -3004,6 +3005,9 @@ HMMs).") from high-throughput sequencing assays.") (license license:gpl3+))) +(define-public python2-htseq + (package-with-python2 htseq)) + (define-public java-htsjdk (package (name "java-htsjdk") @@ -5757,14 +5761,14 @@ high-throughput sequencing experiments.") (define-public r-deseq2 (package (name "r-deseq2") - (version "1.16.0") + (version "1.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DESeq2" version)) (sha256 (base32 - "0m0apn3xi4kdkinsj4xkw5cwysicyjr6xxlxhpa4scyv589am1s5")))) + "01pvyljxkwazxl510v7h0971nx65iqd2bdkbdhw3xzind0n9pdvq")))) (properties `((upstream-name . "DESeq2"))) (build-system r-build-system) (propagated-inputs @@ -5794,14 +5798,14 @@ distribution.") (define-public r-annotationforge (package (name "r-annotationforge") - (version "1.18.0") + (version "1.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationForge" version)) (sha256 (base32 - "01kd86vvgpa4a5zivcy4g6z8rhcykasdskrz8yqsqz211sd1xsr3")))) + "1366qvykd9cpcvwgc5g9mm9adw9rxw6p4814dd6l5fyb0pwpmysx")))) (properties `((upstream-name . "AnnotationForge"))) (build-system r-build-system) @@ -5872,14 +5876,14 @@ Enrichment Analysis} (GSEA).") (define-public r-category (package (name "r-category") - (version "2.42.0") + (version "2.42.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Category" version)) (sha256 (base32 - "0swcmihyjg0fhaaydl9hm24aj9zffw3bibza9y6sqs6jaqd97f09")))) + "1w186nhc85bglcgmbcrsdbb8l6rph21pl5kdwjqwkp0jnr9z0ifn")))) (properties `((upstream-name . "Category"))) (build-system r-build-system) (propagated-inputs @@ -6384,13 +6388,13 @@ also known as views, in a controlled vocabulary.") (define-public r-bookdown (package (name "r-bookdown") - (version "0.3") + (version "0.4") (source (origin (method url-fetch) (uri (cran-uri "bookdown" version)) (sha256 (base32 - "0r9bchzg7im6psc3jphvshzbidc5bv5xaih1qg7b5518jy4iyvb9")))) + "1fp1k7hivrb7s2dwgrsqy9s7xg6pk9hczhrc149y1dwh901j6qvv")))) (build-system r-build-system) (propagated-inputs `(("r-htmltools" ,r-htmltools) @@ -6406,13 +6410,13 @@ authoring books and technical documents with R Markdown.") (define-public r-biocstyle (package (name "r-biocstyle") - (version "2.4.0") + (version "2.4.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocStyle" version)) (sha256 (base32 - "1n2c8rj920wmk3q2khmjfnhn5i4b3lmhx1whnghk0zk3jf88hvbi")))) + "0bmgmsfll923v573g0kyzlmjd7gly5jwgd8vkrcwvbam1gz75f2c")))) (properties `((upstream-name . "BiocStyle"))) (build-system r-build-system) @@ -6500,14 +6504,14 @@ support for default values, positional argument support, etc.") (define-public r-optparse (package (name "r-optparse") - (version "1.3.2") + (version "1.4.4") (source (origin (method url-fetch) (uri (cran-uri "optparse" version)) (sha256 (base32 - "1g8as89r91xxi5j5azsd6vrfrhg84mnfx2683j7pacdp8s33radw")))) + "1ff4wmsszrb3spwfp7ynfs8w11qpy1sdzfxm1wk8dqqvdwris7qb")))) (build-system r-build-system) (propagated-inputs `(("r-getopt" ,r-getopt))) @@ -6523,13 +6527,13 @@ that accept short and long options.") (define-public r-dnacopy (package (name "r-dnacopy") - (version "1.50.0") + (version "1.50.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DNAcopy" version)) (sha256 (base32 - "0112ry62z18m7rdyrn3gvbxq2f6m44cawhcfb1f02z9xzlsj0k28")))) + "0f0x83db7rm5xf9fg5pjhvs4i165qqaf01lbwb8kj13fsqpwx15p")))) (properties `((upstream-name . "DNAcopy"))) (build-system r-build-system) @@ -6572,14 +6576,14 @@ S4Vectors package itself.") (define-public r-seqinr (package (name "r-seqinr") - (version "3.3-6") + (version "3.4-5") (source (origin (method url-fetch) (uri (cran-uri "seqinr" version)) (sha256 (base32 - "13d0qxm2244wgdl2dy2s8vnrnf5fx4n47if9gkb49dqx6c0sx8s2")))) + "17zv0n5cji17izwmwg0jcbxbjl3w5rls91w15svcnlpxjms38ahn")))) (build-system r-build-system) (propagated-inputs `(("r-ade4" ,r-ade4) @@ -6597,13 +6601,13 @@ utilities for sequence data management under the ACNUC system.") (define-public r-iranges (package (name "r-iranges") - (version "2.10.0") + (version "2.10.2") (source (origin (method url-fetch) (uri (bioconductor-uri "IRanges" version)) (sha256 (base32 - "0zp4mxm9h1p4krj7m7cinkvwa2ibqkq59jwpan97yvhb4z8q0d6n")))) + "1brmzs3rsf97gymridrh9c9r3vws8b3rpghaanxnniw36lmcajfy")))) (properties `((upstream-name . "IRanges"))) (build-system r-build-system) @@ -6649,13 +6653,13 @@ ID and species. It is used by functions in the GenomeInfoDb package.") (define-public r-genomeinfodb (package (name "r-genomeinfodb") - (version "1.12.0") + (version "1.12.2") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 - "1bwwhscjl376a5p43mx8ijrqajxmgypbqhv049pgagl22hkkf0y3")))) + "1hjxgmcnrngp1307ipqaq9hgxz4j0ldn7d46knhzs30k2r4qnrfp")))) (properties `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) @@ -6704,13 +6708,13 @@ CAGE.") (define-public r-variantannotation (package (name "r-variantannotation") - (version "1.22.0") + (version "1.22.3") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantAnnotation" version)) (sha256 (base32 - "05hpm4as36kvpiqhgnkfjwfx0a05p304c21ggba29iac4nanm8b3")))) + "0sr3vdn85x5zdxh80cfwlpfdpi2hmjy3fwi00ac3jya4v145vawr")))) (properties `((upstream-name . "VariantAnnotation"))) (inputs @@ -6742,13 +6746,13 @@ coding changes and predict coding outcomes.") (define-public r-limma (package (name "r-limma") - (version "3.32.0") + (version "3.32.5") (source (origin (method url-fetch) (uri (bioconductor-uri "limma" version)) (sha256 (base32 - "0q7rqm86nwq0rg4fjggfr7xqybjrxj425vni3cva70b4c8d1h425")))) + "0p2ayha9g9w5r8s7pgdf16mkmdbqwh6f35jh07g3b8gyra48gwiw")))) (build-system r-build-system) (home-page "http://bioinf.wehi.edu.au/limma") (synopsis "Package for linear models for microarray and RNA-seq data") @@ -6826,13 +6830,13 @@ manipulating genomic intervals and variables defined along a genome.") (define-public r-biobase (package (name "r-biobase") - (version "2.36.0") + (version "2.36.2") (source (origin (method url-fetch) (uri (bioconductor-uri "Biobase" version)) (sha256 (base32 - "0x7pf5xsdcj12dbf5qqki2c6bd5madqg2fbiq5xgisarpc9v6c1m")))) + "0sr48nqx5bqid4g6lr9zr9286xh842w717yvmssvddb5xxynib6f")))) (properties `((upstream-name . "Biobase"))) (build-system r-build-system) @@ -6848,13 +6852,13 @@ on Bioconductor or which replace R functions.") (define-public r-annotationdbi (package (name "r-annotationdbi") - (version "1.38.0") + (version "1.38.2") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationDbi" version)) (sha256 (base32 - "1xffm98s817mfc827cnr0by6167nlrl1glxzjawzz0rkghs41g27")))) + "1lsamnbf07zzsy5asy5hn97n2a4layv58w2bzd90ikcdx0gmzarj")))) (properties `((upstream-name . "AnnotationDbi"))) (build-system r-build-system) @@ -6875,13 +6879,13 @@ annotation data packages using SQLite data storage.") (define-public r-biomart (package (name "r-biomart") - (version "2.32.0") + (version "2.32.1") (source (origin (method url-fetch) (uri (bioconductor-uri "biomaRt" version)) (sha256 (base32 - "0knkxh23vl9pa0by03xr6dy9aiah714cmf54jl828k51l9wv5l2j")))) + "0fhpbjlsgbqxrpj6nzhhk9q3ph81n5x4p7mmd097xjjn6b05w1d8")))) (properties `((upstream-name . "biomaRt"))) (build-system r-build-system) @@ -6905,13 +6909,13 @@ powerful online queries from gene annotation to database mining.") (define-public r-biocparallel (package (name "r-biocparallel") - (version "1.10.0") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocParallel" version)) (sha256 (base32 - "01ph0kq70b5gkd7n6a4myjlvwzgc0hi4xfwz8h17h06n9p5sdwa9")))) + "08mdfxyk9nwz77v0xhlvs19p2wj0phgm5c5b25vm0xh3749njsp0")))) (properties `((upstream-name . "BiocParallel"))) (build-system r-build-system) @@ -6929,13 +6933,13 @@ objects.") (define-public r-biostrings (package (name "r-biostrings") - (version "2.44.0") + (version "2.44.2") (source (origin (method url-fetch) (uri (bioconductor-uri "Biostrings" version)) (sha256 (base32 - "0ixgx12cx2z4n2khxq83crz9gc21qckj2v78y2p31567kfsw7clg")))) + "12c5abgshwq86357jr0r9039y6vl4d6ngysy89rsnr23ldnsirjp")))) (properties `((upstream-name . "Biostrings"))) (build-system r-build-system) @@ -6999,13 +7003,13 @@ files.") (define-public r-delayedarray (package (name "r-delayedarray") - (version "0.2.0") + (version "0.2.7") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedArray" version)) (sha256 (base32 - "0pcsk0f2dg2ldzprs1cccqrk53jrysmm6ccgjj5wh6z3x17g7g2r")))) + "02dfqp4md9xaqjj712ijc3jswghmipr5hwkd5hr0x1xi6l2fb69g")))) (properties `((upstream-name . "DelayedArray"))) (build-system r-build-system) @@ -7029,13 +7033,13 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns), (define-public r-summarizedexperiment (package (name "r-summarizedexperiment") - (version "1.6.0") + (version "1.6.3") (source (origin (method url-fetch) (uri (bioconductor-uri "SummarizedExperiment" version)) (sha256 (base32 - "1szjbzzz4pyip891nji71caalxh0rhqiv7rpv6q54swlrqpfkqkw")))) + "0j7xn7pk52d383fb1wplcggacl2586c4zi0alkgfc3wz7qq9w13s")))) (properties `((upstream-name . "SummarizedExperiment"))) (build-system r-build-system) @@ -7060,13 +7064,13 @@ samples.") (define-public r-genomicalignments (package (name "r-genomicalignments") - (version "1.12.0") + (version "1.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicAlignments" version)) (sha256 (base32 - "1aagyrdk5309a7awg42lg0bpirp91i6i2ddvpmrs38pzriwahnjy")))) + "127690sys4i5q3l4vxnjg4xg8q19qlw2258vgs5d1156w9ypp04h")))) (properties `((upstream-name . "GenomicAlignments"))) (build-system r-build-system) @@ -7093,13 +7097,13 @@ alignments.") (define-public r-rtracklayer (package (name "r-rtracklayer") - (version "1.36.0") + (version "1.36.4") (source (origin (method url-fetch) (uri (bioconductor-uri "rtracklayer" version)) (sha256 (base32 - "0dv7p3wzmx57inznf6fb06417zcm48g7fpazyahxny7bqgzwq0ig")))) + "050q1rv04w31168ljr975vxva31n9lqdx84rnmsk6zcr6p640ffp")))) (build-system r-build-system) (arguments `(#:phases @@ -7138,13 +7142,13 @@ as well as query and modify the browser state, such as the current viewport.") (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.28.0") + (version "1.28.4") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "1pjxlr34ygv8pvfwpyq268wpgqzphiwpij85fyhjqdwdp0a253ik")))) + "01ylvg275iy0cvsbxkbfxcf9pi9al597v5wnlqi2xdpmrcxyc3q0")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) @@ -7817,7 +7821,7 @@ throughput genetic sequencing data sets using regression methods.") (define-public r-qtl (package (name "r-qtl") - (version "1.40-8") + (version "1.41-6") (source (origin (method url-fetch) @@ -7825,7 +7829,7 @@ throughput genetic sequencing data sets using regression methods.") version ".tar.gz")) (sha256 (base32 - "05bj1x2ry0i7yqiydlswb3d2h4pxg70z8w1072az1mrv1m54k8sp")))) + "067az4v432zxp6lxck8d7vlh9w4r13r0mvw5zsglyaqwsh3d9sad")))) (build-system r-build-system) (home-page "http://rqtl.org/") (synopsis "R package for analyzing QTL experiments in genetics") @@ -8067,14 +8071,14 @@ in SNV base substitution data.") (define-public r-wgcna (package (name "r-wgcna") - (version "1.51") + (version "1.60") (source (origin (method url-fetch) (uri (cran-uri "WGCNA" version)) (sha256 (base32 - "0hzvnhw76vwg8bl8x368f0c5szpwb8323bmrb3bir93i5bmfjsxx")))) + "16mxhwzhh5q48wmz1iba2r21cp0n0v8g11am4pi52iv6g0663ixl")))) (properties `((upstream-name . "WGCNA"))) (build-system r-build-system) (propagated-inputs @@ -8584,14 +8588,14 @@ GenomicRanges Bioconductor package.") (define-public r-copywriter (package (name "r-copywriter") - (version "2.8.0") + (version "2.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "CopywriteR" version)) (sha256 (base32 - "183nmrqmdf9syqljslvwv7mhs9ar5xizzq98imgsc80q0m25ncjf")))) + "0xgqnq5v5213b3nzvlmjysjb7w1bc0iblqpmzbjqn7n0ib0qyhbm")))) (properties `((upstream-name . "CopywriteR"))) (build-system r-build-system) (propagated-inputs @@ -8624,18 +8628,21 @@ number detection tools.") (define-public r-sva (package (name "r-sva") - (version "3.24.0") + (version "3.24.4") (source (origin (method url-fetch) (uri (bioconductor-uri "sva" version)) (sha256 (base32 - "04pxl61iyc845wmqca1qv8kbb8zcp0qp72zgvgki3zzmrph9a362")))) + "0wcway4ai9im81xnrzb1vij2iidq5pw24qhjfgacmhxvx3dzhbsc")))) (build-system r-build-system) (propagated-inputs `(("r-genefilter" ,r-genefilter) - ("r-mgcv" ,r-mgcv))) + ("r-mgcv" ,r-mgcv) + ("r-biocparallel" ,r-biocparallel) + ("r-matrixstats" ,r-matrixstats) + ("r-limma" ,r-limma))) (home-page "http://bioconductor.org/packages/sva") (synopsis "Surrogate variable analysis") (description @@ -8651,14 +8658,14 @@ unmodeled, or latent sources of noise.") (define-public r-seqminer (package (name "r-seqminer") - (version "5.9") + (version "6.0") (source (origin (method url-fetch) (uri (cran-uri "seqminer" version)) (sha256 (base32 - "0sfkxrc9gy5a8fadzyzfzh7l5grasm8cj6cd2nnpv85ws6mqr6qd")))) + "057j1l6dip35l1aivilapl2zv9db677b3di2pb3sfgq2sxg0ps3l")))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) diff --git a/gnu/packages/bootloaders.scm b/gnu/packages/bootloaders.scm index 1f6b0fc730..864b1a2698 100644 --- a/gnu/packages/bootloaders.scm +++ b/gnu/packages/bootloaders.scm @@ -183,6 +183,39 @@ menu to select one of the installed operating systems.") "/bin/mcopy\""))) #t)))))))))) +;; Because grub searches hardcoded paths it's easiest to just build grub +;; again to make it find both grub-pc and grub-efi. There is a command +;; line argument which allows you to specify ONE platform - but +;; grub-mkrescue will use multiple platforms if they are available +;; in the installation directory (without command line argument). +(define-public grub-hybrid + (package + (inherit grub-efi) + (name "grub-hybrid") + (synopsis "GRand Unified Boot loader (hybrid version)") + (inputs + `(("grub" ,grub) + ,@(package-inputs grub-efi))) + (arguments + (substitute-keyword-arguments (package-arguments grub-efi) + ((#:modules modules `((guix build utils) (guix build gnu-build-system))) + `((ice-9 ftw) ,@modules)) + ((#:phases phases) + `(modify-phases ,phases + (add-after 'install 'install-non-efi + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((input-dir (string-append (assoc-ref inputs "grub") + "/lib/grub")) + (output-dir (string-append (assoc-ref outputs "out") + "/lib/grub"))) + (for-each + (lambda (basename) + (if (not (string-prefix? "." basename)) + (symlink (string-append input-dir "/" basename) + (string-append output-dir "/" basename)))) + (scandir input-dir)) + #t))))))))) + (define-public syslinux (let ((commit "bb41e935cc83c6242de24d2271e067d76af3585c")) (package diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm index 7237931b7d..f2989d9c15 100644 --- a/gnu/packages/compression.scm +++ b/gnu/packages/compression.scm @@ -736,19 +736,20 @@ time for compression ratio.") (define-public python-lz4 (package (name "python-lz4") - (version "0.8.2") + (version "0.10.1") (source (origin (method url-fetch) (uri (pypi-uri "lz4" version)) (sha256 (base32 - "1irad4sq4hdr30fr53smvv3zzk4rddcf9b4jx19w8s9xsxhr1x3b")))) + "0ghv1xbaq693kgww1x9c22bplz479ls9szjsaa4ig778ls834hm0")))) (build-system python-build-system) (native-inputs - `(("python-nose" ,python-nose))) + `(("python-nose" ,python-nose) + ("python-setuptools-scm" ,python-setuptools-scm))) (home-page "https://github.com/python-lz4/python-lz4") - (synopsis "LZ4 Bindings for Python") + (synopsis "LZ4 bindings for Python") (description "This package provides python bindings for the lz4 compression library by Yann Collet. The project contains bindings for the LZ4 block format and diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 9ebfbbed2d..feae801116 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -42,3 +42,109 @@ including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar CIELAB. Qualitative, sequential, and diverging color palettes based on HCL colors are provided.") (license license:bsd-3))) + +(define-public r-glue + (package + (name "r-glue") + (version "1.1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "glue" version)) + (sha256 + (base32 + "01awmqby7rwzhzr51m7d87wqibx7ggl6xair8fi3z3q1hkyyv7ih")))) + (build-system r-build-system) + (home-page "https://github.com/tidyverse/glue") + (synopsis "Interpreted string literals") + (description + "This package provides an implementation of interpreted string literals, +inspired by Python's Literal String Interpolation (PEP-0498) and +Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.") + (license license:expat))) + +(define-public r-plogr + (package + (name "r-plogr") + (version "0.1-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "plogr" version)) + (sha256 + (base32 + "13zliqlbkl8b04k9ga0sx5jsh7k867gracgl84l2a9kcqy9mqx92")))) + (build-system r-build-system) + (home-page "https://github.com/krlmlr/plogr") + (synopsis "R bindings for the plog C++ logging library") + (description + "This package provides the header files for a stripped-down version of +the plog header-only C++ logging library, and a method to log to R's standard +error stream.") + (license license:expat))) + +(define-public r-rcpp + (package + (name "r-rcpp") + (version "0.12.12") + (source + (origin + (method url-fetch) + (uri (cran-uri "Rcpp" version)) + (sha256 + (base32 "1byyqvlgb2p46p1gv243k73rk69fa8pa4l5m5asmckag2pkb2glz")))) + (build-system r-build-system) + (home-page "http://www.rcpp.org") + (synopsis "Seamless R and C++ integration") + (description + "The Rcpp package provides R functions as well as C++ classes which offer +a seamless integration of R and C++. Many R data types and objects can be +mapped back and forth to C++ equivalents which facilitates both writing of new +code as well as easier integration of third-party libraries. Documentation +about Rcpp is provided by several vignettes included in this package, via the +'Rcpp Gallery' site at <http://gallery.rcpp.org>, the paper by Eddelbuettel +and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see +'citation(\"Rcpp\")' for details on these last two.") + (license license:gpl2+))) + +(define-public r-bindr + (package + (name "r-bindr") + (version "0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "bindr" version)) + (sha256 + (base32 + "0d95ifm0x4mrfzi20xf39f5pzd7rfzqsld0vjqf6xzga5rhnd8fc")))) + (build-system r-build-system) + (home-page "https://github.com/krlmlr/bindr") + (synopsis "Parametrized active bindings") + (description + "This package provides a simple interface for creating active bindings +where the bound function accepts additional arguments.") + (license license:expat))) + +(define-public r-bindrcpp + (package + (name "r-bindrcpp") + (version "0.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "bindrcpp" version)) + (sha256 + (base32 + "0l1l22zl87wiyl79m3gj2vlxmkhxvrkl4alhyy08h55q7hqs3vyh")))) + (build-system r-build-system) + (propagated-inputs + `(("r-bindr" ,r-bindr) + ("r-plogr" ,r-plogr) + ("r-rcpp" ,r-rcpp))) + (home-page "https://github.com/krlmlr/bindrcpp") + (synopsis "Rcpp interface to active bindings") + (description + "This package provides an easy way to fill an environment with active +bindings that call a C++ function.") + (license license:expat))) diff --git a/gnu/packages/ebook.scm b/gnu/packages/ebook.scm index bbb127a7d9..32f4f3b2d1 100644 --- a/gnu/packages/ebook.scm +++ b/gnu/packages/ebook.scm @@ -41,6 +41,7 @@ #:use-module (gnu packages pkg-config) #:use-module (gnu packages python) #:use-module (gnu packages qt) + #:use-module (gnu packages serialization) #:use-module (gnu packages tls) #:use-module (gnu packages web) #:use-module (gnu packages xorg)) @@ -126,6 +127,8 @@ ("python2-lxml" ,python2-lxml) ("python2-markdown" ,python2-markdown) ("python2-mechanize" ,python2-mechanize) + ;; python2-msgpack is needed for the network content server to work. + ("python2-msgpack" ,python2-msgpack) ("python2-netifaces" ,python2-netifaces) ("python2-pillow" ,python2-pillow) ("python2-pygments" ,python2-pygments) diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index 917c511f32..4aa713346f 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -4631,7 +4631,7 @@ It should enable you to implement low-level X11 applications.") (define-public emacs-exwm (package (name "emacs-exwm") - (version "0.14") + (version "0.15") (synopsis "Emacs X window manager") (source (origin (method url-fetch) @@ -4639,7 +4639,7 @@ It should enable you to implement low-level X11 applications.") version ".tar")) (sha256 (base32 - "14hjjpbasm84p54fxy73fg7g1fdwqkvisdw8dwwgzkflmd647mkx")))) + "1y7nqry9y0a99bsdqkk9f554vczfw4sz6raadw3138835qy697jg")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-xelb" ,emacs-xelb))) @@ -4673,12 +4673,9 @@ It should enable you to implement low-level X11 applications.") TryExec=~@*~a~@ Type=Application~%" ,name ,synopsis exwm-executable))) ;; Add a shell wrapper to bin - ;; Set DISPLAY variable to work around - ;; https://github.com/ch11ng/exwm/issues/213 (with-output-to-file exwm-executable (lambda _ (format #t "#!~a ~@ - export DISPLAY=:0 ~@ ~a +SI:localuser:$USER ~@ exec ~a --exit-with-session ~a \"$@\" --eval '~s' ~%" (string-append (assoc-ref inputs "bash") "/bin/sh") @@ -4770,12 +4767,9 @@ other operations.") TryExec=~@*~a~@ Type=Application~%" ,name ,synopsis exwm-executable))) ;; Add a shell wrapper to bin - ;; Set DISPLAY variable to work around - ;; https://github.com/ch11ng/exwm/issues/213 (with-output-to-file exwm-executable (lambda _ (format #t "#!~a ~@ - export DISPLAY=:0 ~@ ~a +SI:localuser:$USER ~@ exec ~a --exit-with-session ~a \"$@\" --eval '~s' ~%" (string-append (assoc-ref inputs "bash") "/bin/sh") diff --git a/gnu/packages/ftp.scm b/gnu/packages/ftp.scm index 49e7214991..eb108491a4 100644 --- a/gnu/packages/ftp.scm +++ b/gnu/packages/ftp.scm @@ -46,7 +46,7 @@ (define-public lftp (package (name "lftp") - (version "4.7.5") + (version "4.7.8") (source (origin (method url-fetch) ;; See https://lftp.tech/get.html for mirrors. @@ -58,7 +58,7 @@ "ftp/lftp/lftp-" version ".tar.xz"))) (sha256 (base32 - "1n6h3y5jz1rxlx7ap46vykgm0q2rvzr7c5s5ry5l32z3lbmwbdak")))) + "19ijsmbb5589vg5ga355ys3075z6s2x2h0bdbga343hfqmnid2pi")))) (build-system gnu-build-system) (native-inputs `(("pkg-config" ,pkg-config))) diff --git a/gnu/packages/gcc.scm b/gnu/packages/gcc.scm index 6b1bc762ba..eee91c32bf 100644 --- a/gnu/packages/gcc.scm +++ b/gnu/packages/gcc.scm @@ -340,6 +340,7 @@ where the OS part is overloaded to denote a specific ABI---into GCC for several languages, including C, C++, Objective-C, Fortran, Java, Ada, and Go. It also includes runtime support libraries for these languages.") (license gpl3+) + (supported-systems (delete "aarch64-linux" %supported-systems)) (home-page "https://gcc.gnu.org/")))) (define-public gcc-4.8 @@ -352,7 +353,8 @@ Go. It also includes runtime support libraries for these languages.") (sha256 (base32 "08yggr18v373a1ihj0rg2vd6psnic42b518xcgp3r9k81xz1xyr2")) - (patches (search-patches "gcc-arm-link-spec-fix.patch")))))) + (patches (search-patches "gcc-arm-link-spec-fix.patch")))) + (supported-systems %supported-systems))) (define-public gcc-4.9 (package (inherit gcc-4.7) @@ -366,7 +368,8 @@ Go. It also includes runtime support libraries for these languages.") "14l06m7nvcvb0igkbip58x59w3nq6315k6jcz3wr9ch1rn9d44bc")) (patches (search-patches "gcc-arm-bug-71399.patch" "gcc-libvtv-runpath.patch")))) - (native-inputs `(("texinfo" ,texinfo))))) + (native-inputs `(("texinfo" ,texinfo))) + (supported-systems %supported-systems))) (define-public gcc-5 ;; Note: GCC >= 5 ships with .info files but 'make install' fails to install diff --git a/gnu/packages/gnupg.scm b/gnu/packages/gnupg.scm index c2e5bbc47c..ca4f1d34f2 100644 --- a/gnu/packages/gnupg.scm +++ b/gnu/packages/gnupg.scm @@ -330,14 +330,14 @@ libskba (working with X.509 certificates and CMS data).") (define-public gnupg-1 (package (inherit gnupg) - (version "1.4.21") + (version "1.4.22") (source (origin (method url-fetch) (uri (string-append "mirror://gnupg/gnupg/gnupg-" version ".tar.bz2")) (sha256 (base32 - "0xi2mshq8f6zbarb5f61c9w2qzwrdbjm4q8fqsrwlzc51h8a6ivb")))) + "1d1hz4szh1kvwhsw7w2zxa6q5ndrk3qy6hj289l1b8k3xi5s554m")))) (native-inputs '()) (inputs `(("zlib" ,zlib) diff --git a/gnu/packages/graphics.scm b/gnu/packages/graphics.scm index 6c813e8a37..d0e50106fa 100644 --- a/gnu/packages/graphics.scm +++ b/gnu/packages/graphics.scm @@ -339,7 +339,11 @@ visual effects work for film.") #:configure-flags (list (string-append "-DCMAKE_INSTALL_RPATH=" (assoc-ref %outputs "out") "/lib:" - (assoc-ref %outputs "out") "/lib64")))) + (assoc-ref %outputs "out") "/lib64") + ;; We need to set this flag or otherwise 'rd' will be added + ;; to the name of the library binaries and break linking + ;; with other programs. + "-DCMAKE_BUILD_TYPE=Release"))) (native-inputs `(("unzip" ,unzip))) (inputs diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm index 5bc9a77174..b9e16a11c3 100644 --- a/gnu/packages/image.scm +++ b/gnu/packages/image.scm @@ -14,7 +14,7 @@ ;;; Copyright © 2016 Eric Bavier <bavier@member.fsf.org> ;;; Copyright © 2016 Arun Isaac <arunisaac@systemreboot.net> ;;; Copyright © 2016, 2017 Kei Kebreau <kei@openmailbox.org> -;;; Copyright © 2017 ng0 <contact.ng0@cryptolab.net> +;;; Copyright © 2017 ng0 <ng0@infotropique.org> ;;; Copyright © 2017 Hartmut Goebel <h.goebel@crazy-compilers.com> ;;; ;;; This file is part of GNU Guix. @@ -92,13 +92,32 @@ library. It supports almost all PNG features and is extensible.") (license license:zlib) (home-page "http://www.libpng.org/pub/png/libpng.html"))) +;; libpng-apng should be updated when the APNG patch is released: +;; <https://bugs.gnu.org/27556> (define-public libpng-apng (package - (inherit libpng) (name "libpng-apng") - (version (package-version libpng)) + (version "1.6.28") + (source + (origin + (method url-fetch) + (uri (list (string-append "mirror://sourceforge/libpng/libpng16/" + version "/libpng-" version ".tar.xz") + (string-append + "ftp://ftp.simplesystems.org/pub/libpng/png/src" + "/libpng16/libpng-" version ".tar.xz") + (string-append + "ftp://ftp.simplesystems.org/pub/libpng/png/src/history" + "/libpng16/libpng-" version ".tar.xz"))) + (sha256 + (base32 + "0ylgyx93hnk38haqrh8prd3ax5ngzwvjqw5cxw7p9nxmwsfyrlyq")))) + (build-system gnu-build-system) (arguments - `(#:phases + `(#:modules ((guix build gnu-build-system) + (guix build utils) + (srfi srfi-1)) + #:phases (modify-phases %standard-phases (add-after 'unpack 'patch-apng (lambda* (#:key inputs #:allow-other-keys) @@ -108,11 +127,10 @@ library. It supports almost all PNG features and is extensible.") (let ((apng.gz (assoc-ref inputs "apng"))) (format #t "Applying APNG patch '~a'...~%" apng.gz) - (system (string-append "gunzip < " apng.gz " > the-patch")) - (and (apply-patch "the-patch") - (for-each apply-patch - (find-files "\\.patch")))) - #t)) + (and + (zero? + (system (string-append "gunzip < " apng.gz " > the-patch"))) + (apply-patch "the-patch"))))) (add-before 'configure 'no-checks (lambda _ (substitute* "Makefile.in" @@ -127,15 +145,19 @@ library. It supports almost all PNG features and is extensible.") version "/libpng-" version "-apng.patch.gz")) (sha256 (base32 - "026r0gbkf6d6v54wca02cdxln8sj4m2c1yk62sj2aasv2ki2ffh5")))))) + "0m5nv70n9903x3xzxw9qqc6sgf2rp106ha0x6gix0xf8wcrljaab")))))) (native-inputs `(("libtool" ,libtool))) + ;; libpng.la says "-lz", so propagate it. + (propagated-inputs + `(("zlib" ,zlib))) (synopsis "APNG patch for libpng") (description "APNG (Animated Portable Network Graphics) is an unofficial extension of the APNG (Portable Network Graphics) format. APNG patch provides APNG support to libpng.") - (home-page "https://sourceforge.net/projects/libpng-apng/"))) + (home-page "https://sourceforge.net/projects/libpng-apng/") + (license license:zlib))) (define-public libpng-1.2 (package diff --git a/gnu/packages/javascript.scm b/gnu/packages/javascript.scm index 43bc0bbf6d..12f12bf8f1 100644 --- a/gnu/packages/javascript.scm +++ b/gnu/packages/javascript.scm @@ -26,7 +26,9 @@ #:use-module (gnu packages lisp) #:use-module (guix packages) #:use-module (guix download) - #:use-module (guix build-system trivial)) + #:use-module (guix git-download) + #:use-module (guix build-system trivial) + #:use-module (guix build-system minify)) (define-public js-mathjax (package @@ -134,3 +136,190 @@ be able to view it naturally and easily."))) script to enable responsive web designs in browsers that don't support CSS3 Media Queries.") (license license:expat))) + +(define-public js-html5shiv + (package + (name "js-html5shiv") + (version "3.7.3") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/aFarkas/html5shiv/" + "archive/" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0inlbpxpqzdyi24lqagzf7l24zxg0y02xcpqs2h4npjscazzw7hg")))) + (build-system minify-build-system) + (home-page "https://github.com/aFarkas/html5shiv") + (synopsis "Enable HTML5 sectioning elements in legacy browsers") + (description "The HTML5 Shiv enables use of HTML5 sectioning elements in +legacy Internet Explorer and provides basic HTML5 styling for Internet +Explorer 6-9, Safari 4.x (and iPhone 3.x), and Firefox 3.x.") + ;; From the file "MIT and GPL2 licenses.md": + ;; + ;; This software is licensed under a dual license system (MIT or GPL + ;; version 2). This means you are free to choose with which of both + ;; licenses (MIT or GPL version 2) you want to use this library. + (license (list license:expat license:gpl2)))) + +(define-public js-json2 + (let ((commit "031b1d9e6971bd4c433ca85e216cc853f5a867bd") + (revision "1")) + (package + (name "js-json2") + (version (string-append "2016-10-28." revision "-" (string-take commit 7))) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/douglascrockford/JSON-js.git") + (commit commit))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "1fvb6b2y5sd3sqdgcj683sdxcbxdii34q0ysc9wg0dq1sy81l11v")))) + (build-system minify-build-system) + (arguments + `(#:javascript-files '("json2.js" + "json_parse.js" + "json_parse_state.js" + "cycle.js"))) + (home-page "https://github.com/douglascrockford/JSON-js") + (synopsis "JSON encoders and decoders") + (description "The files in this collection implement JSON +encoders/decoders in JavaScript. + +@code{json2.js}: This file creates a JSON property in the global object, if +there isn't already one, setting its value to an object containing a stringify +method and a parse method. The @code{parse} method uses the @code{eval} +method to do the parsing, guarding it with several regular expressions to +defend against accidental code execution hazards. On current browsers, this +file does nothing, preferring the built-in JSON object. + +@code{json_parse.js}: This file contains an alternative JSON @code{parse} +function that uses recursive descent instead of @code{eval}. + +@code{json_parse_state.js}: This files contains an alternative JSON +@code{parse} function that uses a state machine instead of @code{eval}. + +@code{cycle.js}: This file contains two functions, @code{JSON.decycle} and +@code{JSON.retrocycle}, which make it possible to encode cyclical structures +and DAGs in JSON, and to then recover them. This is a capability that is not +provided by ES5. @code{JSONPath} is used to represent the links.") + (license license:public-domain)))) + +(define-public js-strftime + (package + (name "js-strftime") + (version "0.10.0") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/samsonjs/strftime/" + "archive/v" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1iya43w7y26y2dp9l4d40bhjc4scb5a9mng5ng5c8hsqr82f1375")))) + (build-system minify-build-system) + (arguments + `(#:javascript-files '("strftime.js"))) + (home-page "https://github.com/samsonjs/strftime") + (synopsis "Implementation of strftime to JavaScript") + (description "This is an implementation of the @code{strftime} procedure +for JavaScript. It works in (at least) node.js and browsers. It supports +localization and timezones. Most standard specifiers from C are supported as +well as some other extensions from Ruby.") + (license license:expat))) + +(define-public js-highlight + (package + (name "js-highlight") + (version "9.12.0") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/isagalaev/highlight.js/" + "archive/" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1jjn9mj7fwq4zpr6is438bscf03b3q8jkj0k5c3fc6pkmjnhw939")))) + (build-system minify-build-system) + (arguments + `(#:javascript-files '("src/highlight.js"))) + (home-page "https://github.com/isagalaev/highlight.js") + (synopsis "Syntax highlighting for JavaScript") + (description "Highlight.js is a syntax highlighter written in JavaScript. +It works in the browser as well as on the server. It works with pretty much +any markup, doesn’t depend on any framework and has automatic language +detection.") + (license license:bsd-3))) + +(define-public js-datatables + (package + (name "js-datatables") + (version "1.10.15") + (source (origin + (method url-fetch) + (uri (string-append "https://datatables.net/releases/DataTables-" + version ".zip")) + (sha256 + (base32 + "1y9xqyqyz7x1ls3ska71pshl2hpiy3qnw1f7wygyslbhy4ssgf57")))) + (build-system minify-build-system) + (arguments + `(#:javascript-files '("media/js/dataTables.bootstrap.js" + "media/js/jquery.dataTables.js"))) + (native-inputs + `(("unzip" ,unzip))) + (home-page "https://datatables.net") + (synopsis "DataTables plug-in for jQuery") + (description "DataTables is a table enhancing plug-in for the jQuery +Javascript library, adding sorting, paging and filtering abilities to plain +HTML tables with minimal effort.") + (license license:expat))) + +(define-public js-selectize + (package + (name "js-selectize") + (version "0.12.4") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/selectize/selectize.js/" + "archive/v" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0756p49aaz34mw2dx8k1gxf210mngfrri25vkba0j7wihd2af8gn")))) + (build-system minify-build-system) + (arguments `(#:javascript-files '("src/selectize.js"))) + (home-page "http://selectize.github.io/selectize.js/") + (synopsis "Hybrid widget between a textbox and <select> box") + (description "Selectize is the hybrid of a textbox and @code{<select>} +box. It's jQuery based and it has autocomplete and native-feeling keyboard +navigation; it is useful for tagging, contact lists, etc.") + (license license:asl2.0))) + +(define-public js-es5-shim + (package + (name "js-es5-shim") + (version "4.5.9") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/es-shims/es5-shim/" + "archive/v" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0yfndyijz0ykddzprpvfjb2453gzpn528klmwycwbqc1bqd3m1hl")))) + (build-system minify-build-system) + (arguments `(#:javascript-files + '("es5-sham.js" + "es5-shim.js"))) + (home-page "https://github.com/es-shims/es5-shim") + (synopsis "ECMAScript 5 compatibility shims for legacy JavaScript engines") + (description "@code{es5-shim.js} patches a JavaScript context to contain +all ECMAScript 5 methods that can be faithfully emulated with a legacy +JavaScript engine. @code{es5-sham.js} patches other ES5 methods as closely as +possible. Many of these shams are intended only to allow code to be written +to ES5 without causing run-time errors in older engines. In many cases, this +means that these shams cause many ES5 methods to silently fail.") + (license license:expat))) diff --git a/gnu/packages/lego.scm b/gnu/packages/lego.scm index d47be5dfb4..d5e5de1c1f 100644 --- a/gnu/packages/lego.scm +++ b/gnu/packages/lego.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2016 Eric Bavier <bavier@member.fsf.org> +;;; Copyright © 2016, 2017 Eric Bavier <bavier@member.fsf.org> ;;; ;;; This file is part of GNU Guix. ;;; @@ -23,7 +23,10 @@ #:use-module (guix build-system gnu) #:use-module (gnu packages) #:use-module (gnu packages bison) - #:use-module (gnu packages flex)) + #:use-module (gnu packages compression) + #:use-module (gnu packages flex) + #:use-module (gnu packages gl) + #:use-module (gnu packages qt)) (define-public nqc (package @@ -65,3 +68,57 @@ MINDSTORMS products. The preprocessor and control structures of NQC are very similar to C. NQC is not a general purpose language -- there are many restrictions that stem from limitations of the standard RCX firmware.") (license license:mpl1.0))) + +(define-public leocad + (package + (name "leocad") + (version "17.07") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/leozide/leocad/" + "archive/v" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "02gm4950zlmsw4sxmdwypgkybn51b02qnmmk6rzjdr8si4k6gikq")))) + (build-system gnu-build-system) + (native-inputs + `(("qttools" ,qttools))) ;for lrelease + (inputs + `(("mesa" ,mesa) + ("qtbase" ,qtbase) + ("zlib" ,zlib))) + (arguments + '(#:tests? #f + #:phases + (modify-phases %standard-phases + (replace 'configure + (lambda* (#:key outputs inputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (zero? (system* "qmake" + (string-append "INSTALL_PREFIX=" out) + ;; Otherwise looks for lrelease-qt4 + "QMAKE_LRELEASE=lrelease" + ;; Don't pester users about updates + "DISABLE_UPDATE_CHECK=1"))))) + (add-after 'configure 'reset-resource-timestamps + (lambda _ + ;; The contents of build/release/.qrc/qrc_leocad.cpp generated by + ;; qt's rcc tool depends on the timestamps in resources/*, in + ;; particular the leocad_*.qm files that are created by qmake + ;; above. So reset those timestamps for a reproducible build. + (with-directory-excursion "resources" + (for-each (lambda (file) + (let* ((base (basename file ".qm")) + (src (string-append base ".ts")) + (st (stat src))) + (set-file-time file st))) + (find-files "." "leocad_.*\\.qm")))))))) + (home-page "http://www.leocad.org") + (synopsis "Create virtual Lego models") + (description + "LeoCAD is a program for creating virtual LEGO models. It has an +intuitive interface, designed to allow new users to start creating new models +without having to spend too much time learning the application. LeoCAD is +fully compatible with the LDraw Standard and related tools.") + (license license:gpl2+))) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 0ee0a5acd0..01b11c4ffb 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -824,36 +824,36 @@ ext3 or ext4 partition.") (define-public zerofree (package (name "zerofree") - (version "1.0.3") - (home-page "http://intgat.tigress.co.uk/rmy/uml/") + (version "1.1.0") + (home-page "https://frippery.org/uml/") (source (origin (method url-fetch) (uri (string-append home-page name "-" version ".tgz")) (sha256 (base32 - "1xncw3dn2cp922ly42m96p6fh7jv8ysg6bwqbk5xvw701f3dmkrs")))) + "059g29x5r1xj6wcj4xj85l8w6qrxyl86yqbybjqqz6nxz4falxzf")))) (build-system gnu-build-system) (arguments - '(#:phases (alist-replace - 'install - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (bin (string-append out "/bin"))) - (mkdir-p bin) - (copy-file "zerofree" - (string-append bin "/zerofree")) - (chmod (string-append bin "/zerofree") - #o555) - #t)) - (alist-delete 'configure %standard-phases)) - #:tests? #f)) ;no tests + '(#:phases + (modify-phases %standard-phases + (delete 'configure) ; no configure script + (replace 'install + ;; The Makefile lacks an ‘install’ target. + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin"))) + (chmod "zerofree" #o555) + (install-file "zerofree" bin) + #t)))) + #:tests? #f)) ; no tests (inputs `(("libext2fs" ,e2fsprogs))) (synopsis "Zero non-allocated regions in ext2/ext3/ext4 file systems") (description - "The zerofree command scans the free blocks in an ext2 file system and -fills any non-zero blocks with zeroes. This is a useful way to make disk -images more compressible.") + "Zerofree finds the unallocated blocks with non-zero value content in an +ext2, ext3, or ext4 file system and fills them with zeroes (or another value). +This is a simple way to make disk images more compressible. +Zerofree requires the file system to be unmounted or mounted read-only.") (license license:gpl2))) (define-public strace @@ -1747,7 +1747,7 @@ UnionFS-FUSE additionally supports copy-on-write.") (define-public sshfs-fuse (package (name "sshfs-fuse") - (version "2.9") + (version "2.10") (source (origin (method url-fetch) (uri (string-append "https://github.com/libfuse/sshfs/releases/" @@ -1755,7 +1755,7 @@ UnionFS-FUSE additionally supports copy-on-write.") ".tar.gz")) (sha256 (base32 - "1pp5wsl1jx11apkv2fpp559miifqhi8ka400npy5awp9ghlf3la6")))) + "00fir2iykdx11g8nv5gijg0zjrp2g3ldypnv0yi6lq3h5pg5v13h")))) (build-system gnu-build-system) (inputs `(("fuse" ,fuse) diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index d39e77d978..c5132faf58 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -32,6 +32,7 @@ #:use-module (gnu packages autotools) #:use-module (gnu packages boost) #:use-module (gnu packages compression) + #:use-module (gnu packages cran) #:use-module (gnu packages dejagnu) #:use-module (gnu packages gcc) #:use-module (gnu packages image) diff --git a/gnu/packages/markup.scm b/gnu/packages/markup.scm index 4afe8c3c0e..121e6cdbf4 100644 --- a/gnu/packages/markup.scm +++ b/gnu/packages/markup.scm @@ -105,7 +105,7 @@ convert it to structurally valid XHTML (or HTML).") (define-public cmark (package (name "cmark") - (version "0.27.1") + (version "0.28.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/jgm/cmark/archive/" @@ -113,7 +113,7 @@ convert it to structurally valid XHTML (or HTML).") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1da62ispca9aal2a36gaj87175rv5013pl7x740vk32y6lclr6v6")))) + "03pypf2mcacfa7lrwz66lh5hydsycc33arp1nx1lljbq98gikkv8")))) (build-system cmake-build-system) (arguments '(#:test-target "test")) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 3d461c7602..45884c20ff 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -561,18 +561,17 @@ computations.") (define-public hdf4 (package (name "hdf4") - (version "4.2.12") + (version "4.2.13") (source (origin (method url-fetch) (uri (string-append "https://support.hdfgroup.org/ftp/HDF/releases/HDF" version "/src/hdf-" version ".tar.bz2")) (sha256 - (base32 "020jh563sjyxsgml8l809d2i1d4ms9shivwj3gbm7n0ilxbll8id")) + (base32 "1wz0586zh91pqb95wvr0pbh71a8rz358fdj6n2ksp85x2cis9lsm")) (patches (search-patches "hdf4-architectures.patch" "hdf4-reproducibility.patch" "hdf4-shared-fortran.patch")))) - (build-system gnu-build-system) (native-inputs `(("gfortran" ,gfortran) @@ -1627,12 +1626,12 @@ programming problems.") (define-public r-pracma (package (name "r-pracma") - (version "2.0.4") + (version "2.0.7") (source (origin (method url-fetch) (uri (cran-uri "pracma" version)) (sha256 - (base32 "1z3i90mkzwvp9di17caf4934z2xlb2imm3hwxllcrbwvmnmhrwyc")))) + (base32 "0hxa0rbbp54j0c05qj7vfwhqfdmiz5ax8vhqxd09g33x7c0hqbc5")))) (build-system r-build-system) (propagated-inputs `(("r-quadprog" ,r-quadprog))) @@ -3068,6 +3067,8 @@ instruction sets. Thus, an application written with Vc can be compiled for: @item NVIDIA GPUs / CUDA (in development) @end enumerate\n") (home-page "https://github.com/VcDevel/Vc") + ;; "No support_???.cpp file exists for this architecture." + (supported-systems '("x86_64-linux" "i686-linux")) (license license:bsd-3))) (define-public reducelcs @@ -3196,3 +3197,46 @@ as equations, scalars, vectors, and matrices.") theories} (SMT) solver. It provides a C/C++ API.") (home-page "https://github.com/Z3Prover/z3") (license license:expat))) + +(define-public cubicle + (package + (name "cubicle") + (version "1.1.1") + (source (origin + (method url-fetch) + (uri (string-append "http://cubicle.lri.fr/cubicle-" + version ".tar.gz")) + (sha256 + (base32 + "1sny9c4fm14k014pk62ibpwbrjjirkx8xmhs9jg7q1hk7y7x3q2h")))) + (build-system gnu-build-system) + (native-inputs + `(("ocaml" ,ocaml) + ("which" ,which))) + (propagated-inputs + `(("z3" ,z3))) + (arguments + `(#:configure-flags (list "--with-z3") + #:tests? #f + #:phases + (modify-phases %standard-phases + (add-before 'configure 'configure-for-release + (lambda _ + (substitute* "Makefile.in" + (("SVNREV=") "#SVNREV=")))) + (add-before 'configure 'fix-/bin/sh + (lambda _ + (substitute* "configure" + (("/bin/sh") (which "sh"))))) + (add-before 'configure 'fix-smt-z3wrapper.ml + (lambda _ + (substitute* "Makefile.in" + (("\\\\n") ""))))))) + (home-page "http://cubicle.lri.fr/") + (synopsis "Model checker for array-based systems") + (description "Cubicle is an open source model checker for verifying safety +properties of array-based systems. This is a syntactically restricted class of +parametrized transition systems with states represented as arrays indexed by an +arbitrary number of processes. Cache coherence protocols and mutual exclusion +algorithms are typical examples of such systems.") + (license license:asl2.0))) diff --git a/gnu/packages/mp3.scm b/gnu/packages/mp3.scm index 789e596f84..37885c9e34 100644 --- a/gnu/packages/mp3.scm +++ b/gnu/packages/mp3.scm @@ -462,7 +462,7 @@ compression format (.mpc files).") (define-public eyed3 (package (name "eyed3") - (version "0.7.10") + (version "0.8") (source (origin (method url-fetch) (uri (string-append @@ -470,14 +470,13 @@ compression format (.mpc files).") version ".tar.gz")) (sha256 (base32 - "0wjicszs64ksj2y5jbk09yjd08znc1qnarlq8ssmx13f2d4x59wq")))) + "1dcswb0f6w3b05s1v43pq8fmavkd5g88ysndn9160wlaa1v9n40h")))) (build-system python-build-system) (arguments - `(#:python ,python-2)) - (native-inputs - `(("python2-nose" ,python2-nose) - ("python2-sphinx" ,python2-sphinx) - ("python2-coverage" ,python2-coverage))) + `(#:tests? #f)) ; the required test data contains copyrighted material. + (propagated-inputs + `(("python-six" ,python-six) + ("python-grako" ,python-grako))) (synopsis "MP3 tag ID3 metadata editor") (description "eyeD3 is a Python tool for working with audio files, specifically mp3 files containing ID3 metadata (i.e. song info). It provides a diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm index 506d1f94e7..3c1a4d9567 100644 --- a/gnu/packages/package-management.scm +++ b/gnu/packages/package-management.scm @@ -523,7 +523,7 @@ transactions from C or Python.") ;; Below are modules used for tests. ("python-pytest" ,python-pytest) ("python-chardet" ,python-chardet))) - (home-page "http://diffoscope.org/") + (home-page "https://diffoscope.org/") (synopsis "Compare files, archives, and directories in depth") (description "Diffoscope tries to get to the bottom of what makes files or directories @@ -661,7 +661,12 @@ This package provides Conda as a library.") (license bsd-3))) (define-public python2-conda - (package-with-python2 python-conda)) + (let ((base (package-with-python2 + (strip-python2-variant python-conda)))) + (package (inherit base) + (native-inputs + `(("python2-enum34" ,python2-enum34) + ,@(package-native-inputs base)))))) (define-public conda (package (inherit python-conda) diff --git a/gnu/packages/patches/fabric-tests.patch b/gnu/packages/patches/fabric-tests.patch deleted file mode 100644 index 4a0ca9f8f1..0000000000 --- a/gnu/packages/patches/fabric-tests.patch +++ /dev/null @@ -1,15 +0,0 @@ -The `fab` excecutable doesn't exist during the test phase as it is created -dynamically during installation. Refer to the equivalent Python module -directly. - ---- a/tests/test_utils.py -+++ b/tests/test_utils.py -@@ -93,7 +93,7 @@ - # perform when they are allowed to bubble all the way to the top. So, we - # invoke a subprocess and look at its stderr instead. - with quiet(): -- result = local("fab -f tests/support/aborts.py kaboom", capture=True) -+ result = local("python -m fabric -f tests/support/aborts.py kaboom", capture=True) - # When error in #1318 is present, this has an extra "It burns!" at end of - # stderr string. - eq_(result.stderr, "Fatal error: It burns!\n\nAborting.")
\ No newline at end of file diff --git a/gnu/packages/patches/gd-CVE-2017-7890.patch b/gnu/packages/patches/gd-CVE-2017-7890.patch new file mode 100644 index 0000000000..66034c5703 --- /dev/null +++ b/gnu/packages/patches/gd-CVE-2017-7890.patch @@ -0,0 +1,30 @@ +From 99ba5c353373ed198f54af66fe4e355ebb96e363 Mon Sep 17 00:00:00 2001 +From: LEPILLER Julien <julien@lepiller.eu> +Date: Thu, 3 Aug 2017 17:04:17 +0200 +Subject: [PATCH] Fix #399: Buffer over-read into uninitialized memory. + +The stack allocated color map buffers were not zeroed before usage, and +so undefined palette indexes could cause information leakage. + +This is CVE-2017-7890. +--- + src/gd_gif_in.c | 3 +++ + 1 file changed, 3 insertions(+) + +diff --git a/src/gd_gif_in.c b/src/gd_gif_in.c +index 008d1ec..c195448 100644 +--- a/src/gd_gif_in.c ++++ b/src/gd_gif_in.c +@@ -216,6 +216,9 @@ BGD_DECLARE(gdImagePtr) gdImageCreateFromGifCtx(gdIOCtxPtr fd) + + gdImagePtr im = 0; + ++ memset(ColorMap, 0, 3 * MAXCOLORMAPSIZE); ++ memset(localColorMap, 0, 3 * MAXCOLORMAPSIZE); ++ + if(!ReadOK(fd, buf, 6)) { + return 0; + } +-- +2.13.3 + diff --git a/gnu/packages/patches/glibc-CVE-2015-5180.patch b/gnu/packages/patches/glibc-CVE-2015-5180.patch new file mode 100644 index 0000000000..92e3740fc1 --- /dev/null +++ b/gnu/packages/patches/glibc-CVE-2015-5180.patch @@ -0,0 +1,311 @@ +From b3b37f1a5559a7620e31c8053ed1b44f798f2b6d Mon Sep 17 00:00:00 2001 +From: Florian Weimer <fweimer@redhat.com> +Date: Sat, 31 Dec 2016 20:22:09 +0100 +Subject: [PATCH] CVE-2015-5180: resolv: Fix crash with internal QTYPE [BZ + #18784] + +Also rename T_UNSPEC because an upcoming public header file +update will use that name. + +(cherry picked from commit fc82b0a2dfe7dbd35671c10510a8da1043d746a5) +--- + ChangeLog | 14 ++++ + NEWS | 6 ++ + include/arpa/nameser_compat.h | 6 +- + resolv/Makefile | 5 ++ + resolv/nss_dns/dns-host.c | 2 +- + resolv/res_mkquery.c | 4 + + resolv/res_query.c | 6 +- + resolv/tst-resolv-qtypes.c | 185 ++++++++++++++++++++++++++++++++++++++++++ + 8 files changed, 221 insertions(+), 7 deletions(-) + create mode 100644 resolv/tst-resolv-qtypes.c + +diff --git a/include/arpa/nameser_compat.h b/include/arpa/nameser_compat.h +index 2e735ed..7c0deed 100644 +--- a/include/arpa/nameser_compat.h ++++ b/include/arpa/nameser_compat.h +@@ -1,8 +1,8 @@ + #ifndef _ARPA_NAMESER_COMPAT_ + #include <resolv/arpa/nameser_compat.h> + +-/* Picksome unused number to represent lookups of IPv4 and IPv6 (i.e., +- T_A and T_AAAA). */ +-#define T_UNSPEC 62321 ++/* The number is outside the 16-bit RR type range and is used ++ internally by the implementation. */ ++#define T_QUERY_A_AND_AAAA 439963904 + + #endif +diff --git a/resolv/Makefile b/resolv/Makefile +index 8be41d3..a4c86b9 100644 +--- a/resolv/Makefile ++++ b/resolv/Makefile +@@ -40,6 +40,9 @@ ifeq ($(have-thread-library),yes) + extra-libs += libanl + routines += gai_sigqueue + tests += tst-res_hconf_reorder ++ ++# This test sends millions of packets and is rather slow. ++xtests += tst-resolv-qtypes + endif + extra-libs-others = $(extra-libs) + libresolv-routines := gethnamaddr res_comp res_debug \ +@@ -117,3 +120,5 @@ tst-leaks2-ENV = MALLOC_TRACE=$(objpfx)tst-leaks2.mtrace + $(objpfx)mtrace-tst-leaks2.out: $(objpfx)tst-leaks2.out + $(common-objpfx)malloc/mtrace $(objpfx)tst-leaks2.mtrace > $@; \ + $(evaluate-test) ++ ++$(objpfx)tst-resolv-qtypes: $(objpfx)libresolv.so $(shared-thread-library) +diff --git a/resolv/nss_dns/dns-host.c b/resolv/nss_dns/dns-host.c +index 5f9e357..d16fa4b 100644 +--- a/resolv/nss_dns/dns-host.c ++++ b/resolv/nss_dns/dns-host.c +@@ -323,7 +323,7 @@ _nss_dns_gethostbyname4_r (const char *name, struct gaih_addrtuple **pat, + + int olderr = errno; + enum nss_status status; +- int n = __libc_res_nsearch (&_res, name, C_IN, T_UNSPEC, ++ int n = __libc_res_nsearch (&_res, name, C_IN, T_QUERY_A_AND_AAAA, + host_buffer.buf->buf, 2048, &host_buffer.ptr, + &ans2p, &nans2p, &resplen2, &ans2p_malloced); + if (n >= 0) +diff --git a/resolv/res_mkquery.c b/resolv/res_mkquery.c +index 12f9730..d80b531 100644 +--- a/resolv/res_mkquery.c ++++ b/resolv/res_mkquery.c +@@ -103,6 +103,10 @@ res_nmkquery(res_state statp, + int n; + u_char *dnptrs[20], **dpp, **lastdnptr; + ++ if (class < 0 || class > 65535 ++ || type < 0 || type > 65535) ++ return -1; ++ + #ifdef DEBUG + if (statp->options & RES_DEBUG) + printf(";; res_nmkquery(%s, %s, %s, %s)\n", +diff --git a/resolv/res_query.c b/resolv/res_query.c +index 944d1a9..07dc6f6 100644 +--- a/resolv/res_query.c ++++ b/resolv/res_query.c +@@ -122,7 +122,7 @@ __libc_res_nquery(res_state statp, + int n, use_malloc = 0; + u_int oflags = statp->_flags; + +- size_t bufsize = (type == T_UNSPEC ? 2 : 1) * QUERYSIZE; ++ size_t bufsize = (type == T_QUERY_A_AND_AAAA ? 2 : 1) * QUERYSIZE; + u_char *buf = alloca (bufsize); + u_char *query1 = buf; + int nquery1 = -1; +@@ -137,7 +137,7 @@ __libc_res_nquery(res_state statp, + printf(";; res_query(%s, %d, %d)\n", name, class, type); + #endif + +- if (type == T_UNSPEC) ++ if (type == T_QUERY_A_AND_AAAA) + { + n = res_nmkquery(statp, QUERY, name, class, T_A, NULL, 0, NULL, + query1, bufsize); +@@ -190,7 +190,7 @@ __libc_res_nquery(res_state statp, + if (__builtin_expect (n <= 0, 0) && !use_malloc) { + /* Retry just in case res_nmkquery failed because of too + short buffer. Shouldn't happen. */ +- bufsize = (type == T_UNSPEC ? 2 : 1) * MAXPACKET; ++ bufsize = (type == T_QUERY_A_AND_AAAA ? 2 : 1) * MAXPACKET; + buf = malloc (bufsize); + if (buf != NULL) { + query1 = buf; +diff --git a/resolv/tst-resolv-qtypes.c b/resolv/tst-resolv-qtypes.c +new file mode 100644 +index 0000000..b3e60c6 +--- /dev/null ++++ b/resolv/tst-resolv-qtypes.c +@@ -0,0 +1,185 @@ ++/* Exercise low-level query functions with different QTYPEs. ++ Copyright (C) 2016 Free Software Foundation, Inc. ++ This file is part of the GNU C Library. ++ ++ The GNU C Library is free software; you can redistribute it and/or ++ modify it under the terms of the GNU Lesser General Public ++ License as published by the Free Software Foundation; either ++ version 2.1 of the License, or (at your option) any later version. ++ ++ The GNU C Library is distributed in the hope that it will be useful, ++ but WITHOUT ANY WARRANTY; without even the implied warranty of ++ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU ++ Lesser General Public License for more details. ++ ++ You should have received a copy of the GNU Lesser General Public ++ License along with the GNU C Library; if not, see ++ <http://www.gnu.org/licenses/>. */ ++ ++#include <resolv.h> ++#include <string.h> ++#include <support/check.h> ++#include <support/check_nss.h> ++#include <support/resolv_test.h> ++#include <support/support.h> ++#include <support/test-driver.h> ++#include <support/xmemstream.h> ++ ++/* If ture, the response function will send the actual response packet ++ over TCP instead of UDP. */ ++static volatile bool force_tcp; ++ ++/* Send back a fake resource record matching the QTYPE. */ ++static void ++response (const struct resolv_response_context *ctx, ++ struct resolv_response_builder *b, ++ const char *qname, uint16_t qclass, uint16_t qtype) ++{ ++ if (force_tcp && ctx->tcp) ++ { ++ resolv_response_init (b, (struct resolv_response_flags) { .tc = 1 }); ++ resolv_response_add_question (b, qname, qclass, qtype); ++ return; ++ } ++ ++ resolv_response_init (b, (struct resolv_response_flags) { }); ++ resolv_response_add_question (b, qname, qclass, qtype); ++ resolv_response_section (b, ns_s_an); ++ resolv_response_open_record (b, qname, qclass, qtype, 0); ++ resolv_response_add_data (b, &qtype, sizeof (qtype)); ++ resolv_response_close_record (b); ++} ++ ++static const const char *domain = "www.example.com"; ++ ++static int ++wrap_res_query (int type, unsigned char *answer, int answer_length) ++{ ++ return res_query (domain, C_IN, type, answer, answer_length); ++} ++ ++static int ++wrap_res_search (int type, unsigned char *answer, int answer_length) ++{ ++ return res_query (domain, C_IN, type, answer, answer_length); ++} ++ ++static int ++wrap_res_querydomain (int type, unsigned char *answer, int answer_length) ++{ ++ return res_querydomain ("www", "example.com", C_IN, type, ++ answer, answer_length); ++} ++ ++static int ++wrap_res_send (int type, unsigned char *answer, int answer_length) ++{ ++ unsigned char buf[512]; ++ int ret = res_mkquery (QUERY, domain, C_IN, type, ++ (const unsigned char *) "", 0, NULL, ++ buf, sizeof (buf)); ++ if (type < 0 || type >= 65536) ++ { ++ /* res_mkquery fails for out-of-range record types. */ ++ TEST_VERIFY_EXIT (ret == -1); ++ return -1; ++ } ++ TEST_VERIFY_EXIT (ret > 12); /* DNS header length. */ ++ return res_send (buf, ret, answer, answer_length); ++} ++ ++static int ++wrap_res_nquery (int type, unsigned char *answer, int answer_length) ++{ ++ return res_nquery (&_res, domain, C_IN, type, answer, answer_length); ++} ++ ++static int ++wrap_res_nsearch (int type, unsigned char *answer, int answer_length) ++{ ++ return res_nquery (&_res, domain, C_IN, type, answer, answer_length); ++} ++ ++static int ++wrap_res_nquerydomain (int type, unsigned char *answer, int answer_length) ++{ ++ return res_nquerydomain (&_res, "www", "example.com", C_IN, type, ++ answer, answer_length); ++} ++ ++static int ++wrap_res_nsend (int type, unsigned char *answer, int answer_length) ++{ ++ unsigned char buf[512]; ++ int ret = res_nmkquery (&_res, QUERY, domain, C_IN, type, ++ (const unsigned char *) "", 0, NULL, ++ buf, sizeof (buf)); ++ if (type < 0 || type >= 65536) ++ { ++ /* res_mkquery fails for out-of-range record types. */ ++ TEST_VERIFY_EXIT (ret == -1); ++ return -1; ++ } ++ TEST_VERIFY_EXIT (ret > 12); /* DNS header length. */ ++ return res_nsend (&_res, buf, ret, answer, answer_length); ++} ++ ++static void ++test_function (const char *fname, ++ int (*func) (int type, ++ unsigned char *answer, int answer_length)) ++{ ++ unsigned char buf[512]; ++ for (int tcp = 0; tcp < 2; ++tcp) ++ { ++ force_tcp = tcp; ++ for (unsigned int type = 1; type <= 65535; ++type) ++ { ++ if (test_verbose) ++ printf ("info: sending QTYPE %d with %s (tcp=%d)\n", ++ type, fname, tcp); ++ int ret = func (type, buf, sizeof (buf)); ++ if (ret != 47) ++ FAIL_EXIT1 ("%s tcp=%d qtype=%d return value %d", ++ fname,tcp, type, ret); ++ /* One question, one answer record. */ ++ TEST_VERIFY (memcmp (buf + 4, "\0\1\0\1\0\0\0\0", 8) == 0); ++ /* Question section. */ ++ static const char qname[] = "\3www\7example\3com"; ++ size_t qname_length = sizeof (qname); ++ TEST_VERIFY (memcmp (buf + 12, qname, qname_length) == 0); ++ /* RDATA part of answer. */ ++ uint16_t type16 = type; ++ TEST_VERIFY (memcmp (buf + ret - 2, &type16, sizeof (type16)) == 0); ++ } ++ } ++ ++ TEST_VERIFY (func (-1, buf, sizeof (buf) == -1)); ++ TEST_VERIFY (func (65536, buf, sizeof (buf) == -1)); ++} ++ ++static int ++do_test (void) ++{ ++ struct resolv_redirect_config config = ++ { ++ .response_callback = response, ++ }; ++ struct resolv_test *obj = resolv_test_start (config); ++ ++ test_function ("res_query", &wrap_res_query); ++ test_function ("res_search", &wrap_res_search); ++ test_function ("res_querydomain", &wrap_res_querydomain); ++ test_function ("res_send", &wrap_res_send); ++ ++ test_function ("res_nquery", &wrap_res_nquery); ++ test_function ("res_nsearch", &wrap_res_nsearch); ++ test_function ("res_nquerydomain", &wrap_res_nquerydomain); ++ test_function ("res_nsend", &wrap_res_nsend); ++ ++ resolv_test_end (obj); ++ return 0; ++} ++ ++#define TIMEOUT 300 ++#include <support/test-driver.c> +-- +2.9.3 + diff --git a/gnu/packages/patches/glibc-CVE-2015-7547.patch b/gnu/packages/patches/glibc-CVE-2015-7547.patch new file mode 100644 index 0000000000..12abeb76d4 --- /dev/null +++ b/gnu/packages/patches/glibc-CVE-2015-7547.patch @@ -0,0 +1,590 @@ +From b995d95a5943785be3ab862b2d3276f3b4a22481 Mon Sep 17 00:00:00 2001 +From: Carlos O'Donell <carlos@systemhalted.org> +Date: Tue, 16 Feb 2016 21:26:37 -0500 +Subject: [PATCH] CVE-2015-7547: getaddrinfo() stack-based buffer overflow (Bug + 18665). + +* A stack-based buffer overflow was found in libresolv when invoked from + libnss_dns, allowing specially crafted DNS responses to seize control + of execution flow in the DNS client. The buffer overflow occurs in + the functions send_dg (send datagram) and send_vc (send TCP) for the + NSS module libnss_dns.so.2 when calling getaddrinfo with AF_UNSPEC + family. The use of AF_UNSPEC triggers the low-level resolver code to + send out two parallel queries for A and AAAA. A mismanagement of the + buffers used for those queries could result in the response of a query + writing beyond the alloca allocated buffer created by + _nss_dns_gethostbyname4_r. Buffer management is simplified to remove + the overflow. Thanks to the Google Security Team and Red Hat for + reporting the security impact of this issue, and Robert Holiday of + Ciena for reporting the related bug 18665. (CVE-2015-7547) + +See also: +https://sourceware.org/ml/libc-alpha/2016-02/msg00416.html +https://sourceware.org/ml/libc-alpha/2016-02/msg00418.html + +(cherry picked from commit e9db92d3acfe1822d56d11abcea5bfc4c41cf6ca) +--- + ChangeLog | 15 +++ + NEWS | 14 +++ + resolv/nss_dns/dns-host.c | 111 ++++++++++++++++++- + resolv/res_query.c | 3 + + resolv/res_send.c | 264 ++++++++++++++++++++++++++++++++++------------ + 5 files changed, 338 insertions(+), 69 deletions(-) + +diff --git a/resolv/nss_dns/dns-host.c b/resolv/nss_dns/dns-host.c +index 357ac04..a0fe9a8 100644 +--- a/resolv/nss_dns/dns-host.c ++++ b/resolv/nss_dns/dns-host.c +@@ -1031,7 +1031,10 @@ gaih_getanswer_slice (const querybuf *answer, int anslen, const char *qname, + int h_namelen = 0; + + if (ancount == 0) +- return NSS_STATUS_NOTFOUND; ++ { ++ *h_errnop = HOST_NOT_FOUND; ++ return NSS_STATUS_NOTFOUND; ++ } + + while (ancount-- > 0 && cp < end_of_message && had_error == 0) + { +@@ -1208,7 +1211,14 @@ gaih_getanswer_slice (const querybuf *answer, int anslen, const char *qname, + /* Special case here: if the resolver sent a result but it only + contains a CNAME while we are looking for a T_A or T_AAAA record, + we fail with NOTFOUND instead of TRYAGAIN. */ +- return canon == NULL ? NSS_STATUS_TRYAGAIN : NSS_STATUS_NOTFOUND; ++ if (canon != NULL) ++ { ++ *h_errnop = HOST_NOT_FOUND; ++ return NSS_STATUS_NOTFOUND; ++ } ++ ++ *h_errnop = NETDB_INTERNAL; ++ return NSS_STATUS_TRYAGAIN; + } + + +@@ -1222,11 +1232,101 @@ gaih_getanswer (const querybuf *answer1, int anslen1, const querybuf *answer2, + + enum nss_status status = NSS_STATUS_NOTFOUND; + ++ /* Combining the NSS status of two distinct queries requires some ++ compromise and attention to symmetry (A or AAAA queries can be ++ returned in any order). What follows is a breakdown of how this ++ code is expected to work and why. We discuss only SUCCESS, ++ TRYAGAIN, NOTFOUND and UNAVAIL, since they are the only returns ++ that apply (though RETURN and MERGE exist). We make a distinction ++ between TRYAGAIN (recoverable) and TRYAGAIN' (not-recoverable). ++ A recoverable TRYAGAIN is almost always due to buffer size issues ++ and returns ERANGE in errno and the caller is expected to retry ++ with a larger buffer. ++ ++ Lastly, you may be tempted to make significant changes to the ++ conditions in this code to bring about symmetry between responses. ++ Please don't change anything without due consideration for ++ expected application behaviour. Some of the synthesized responses ++ aren't very well thought out and sometimes appear to imply that ++ IPv4 responses are always answer 1, and IPv6 responses are always ++ answer 2, but that's not true (see the implementation of send_dg ++ and send_vc to see response can arrive in any order, particularly ++ for UDP). However, we expect it holds roughly enough of the time ++ that this code works, but certainly needs to be fixed to make this ++ a more robust implementation. ++ ++ ---------------------------------------------- ++ | Answer 1 Status / | Synthesized | Reason | ++ | Answer 2 Status | Status | | ++ |--------------------------------------------| ++ | SUCCESS/SUCCESS | SUCCESS | [1] | ++ | SUCCESS/TRYAGAIN | TRYAGAIN | [5] | ++ | SUCCESS/TRYAGAIN' | SUCCESS | [1] | ++ | SUCCESS/NOTFOUND | SUCCESS | [1] | ++ | SUCCESS/UNAVAIL | SUCCESS | [1] | ++ | TRYAGAIN/SUCCESS | TRYAGAIN | [2] | ++ | TRYAGAIN/TRYAGAIN | TRYAGAIN | [2] | ++ | TRYAGAIN/TRYAGAIN' | TRYAGAIN | [2] | ++ | TRYAGAIN/NOTFOUND | TRYAGAIN | [2] | ++ | TRYAGAIN/UNAVAIL | TRYAGAIN | [2] | ++ | TRYAGAIN'/SUCCESS | SUCCESS | [3] | ++ | TRYAGAIN'/TRYAGAIN | TRYAGAIN | [3] | ++ | TRYAGAIN'/TRYAGAIN' | TRYAGAIN' | [3] | ++ | TRYAGAIN'/NOTFOUND | TRYAGAIN' | [3] | ++ | TRYAGAIN'/UNAVAIL | UNAVAIL | [3] | ++ | NOTFOUND/SUCCESS | SUCCESS | [3] | ++ | NOTFOUND/TRYAGAIN | TRYAGAIN | [3] | ++ | NOTFOUND/TRYAGAIN' | TRYAGAIN' | [3] | ++ | NOTFOUND/NOTFOUND | NOTFOUND | [3] | ++ | NOTFOUND/UNAVAIL | UNAVAIL | [3] | ++ | UNAVAIL/SUCCESS | UNAVAIL | [4] | ++ | UNAVAIL/TRYAGAIN | UNAVAIL | [4] | ++ | UNAVAIL/TRYAGAIN' | UNAVAIL | [4] | ++ | UNAVAIL/NOTFOUND | UNAVAIL | [4] | ++ | UNAVAIL/UNAVAIL | UNAVAIL | [4] | ++ ---------------------------------------------- ++ ++ [1] If the first response is a success we return success. ++ This ignores the state of the second answer and in fact ++ incorrectly sets errno and h_errno to that of the second ++ answer. However because the response is a success we ignore ++ *errnop and *h_errnop (though that means you touched errno on ++ success). We are being conservative here and returning the ++ likely IPv4 response in the first answer as a success. ++ ++ [2] If the first response is a recoverable TRYAGAIN we return ++ that instead of looking at the second response. The ++ expectation here is that we have failed to get an IPv4 response ++ and should retry both queries. ++ ++ [3] If the first response was not a SUCCESS and the second ++ response is not NOTFOUND (had a SUCCESS, need to TRYAGAIN, ++ or failed entirely e.g. TRYAGAIN' and UNAVAIL) then use the ++ result from the second response, otherwise the first responses ++ status is used. Again we have some odd side-effects when the ++ second response is NOTFOUND because we overwrite *errnop and ++ *h_errnop that means that a first answer of NOTFOUND might see ++ its *errnop and *h_errnop values altered. Whether it matters ++ in practice that a first response NOTFOUND has the wrong ++ *errnop and *h_errnop is undecided. ++ ++ [4] If the first response is UNAVAIL we return that instead of ++ looking at the second response. The expectation here is that ++ it will have failed similarly e.g. configuration failure. ++ ++ [5] Testing this code is complicated by the fact that truncated ++ second response buffers might be returned as SUCCESS if the ++ first answer is a SUCCESS. To fix this we add symmetry to ++ TRYAGAIN with the second response. If the second response ++ is a recoverable error we now return TRYAGIN even if the first ++ response was SUCCESS. */ ++ + if (anslen1 > 0) + status = gaih_getanswer_slice(answer1, anslen1, qname, + &pat, &buffer, &buflen, + errnop, h_errnop, ttlp, + &first); ++ + if ((status == NSS_STATUS_SUCCESS || status == NSS_STATUS_NOTFOUND + || (status == NSS_STATUS_TRYAGAIN + /* We want to look at the second answer in case of an +@@ -1242,8 +1342,15 @@ gaih_getanswer (const querybuf *answer1, int anslen1, const querybuf *answer2, + &pat, &buffer, &buflen, + errnop, h_errnop, ttlp, + &first); ++ /* Use the second response status in some cases. */ + if (status != NSS_STATUS_SUCCESS && status2 != NSS_STATUS_NOTFOUND) + status = status2; ++ /* Do not return a truncated second response (unless it was ++ unavoidable e.g. unrecoverable TRYAGAIN). */ ++ if (status == NSS_STATUS_SUCCESS ++ && (status2 == NSS_STATUS_TRYAGAIN ++ && *errnop == ERANGE && *h_errnop != NO_RECOVERY)) ++ status = NSS_STATUS_TRYAGAIN; + } + + return status; +diff --git a/resolv/res_query.c b/resolv/res_query.c +index 4a9b3b3..95470a9 100644 +--- a/resolv/res_query.c ++++ b/resolv/res_query.c +@@ -396,6 +396,7 @@ __libc_res_nsearch(res_state statp, + { + free (*answerp2); + *answerp2 = NULL; ++ *nanswerp2 = 0; + *answerp2_malloced = 0; + } + } +@@ -447,6 +448,7 @@ __libc_res_nsearch(res_state statp, + { + free (*answerp2); + *answerp2 = NULL; ++ *nanswerp2 = 0; + *answerp2_malloced = 0; + } + +@@ -521,6 +523,7 @@ __libc_res_nsearch(res_state statp, + { + free (*answerp2); + *answerp2 = NULL; ++ *nanswerp2 = 0; + *answerp2_malloced = 0; + } + if (saved_herrno != -1) +diff --git a/resolv/res_send.c b/resolv/res_send.c +index 5e53cc2..6511bb1 100644 +--- a/resolv/res_send.c ++++ b/resolv/res_send.c +@@ -1,3 +1,20 @@ ++/* Copyright (C) 2016 Free Software Foundation, Inc. ++ This file is part of the GNU C Library. ++ ++ The GNU C Library is free software; you can redistribute it and/or ++ modify it under the terms of the GNU Lesser General Public ++ License as published by the Free Software Foundation; either ++ version 2.1 of the License, or (at your option) any later version. ++ ++ The GNU C Library is distributed in the hope that it will be useful, ++ but WITHOUT ANY WARRANTY; without even the implied warranty of ++ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU ++ Lesser General Public License for more details. ++ ++ You should have received a copy of the GNU Lesser General Public ++ License along with the GNU C Library; if not, see ++ <http://www.gnu.org/licenses/>. */ ++ + /* + * Copyright (c) 1985, 1989, 1993 + * The Regents of the University of California. All rights reserved. +@@ -363,6 +380,8 @@ __libc_res_nsend(res_state statp, const u_char *buf, int buflen, + #ifdef USE_HOOKS + if (__glibc_unlikely (statp->qhook || statp->rhook)) { + if (anssiz < MAXPACKET && ansp) { ++ /* Always allocate MAXPACKET, callers expect ++ this specific size. */ + u_char *buf = malloc (MAXPACKET); + if (buf == NULL) + return (-1); +@@ -638,6 +657,77 @@ get_nsaddr (res_state statp, int n) + return (struct sockaddr *) (void *) &statp->nsaddr_list[n]; + } + ++/* The send_vc function is responsible for sending a DNS query over TCP ++ to the nameserver numbered NS from the res_state STATP i.e. ++ EXT(statp).nssocks[ns]. The function supports sending both IPv4 and ++ IPv6 queries at the same serially on the same socket. ++ ++ Please note that for TCP there is no way to disable sending both ++ queries, unlike UDP, which honours RES_SNGLKUP and RES_SNGLKUPREOP ++ and sends the queries serially and waits for the result after each ++ sent query. This implemetnation should be corrected to honour these ++ options. ++ ++ Please also note that for TCP we send both queries over the same ++ socket one after another. This technically violates best practice ++ since the server is allowed to read the first query, respond, and ++ then close the socket (to service another client). If the server ++ does this, then the remaining second query in the socket data buffer ++ will cause the server to send the client an RST which will arrive ++ asynchronously and the client's OS will likely tear down the socket ++ receive buffer resulting in a potentially short read and lost ++ response data. This will force the client to retry the query again, ++ and this process may repeat until all servers and connection resets ++ are exhausted and then the query will fail. It's not known if this ++ happens with any frequency in real DNS server implementations. This ++ implementation should be corrected to use two sockets by default for ++ parallel queries. ++ ++ The query stored in BUF of BUFLEN length is sent first followed by ++ the query stored in BUF2 of BUFLEN2 length. Queries are sent ++ serially on the same socket. ++ ++ Answers to the query are stored firstly in *ANSP up to a max of ++ *ANSSIZP bytes. If more than *ANSSIZP bytes are needed and ANSCP ++ is non-NULL (to indicate that modifying the answer buffer is allowed) ++ then malloc is used to allocate a new response buffer and ANSCP and ++ ANSP will both point to the new buffer. If more than *ANSSIZP bytes ++ are needed but ANSCP is NULL, then as much of the response as ++ possible is read into the buffer, but the results will be truncated. ++ When truncation happens because of a small answer buffer the DNS ++ packets header field TC will bet set to 1, indicating a truncated ++ message and the rest of the socket data will be read and discarded. ++ ++ Answers to the query are stored secondly in *ANSP2 up to a max of ++ *ANSSIZP2 bytes, with the actual response length stored in ++ *RESPLEN2. If more than *ANSSIZP bytes are needed and ANSP2 ++ is non-NULL (required for a second query) then malloc is used to ++ allocate a new response buffer, *ANSSIZP2 is set to the new buffer ++ size and *ANSP2_MALLOCED is set to 1. ++ ++ The ANSP2_MALLOCED argument will eventually be removed as the ++ change in buffer pointer can be used to detect the buffer has ++ changed and that the caller should use free on the new buffer. ++ ++ Note that the answers may arrive in any order from the server and ++ therefore the first and second answer buffers may not correspond to ++ the first and second queries. ++ ++ It is not supported to call this function with a non-NULL ANSP2 ++ but a NULL ANSCP. Put another way, you can call send_vc with a ++ single unmodifiable buffer or two modifiable buffers, but no other ++ combination is supported. ++ ++ It is the caller's responsibility to free the malloc allocated ++ buffers by detecting that the pointers have changed from their ++ original values i.e. *ANSCP or *ANSP2 has changed. ++ ++ If errors are encountered then *TERRNO is set to an appropriate ++ errno value and a zero result is returned for a recoverable error, ++ and a less-than zero result is returned for a non-recoverable error. ++ ++ If no errors are encountered then *TERRNO is left unmodified and ++ a the length of the first response in bytes is returned. */ + static int + send_vc(res_state statp, + const u_char *buf, int buflen, const u_char *buf2, int buflen2, +@@ -647,11 +737,7 @@ send_vc(res_state statp, + { + const HEADER *hp = (HEADER *) buf; + const HEADER *hp2 = (HEADER *) buf2; +- u_char *ans = *ansp; +- int orig_anssizp = *anssizp; +- // XXX REMOVE +- // int anssiz = *anssizp; +- HEADER *anhp = (HEADER *) ans; ++ HEADER *anhp = (HEADER *) *ansp; + struct sockaddr *nsap = get_nsaddr (statp, ns); + int truncating, connreset, n; + /* On some architectures compiler might emit a warning indicating +@@ -743,6 +829,8 @@ send_vc(res_state statp, + * Receive length & response + */ + int recvresp1 = 0; ++ /* Skip the second response if there is no second query. ++ To do that we mark the second response as received. */ + int recvresp2 = buf2 == NULL; + uint16_t rlen16; + read_len: +@@ -779,40 +867,14 @@ send_vc(res_state statp, + u_char **thisansp; + int *thisresplenp; + if ((recvresp1 | recvresp2) == 0 || buf2 == NULL) { ++ /* We have not received any responses ++ yet or we only have one response to ++ receive. */ + thisanssizp = anssizp; + thisansp = anscp ?: ansp; + assert (anscp != NULL || ansp2 == NULL); + thisresplenp = &resplen; + } else { +- if (*anssizp != MAXPACKET) { +- /* No buffer allocated for the first +- reply. We can try to use the rest +- of the user-provided buffer. */ +-#if __GNUC_PREREQ (4, 7) +- DIAG_PUSH_NEEDS_COMMENT; +- DIAG_IGNORE_NEEDS_COMMENT (5, "-Wmaybe-uninitialized"); +-#endif +-#if _STRING_ARCH_unaligned +- *anssizp2 = orig_anssizp - resplen; +- *ansp2 = *ansp + resplen; +-#else +- int aligned_resplen +- = ((resplen + __alignof__ (HEADER) - 1) +- & ~(__alignof__ (HEADER) - 1)); +- *anssizp2 = orig_anssizp - aligned_resplen; +- *ansp2 = *ansp + aligned_resplen; +-#endif +-#if __GNUC_PREREQ (4, 7) +- DIAG_POP_NEEDS_COMMENT; +-#endif +- } else { +- /* The first reply did not fit into the +- user-provided buffer. Maybe the second +- answer will. */ +- *anssizp2 = orig_anssizp; +- *ansp2 = *ansp; +- } +- + thisanssizp = anssizp2; + thisansp = ansp2; + thisresplenp = resplen2; +@@ -820,10 +882,14 @@ send_vc(res_state statp, + anhp = (HEADER *) *thisansp; + + *thisresplenp = rlen; +- if (rlen > *thisanssizp) { +- /* Yes, we test ANSCP here. If we have two buffers +- both will be allocatable. */ +- if (__glibc_likely (anscp != NULL)) { ++ /* Is the answer buffer too small? */ ++ if (*thisanssizp < rlen) { ++ /* If the current buffer is not the the static ++ user-supplied buffer then we can reallocate ++ it. */ ++ if (thisansp != NULL && thisansp != ansp) { ++ /* Always allocate MAXPACKET, callers expect ++ this specific size. */ + u_char *newp = malloc (MAXPACKET); + if (newp == NULL) { + *terrno = ENOMEM; +@@ -835,6 +901,9 @@ send_vc(res_state statp, + if (thisansp == ansp2) + *ansp2_malloced = 1; + anhp = (HEADER *) newp; ++ /* A uint16_t can't be larger than MAXPACKET ++ thus it's safe to allocate MAXPACKET but ++ read RLEN bytes instead. */ + len = rlen; + } else { + Dprint(statp->options & RES_DEBUG, +@@ -997,6 +1066,66 @@ reopen (res_state statp, int *terrno, int ns) + return 1; + } + ++/* The send_dg function is responsible for sending a DNS query over UDP ++ to the nameserver numbered NS from the res_state STATP i.e. ++ EXT(statp).nssocks[ns]. The function supports IPv4 and IPv6 queries ++ along with the ability to send the query in parallel for both stacks ++ (default) or serially (RES_SINGLKUP). It also supports serial lookup ++ with a close and reopen of the socket used to talk to the server ++ (RES_SNGLKUPREOP) to work around broken name servers. ++ ++ The query stored in BUF of BUFLEN length is sent first followed by ++ the query stored in BUF2 of BUFLEN2 length. Queries are sent ++ in parallel (default) or serially (RES_SINGLKUP or RES_SNGLKUPREOP). ++ ++ Answers to the query are stored firstly in *ANSP up to a max of ++ *ANSSIZP bytes. If more than *ANSSIZP bytes are needed and ANSCP ++ is non-NULL (to indicate that modifying the answer buffer is allowed) ++ then malloc is used to allocate a new response buffer and ANSCP and ++ ANSP will both point to the new buffer. If more than *ANSSIZP bytes ++ are needed but ANSCP is NULL, then as much of the response as ++ possible is read into the buffer, but the results will be truncated. ++ When truncation happens because of a small answer buffer the DNS ++ packets header field TC will bet set to 1, indicating a truncated ++ message, while the rest of the UDP packet is discarded. ++ ++ Answers to the query are stored secondly in *ANSP2 up to a max of ++ *ANSSIZP2 bytes, with the actual response length stored in ++ *RESPLEN2. If more than *ANSSIZP bytes are needed and ANSP2 ++ is non-NULL (required for a second query) then malloc is used to ++ allocate a new response buffer, *ANSSIZP2 is set to the new buffer ++ size and *ANSP2_MALLOCED is set to 1. ++ ++ The ANSP2_MALLOCED argument will eventually be removed as the ++ change in buffer pointer can be used to detect the buffer has ++ changed and that the caller should use free on the new buffer. ++ ++ Note that the answers may arrive in any order from the server and ++ therefore the first and second answer buffers may not correspond to ++ the first and second queries. ++ ++ It is not supported to call this function with a non-NULL ANSP2 ++ but a NULL ANSCP. Put another way, you can call send_vc with a ++ single unmodifiable buffer or two modifiable buffers, but no other ++ combination is supported. ++ ++ It is the caller's responsibility to free the malloc allocated ++ buffers by detecting that the pointers have changed from their ++ original values i.e. *ANSCP or *ANSP2 has changed. ++ ++ If an answer is truncated because of UDP datagram DNS limits then ++ *V_CIRCUIT is set to 1 and the return value non-zero to indicate to ++ the caller to retry with TCP. The value *GOTSOMEWHERE is set to 1 ++ if any progress was made reading a response from the nameserver and ++ is used by the caller to distinguish between ECONNREFUSED and ++ ETIMEDOUT (the latter if *GOTSOMEWHERE is 1). ++ ++ If errors are encountered then *TERRNO is set to an appropriate ++ errno value and a zero result is returned for a recoverable error, ++ and a less-than zero result is returned for a non-recoverable error. ++ ++ If no errors are encountered then *TERRNO is left unmodified and ++ a the length of the first response in bytes is returned. */ + static int + send_dg(res_state statp, + const u_char *buf, int buflen, const u_char *buf2, int buflen2, +@@ -1006,8 +1135,6 @@ send_dg(res_state statp, + { + const HEADER *hp = (HEADER *) buf; + const HEADER *hp2 = (HEADER *) buf2; +- u_char *ans = *ansp; +- int orig_anssizp = *anssizp; + struct timespec now, timeout, finish; + struct pollfd pfd[1]; + int ptimeout; +@@ -1040,6 +1167,8 @@ send_dg(res_state statp, + int need_recompute = 0; + int nwritten = 0; + int recvresp1 = 0; ++ /* Skip the second response if there is no second query. ++ To do that we mark the second response as received. */ + int recvresp2 = buf2 == NULL; + pfd[0].fd = EXT(statp).nssocks[ns]; + pfd[0].events = POLLOUT; +@@ -1203,55 +1332,56 @@ send_dg(res_state statp, + int *thisresplenp; + + if ((recvresp1 | recvresp2) == 0 || buf2 == NULL) { ++ /* We have not received any responses ++ yet or we only have one response to ++ receive. */ + thisanssizp = anssizp; + thisansp = anscp ?: ansp; + assert (anscp != NULL || ansp2 == NULL); + thisresplenp = &resplen; + } else { +- if (*anssizp != MAXPACKET) { +- /* No buffer allocated for the first +- reply. We can try to use the rest +- of the user-provided buffer. */ +-#if _STRING_ARCH_unaligned +- *anssizp2 = orig_anssizp - resplen; +- *ansp2 = *ansp + resplen; +-#else +- int aligned_resplen +- = ((resplen + __alignof__ (HEADER) - 1) +- & ~(__alignof__ (HEADER) - 1)); +- *anssizp2 = orig_anssizp - aligned_resplen; +- *ansp2 = *ansp + aligned_resplen; +-#endif +- } else { +- /* The first reply did not fit into the +- user-provided buffer. Maybe the second +- answer will. */ +- *anssizp2 = orig_anssizp; +- *ansp2 = *ansp; +- } +- + thisanssizp = anssizp2; + thisansp = ansp2; + thisresplenp = resplen2; + } + + if (*thisanssizp < MAXPACKET +- /* Yes, we test ANSCP here. If we have two buffers +- both will be allocatable. */ +- && anscp ++ /* If the current buffer is not the the static ++ user-supplied buffer then we can reallocate ++ it. */ ++ && (thisansp != NULL && thisansp != ansp) + #ifdef FIONREAD ++ /* Is the size too small? */ + && (ioctl (pfd[0].fd, FIONREAD, thisresplenp) < 0 + || *thisanssizp < *thisresplenp) + #endif + ) { ++ /* Always allocate MAXPACKET, callers expect ++ this specific size. */ + u_char *newp = malloc (MAXPACKET); + if (newp != NULL) { +- *anssizp = MAXPACKET; +- *thisansp = ans = newp; ++ *thisanssizp = MAXPACKET; ++ *thisansp = newp; + if (thisansp == ansp2) + *ansp2_malloced = 1; + } + } ++ /* We could end up with truncation if anscp was NULL ++ (not allowed to change caller's buffer) and the ++ response buffer size is too small. This isn't a ++ reliable way to detect truncation because the ioctl ++ may be an inaccurate report of the UDP message size. ++ Therefore we use this only to issue debug output. ++ To do truncation accurately with UDP we need ++ MSG_TRUNC which is only available on Linux. We ++ can abstract out the Linux-specific feature in the ++ future to detect truncation. */ ++ if (__glibc_unlikely (*thisanssizp < *thisresplenp)) { ++ Dprint(statp->options & RES_DEBUG, ++ (stdout, ";; response may be truncated (UDP)\n") ++ ); ++ } ++ + HEADER *anhp = (HEADER *) *thisansp; + socklen_t fromlen = sizeof(struct sockaddr_in6); + assert (sizeof(from) <= fromlen); +-- +2.9.3 + diff --git a/gnu/packages/patches/glibc-CVE-2016-3075.patch b/gnu/packages/patches/glibc-CVE-2016-3075.patch new file mode 100644 index 0000000000..d16722806e --- /dev/null +++ b/gnu/packages/patches/glibc-CVE-2016-3075.patch @@ -0,0 +1,43 @@ +From 146b58d11fddbef15b888906e3be4f33900c416f Mon Sep 17 00:00:00 2001 +From: Florian Weimer <fweimer@redhat.com> +Date: Tue, 29 Mar 2016 12:57:56 +0200 +Subject: [PATCH] CVE-2016-3075: Stack overflow in _nss_dns_getnetbyname_r [BZ + #19879] + +The defensive copy is not needed because the name may not alias the +output buffer. + +(cherry picked from commit 317b199b4aff8cfa27f2302ab404d2bb5032b9a4) +(cherry picked from commit 883dceebc8f11921a9890211a4e202e5be17562f) +--- + ChangeLog | 7 +++++++ + NEWS | 10 ++++++++-- + resolv/nss_dns/dns-network.c | 5 +---- + 3 files changed, 16 insertions(+), 6 deletions(-) + +diff --git a/resolv/nss_dns/dns-network.c b/resolv/nss_dns/dns-network.c +index 2eb2f67..8f301a7 100644 +--- a/resolv/nss_dns/dns-network.c ++++ b/resolv/nss_dns/dns-network.c +@@ -118,17 +118,14 @@ _nss_dns_getnetbyname_r (const char *name, struct netent *result, + } net_buffer; + querybuf *orig_net_buffer; + int anslen; +- char *qbuf; + enum nss_status status; + + if (__res_maybe_init (&_res, 0) == -1) + return NSS_STATUS_UNAVAIL; + +- qbuf = strdupa (name); +- + net_buffer.buf = orig_net_buffer = (querybuf *) alloca (1024); + +- anslen = __libc_res_nsearch (&_res, qbuf, C_IN, T_PTR, net_buffer.buf->buf, ++ anslen = __libc_res_nsearch (&_res, name, C_IN, T_PTR, net_buffer.buf->buf, + 1024, &net_buffer.ptr, NULL, NULL, NULL, NULL); + if (anslen < 0) + { +-- +2.9.3 + diff --git a/gnu/packages/patches/glibc-CVE-2016-3706.patch b/gnu/packages/patches/glibc-CVE-2016-3706.patch new file mode 100644 index 0000000000..617242df24 --- /dev/null +++ b/gnu/packages/patches/glibc-CVE-2016-3706.patch @@ -0,0 +1,188 @@ +From 1a8a7c12950a0026a3c406a7cb1608f96aa1460e Mon Sep 17 00:00:00 2001 +From: Florian Weimer <fweimer@redhat.com> +Date: Fri, 29 Apr 2016 10:35:34 +0200 +Subject: [PATCH] CVE-2016-3706: getaddrinfo: stack overflow in hostent + conversion [BZ #20010] + +When converting a struct hostent response to struct gaih_addrtuple, the +gethosts macro (which is called from gaih_inet) used alloca, without +malloc fallback for large responses. This commit changes this code to +use calloc unconditionally. + +This commit also consolidated a second hostent-to-gaih_addrtuple +conversion loop (in gaih_inet) to use the new conversion function. + +(cherry picked from commit 4ab2ab03d4351914ee53248dc5aef4a8c88ff8b9) +--- + ChangeLog | 10 ++++ + sysdeps/posix/getaddrinfo.c | 130 +++++++++++++++++++++++--------------------- + 2 files changed, 79 insertions(+), 61 deletions(-) + +diff --git a/sysdeps/posix/getaddrinfo.c b/sysdeps/posix/getaddrinfo.c +index 1ef3f20..fed2d3b 100644 +--- a/sysdeps/posix/getaddrinfo.c ++++ b/sysdeps/posix/getaddrinfo.c +@@ -168,9 +168,58 @@ gaih_inet_serv (const char *servicename, const struct gaih_typeproto *tp, + return 0; + } + ++/* Convert struct hostent to a list of struct gaih_addrtuple objects. ++ h_name is not copied, and the struct hostent object must not be ++ deallocated prematurely. *RESULT must be NULL or a pointer to an ++ object allocated using malloc, which is freed. */ ++static bool ++convert_hostent_to_gaih_addrtuple (const struct addrinfo *req, ++ int family, ++ struct hostent *h, ++ struct gaih_addrtuple **result) ++{ ++ free (*result); ++ *result = NULL; ++ ++ /* Count the number of addresses in h->h_addr_list. */ ++ size_t count = 0; ++ for (char **p = h->h_addr_list; *p != NULL; ++p) ++ ++count; ++ ++ /* Report no data if no addresses are available, or if the incoming ++ address size is larger than what we can store. */ ++ if (count == 0 || h->h_length > sizeof (((struct gaih_addrtuple) {}).addr)) ++ return true; ++ ++ struct gaih_addrtuple *array = calloc (count, sizeof (*array)); ++ if (array == NULL) ++ return false; ++ ++ for (size_t i = 0; i < count; ++i) ++ { ++ if (family == AF_INET && req->ai_family == AF_INET6) ++ { ++ /* Perform address mapping. */ ++ array[i].family = AF_INET6; ++ memcpy(array[i].addr + 3, h->h_addr_list[i], sizeof (uint32_t)); ++ array[i].addr[2] = htonl (0xffff); ++ } ++ else ++ { ++ array[i].family = family; ++ memcpy (array[i].addr, h->h_addr_list[i], h->h_length); ++ } ++ array[i].next = array + i + 1; ++ } ++ array[0].name = h->h_name; ++ array[count - 1].next = NULL; ++ ++ *result = array; ++ return true; ++} ++ + #define gethosts(_family, _type) \ + { \ +- int i; \ + int herrno; \ + struct hostent th; \ + struct hostent *h; \ +@@ -219,36 +268,23 @@ gaih_inet_serv (const char *servicename, const struct gaih_typeproto *tp, + } \ + else if (h != NULL) \ + { \ +- for (i = 0; h->h_addr_list[i]; i++) \ ++ /* Make sure that addrmem can be freed. */ \ ++ if (!malloc_addrmem) \ ++ addrmem = NULL; \ ++ if (!convert_hostent_to_gaih_addrtuple (req, _family,h, &addrmem)) \ + { \ +- if (*pat == NULL) \ +- { \ +- *pat = __alloca (sizeof (struct gaih_addrtuple)); \ +- (*pat)->scopeid = 0; \ +- } \ +- uint32_t *addr = (*pat)->addr; \ +- (*pat)->next = NULL; \ +- (*pat)->name = i == 0 ? strdupa (h->h_name) : NULL; \ +- if (_family == AF_INET && req->ai_family == AF_INET6) \ +- { \ +- (*pat)->family = AF_INET6; \ +- addr[3] = *(uint32_t *) h->h_addr_list[i]; \ +- addr[2] = htonl (0xffff); \ +- addr[1] = 0; \ +- addr[0] = 0; \ +- } \ +- else \ +- { \ +- (*pat)->family = _family; \ +- memcpy (addr, h->h_addr_list[i], sizeof(_type)); \ +- } \ +- pat = &((*pat)->next); \ ++ _res.options |= old_res_options & RES_USE_INET6; \ ++ result = -EAI_SYSTEM; \ ++ goto free_and_return; \ + } \ ++ *pat = addrmem; \ ++ /* The conversion uses malloc unconditionally. */ \ ++ malloc_addrmem = true; \ + \ + if (localcanon != NULL && canon == NULL) \ + canon = strdupa (localcanon); \ + \ +- if (_family == AF_INET6 && i > 0) \ ++ if (_family == AF_INET6 && *pat != NULL) \ + got_ipv6 = true; \ + } \ + } +@@ -612,44 +648,16 @@ gaih_inet (const char *name, const struct gaih_service *service, + { + if (h != NULL) + { +- int i; +- /* We found data, count the number of addresses. */ +- for (i = 0; h->h_addr_list[i]; ++i) +- ; +- if (i > 0 && *pat != NULL) +- --i; +- +- if (__libc_use_alloca (alloca_used +- + i * sizeof (struct gaih_addrtuple))) +- addrmem = alloca_account (i * sizeof (struct gaih_addrtuple), +- alloca_used); +- else +- { +- addrmem = malloc (i +- * sizeof (struct gaih_addrtuple)); +- if (addrmem == NULL) +- { +- result = -EAI_MEMORY; +- goto free_and_return; +- } +- malloc_addrmem = true; +- } +- +- /* Now convert it into the list. */ +- struct gaih_addrtuple *addrfree = addrmem; +- for (i = 0; h->h_addr_list[i]; ++i) ++ /* We found data, convert it. */ ++ if (!convert_hostent_to_gaih_addrtuple ++ (req, AF_INET, h, &addrmem)) + { +- if (*pat == NULL) +- { +- *pat = addrfree++; +- (*pat)->scopeid = 0; +- } +- (*pat)->next = NULL; +- (*pat)->family = AF_INET; +- memcpy ((*pat)->addr, h->h_addr_list[i], +- h->h_length); +- pat = &((*pat)->next); ++ result = -EAI_MEMORY; ++ goto free_and_return; + } ++ *pat = addrmem; ++ /* The conversion uses malloc unconditionally. */ ++ malloc_addrmem = true; + } + } + else +-- +2.9.3 + diff --git a/gnu/packages/patches/glibc-CVE-2016-4429.patch b/gnu/packages/patches/glibc-CVE-2016-4429.patch new file mode 100644 index 0000000000..5eebd10543 --- /dev/null +++ b/gnu/packages/patches/glibc-CVE-2016-4429.patch @@ -0,0 +1,58 @@ +From bdce95930e1d9a7d013d1ba78740243491262879 Mon Sep 17 00:00:00 2001 +From: Florian Weimer <fweimer@redhat.com> +Date: Mon, 23 May 2016 20:18:34 +0200 +Subject: [PATCH] CVE-2016-4429: sunrpc: Do not use alloca in clntudp_call [BZ + #20112] + +The call is technically in a loop, and under certain circumstances +(which are quite difficult to reproduce in a test case), alloca +can be invoked repeatedly during a single call to clntudp_call. +As a result, the available stack space can be exhausted (even +though individual alloca sizes are bounded implicitly by what +can fit into a UDP packet, as a side effect of the earlier +successful send operation). + +(cherry picked from commit bc779a1a5b3035133024b21e2f339fe4219fb11c) +--- + ChangeLog | 7 +++++++ + NEWS | 4 ++++ + sunrpc/clnt_udp.c | 10 +++++++++- + 3 files changed, 20 insertions(+), 1 deletion(-) + +diff --git a/sunrpc/clnt_udp.c b/sunrpc/clnt_udp.c +index a6cf5f1..4d9acb1 100644 +--- a/sunrpc/clnt_udp.c ++++ b/sunrpc/clnt_udp.c +@@ -388,9 +388,15 @@ send_again: + struct sock_extended_err *e; + struct sockaddr_in err_addr; + struct iovec iov; +- char *cbuf = (char *) alloca (outlen + 256); ++ char *cbuf = malloc (outlen + 256); + int ret; + ++ if (cbuf == NULL) ++ { ++ cu->cu_error.re_errno = errno; ++ return (cu->cu_error.re_status = RPC_CANTRECV); ++ } ++ + iov.iov_base = cbuf + 256; + iov.iov_len = outlen; + msg.msg_name = (void *) &err_addr; +@@ -415,10 +421,12 @@ send_again: + cmsg = CMSG_NXTHDR (&msg, cmsg)) + if (cmsg->cmsg_level == SOL_IP && cmsg->cmsg_type == IP_RECVERR) + { ++ free (cbuf); + e = (struct sock_extended_err *) CMSG_DATA(cmsg); + cu->cu_error.re_errno = e->ee_errno; + return (cu->cu_error.re_status = RPC_CANTRECV); + } ++ free (cbuf); + } + #endif + do +-- +2.9.3 + diff --git a/gnu/packages/php.scm b/gnu/packages/php.scm index 7d569eef3e..d0afab0931 100644 --- a/gnu/packages/php.scm +++ b/gnu/packages/php.scm @@ -49,10 +49,21 @@ #:use-module (guix build-system gnu) #:use-module ((guix licenses) #:prefix license:)) +(define gd-for-php + (package + (inherit gd) + (source (origin + (inherit (package-source gd)) + (patches + (append + (origin-patches (package-source gd)) + (search-patches "gd-CVE-2017-7890.patch"))))))) + + (define-public php (package (name "php") - (version "7.1.6") + (version "7.1.8") (home-page "https://secure.php.net/") (source (origin (method url-fetch) @@ -60,7 +71,7 @@ name "-" version ".tar.xz")) (sha256 (base32 - "0nr49gqhk4pv8kcdc60cl1mgwlinawpraq9ba15whzmb472lsn01")) + "1aramb6dm57pr2iz61id9vzfy7h5qkb6bf7dxhrwnjk0723qahw9")) (modules '((guix build utils))) (snippet '(with-directory-excursion "ext" @@ -282,7 +293,7 @@ ("curl" ,curl) ("cyrus-sasl" ,cyrus-sasl) ("freetype" ,freetype) - ("gd" ,gd) + ("gd" ,gd-for-php) ("gdbm" ,gdbm) ("glibc" ,glibc) ("gmp" ,gmp) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index f8300a1752..d2b6c6dd59 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -5172,6 +5172,34 @@ Python language binding specification.") (define-public python2-drmaa (package-with-python2 python-drmaa)) +(define-public python-grako + (package + (name "python-grako") + (version "3.99.9") + (source + (origin + (method url-fetch) + (uri + (pypi-uri "grako" version ".zip")) + (sha256 + (base32 + "0r63i68wcnv63rfjkasq1ah81frz61a6mzbcnaxhrkdpx84p7hzw")))) + (build-system python-build-system) + (arguments '(#:tests? #f)) ; Test file 'grako.ebnf' is missing from archive. + (native-inputs + `(("unzip" ,unzip) + ("python-pytest" ,python-pytest-3.0) + ("python-pytest-runner" ,python-pytest-runner))) + (home-page "https://bitbucket.org/neogeny/grako") + (synopsis "EBNF parser generator") + (description + "Grako takes a grammar in a variation of EBNF as input, and outputs a +memoizing PEG/Packrat parser in Python.") + (license license:bsd-3))) + +(define-public python2-grako + (package-with-python2 python-grako)) + (define-public python-gridmap (package (name "python-gridmap") diff --git a/gnu/packages/rdesktop.scm b/gnu/packages/rdesktop.scm index 3eb82f22f3..7946cde790 100644 --- a/gnu/packages/rdesktop.scm +++ b/gnu/packages/rdesktop.scm @@ -72,15 +72,14 @@ to remotely control a user's Windows desktop.") (define-public freerdp (package (name "freerdp") - (version "1.2.0-beta1+android9") + (version "2.0.0-rc0") (source (origin - (method git-fetch) - (uri (git-reference - (url "git://github.com/FreeRDP/FreeRDP.git") - (commit version))) - (file-name (git-file-name name version)) + (method url-fetch) + (uri (string-append "https://github.com/FreeRDP/FreeRDP/archive/" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) (sha256 - (base32 "1m0lzrr7hkxfvc5f9p8snimv0rmin2463zhg25mv36wig8g5k7l3")))) + (base32 "0r36zwhl7fhmdng5pvl2a106gqbcqq184g2i2klz6ilna8pxjcml")))) (build-system cmake-build-system) (native-inputs `(("pkg-config" ,pkg-config) @@ -111,15 +110,6 @@ to remotely control a user's Windows desktop.") '("-DCMAKE_INSTALL_LIBDIR=lib" "-DWITH_PULSE=ON" "-DWITH_CUPS=ON") - #:phases - (modify-phases %standard-phases - (add-before 'configure 'patch-cmakelists - (lambda _ - ;; CMake would return an error on REMOVE_DUPLICATES because this - ;; list is empty. - (substitute* "channels/client/CMakeLists.txt" - (("list\\(REMOVE_DUPLICATES CHANNEL_STATIC_CLIENT_ENTRIES\\)") - ""))))) #:tests? #f)) ; no 'test' target (home-page "https://www.freerdp.com") (synopsis "Remote Desktop Protocol implementation") diff --git a/gnu/packages/shells.scm b/gnu/packages/shells.scm index 8d2a957eae..4603fd49b3 100644 --- a/gnu/packages/shells.scm +++ b/gnu/packages/shells.scm @@ -366,14 +366,14 @@ ksh, and tcsh.") (define-public xonsh (package (name "xonsh") - (version "0.5.9") + (version "0.5.12") (source (origin (method url-fetch) (uri (pypi-uri "xonsh" version)) (sha256 (base32 - "09s5k7fh4p0vkq0fha4ikwqlqsyv84vmlbqn8ggn0ymd47ajv38z")) + "1yz595hx5bni524m73cx8a08vcr6vfksfci14nx2ylz53igzva2c")) (modules '((guix build utils))) (snippet `(begin diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 99fd2e8d12..55a8a2a483 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -264,14 +264,14 @@ available, greatly increasing its breadth and scope.") (define-public r-boot (package (name "r-boot") - (version "1.3-19") + (version "1.3-20") (source (origin (method url-fetch) (uri (cran-uri "boot" version)) (sha256 (base32 - "16hsw4bw9pkfc2lqxfwycm1sbvbrm4linvm0ci71n8sxc7srvkis")))) + "0ai1qpm0p4z07xr0dvag8sdn9jrxcwanrsk9khzmww094jvr1jxd")))) (build-system r-build-system) (home-page "http://cran.r-project.org/web/packages/boot") (synopsis "Bootstrap functions for R") @@ -366,14 +366,14 @@ Hubert, based on Kaufman and Rousseeuw (1990) \"Finding Groups in Data\".") (define-public r-foreign (package (name "r-foreign") - (version "0.8-67") + (version "0.8-69") (source (origin (method url-fetch) (uri (cran-uri "foreign" version)) (sha256 (base32 - "0j0z815zyp8n97rk6hlk68d1r8b26vls39s03viq0pnx3cbpwyga")))) + "0s1lxmd85dd0kxx8hwk02w9l7pmpk4bpy7787fbyh2dbq5g9ys0k")))) (build-system r-build-system) (home-page "http://cran.r-project.org/web/packages/foreign") (synopsis "Read data stored by other statistics software") @@ -428,14 +428,14 @@ also flexible enough to handle most nonstandard requirements.") (define-public r-matrix (package (name "r-matrix") - (version "1.2-8") + (version "1.2-10") (source (origin (method url-fetch) (uri (cran-uri "Matrix" version)) (sha256 (base32 - "1dyv42d7ranb85y8hvi57hbg5xnvhdzqn56wcq3qmhazqj3s3liw")))) + "0r3qjcz92xwgdzrfz444mqzwnja5sv9abaf252fh6k48qbyahahh")))) (properties `((upstream-name . "Matrix"))) (build-system r-build-system) (propagated-inputs @@ -473,14 +473,14 @@ nonlinear mixed-effects models.") (define-public r-mgcv (package (name "r-mgcv") - (version "1.8-17") + (version "1.8-18") (source (origin (method url-fetch) (uri (cran-uri "mgcv" version)) (sha256 (base32 - "1zj223l4a3j15d3c01wv7dkzn9w6084gxrq5600ck9rvr0lfpwwg")))) + "011mgcypr56xvm9nizsfsb2285kzql93x0d3lzg849g39vbpp4s2")))) (build-system r-build-system) (propagated-inputs `(("r-matrix" ,r-matrix) @@ -622,14 +622,14 @@ binary booleans, @code{TRUE} and @code{FALSE} can be stored with 1 bit only.") (define-public r-bit64 (package (name "r-bit64") - (version "0.9-5") + (version "0.9-7") (source (origin (method url-fetch) (uri (cran-uri "bit64" version)) (sha256 (base32 - "0fz5m3fhvxgwjl76maag7yn0zdw24rx34gy6v77378fajag9yllg")))) + "07znvz9vp1nz1y5ljng4qyskvm943cdbmy996s67560ijxzsm6kv")))) (build-system r-build-system) (propagated-inputs `(("r-bit" ,r-bit))) @@ -793,30 +793,6 @@ see package vignette. To quote Rene Magritte, \"Ceci n'est pas un pipe.\"") Munsell colour system.") (license license:expat))) -(define-public r-rcpp - (package - (name "r-rcpp") - (version "0.12.10") - (source - (origin - (method url-fetch) - (uri (cran-uri "Rcpp" version)) - (sha256 - (base32 "108p485agxwgmnl9p54vsyy94w96lcimlk08v71ddm77gfl13y2f")))) - (build-system r-build-system) - (home-page "http://www.rcpp.org") - (synopsis "Seamless R and C++ Integration") - (description - "The Rcpp package provides R functions as well as C++ classes which offer -a seamless integration of R and C++. Many R data types and objects can be -mapped back and forth to C++ equivalents which facilitates both writing of new -code as well as easier integration of third-party libraries. Documentation -about Rcpp is provided by several vignettes included in this package, via the -'Rcpp Gallery' site at <http://gallery.rcpp.org>, the paper by Eddelbuettel -and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see -'citation(\"Rcpp\")' for details on these last two.") - (license license:gpl2+))) - (define-public r-permute (package (name "r-permute") @@ -1144,13 +1120,13 @@ evaluation (NSE) in R.") (define-public r-dbi (package (name "r-dbi") - (version "0.6-1") + (version "0.7") (source (origin (method url-fetch) (uri (cran-uri "DBI" version)) (sha256 (base32 - "1fg158k4n6l3rzx9nrwhp4nwkwpbmv1q7z2xz5rw138zws68fkgr")))) + "04fyrxdpqcygg5wviy637y6lgk64xqjjq31lvv4hwqj5kbaxamr5")))) (build-system r-build-system) (home-page "https://github.com/rstats-db/DBI") (synopsis "R database interface") @@ -1182,13 +1158,13 @@ for template use among CRAN packages.") (define-public r-evaluate (package (name "r-evaluate") - (version "0.10") + (version "0.10.1") (source (origin (method url-fetch) (uri (cran-uri "evaluate" version)) (sha256 (base32 - "0mwna7rjyrmc76651a1fm7c76ippdsc2wsp3sj3iwb1c73mvlqv1")))) + "070vvmnbdlp7sz2zhza7fhd2a6mlwiln8fn4hyzhsiizbn4n79y9")))) (build-system r-build-system) (propagated-inputs `(("r-stringr" ,r-stringr))) @@ -1204,13 +1180,13 @@ adapted for other output formats, such as HTML or LaTeX.") (define-public r-formatr (package (name "r-formatr") - (version "1.4") + (version "1.5") (source (origin (method url-fetch) (uri (cran-uri "formatR" version)) (sha256 (base32 - "1fvynq0fj1r9grg9vvfdh5fl2riv6qki9f2rfpyvbvqq3xxpmi3f")))) + "19sd23vgs4ac0fwlw40j3676k6mramb0ajlq8hdw23kjwdx1jk47")))) (build-system r-build-system) (home-page "http://yihui.name/formatR") (synopsis "Format R code automatically") @@ -1305,13 +1281,13 @@ emitter (http://pyyaml.org/wiki/LibYAML) for R.") (define-public r-knitr (package (name "r-knitr") - (version "1.15.1") + (version "1.16") (source (origin (method url-fetch) (uri (cran-uri "knitr" version)) (sha256 (base32 - "1pbxd3k7kv5sa1a5gxm0zc2bhjxdgx2nfch9xap5k85djmgsfqc1")))) + "02balmhvc955rkqv4v0wkxbw4vjphydajgcpy4ml0s3b4sziyj0h")))) (build-system r-build-system) (propagated-inputs `(("r-evaluate" ,r-evaluate) @@ -1333,14 +1309,14 @@ generation in R using Literate Programming techniques.") (define-public r-knitrbootstrap (package (name "r-knitrbootstrap") - (version "1.0.0") + (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "knitrBootstrap" version)) (sha256 (base32 - "0pshn2slzqwpryklslsxwh1dmqcnwv6bwi7yfm6m342wjybpk0wl")))) + "089147g7nqp99rwdxxsfmklsrwc8aia09sr8ndmrc335r33v6r6p")))) (properties `((upstream-name . "knitrBootstrap"))) (build-system r-build-system) (propagated-inputs @@ -1485,13 +1461,13 @@ flexible and easy to set up.") (define-public r-r6 (package (name "r-r6") - (version "2.2.0") + (version "2.2.2") (source (origin (method url-fetch) (uri (cran-uri "R6" version)) (sha256 (base32 - "1ir51pb0y6yj05qaxsflk4a6hv8n73cwlb0qajcskbrz632dsyvx")))) + "13xfdr19ca7ymisidsanm6w7hsk3qmy5l8c0mlz3nk48f7s5cxq8")))) (build-system r-build-system) (home-page "https://github.com/wch/R6/") (synopsis "Classes with reference semantics in R") @@ -1504,20 +1480,38 @@ private members, and they support inheritance, even when the classes are defined in different packages.") (license license:expat))) +(define-public r-rlang + (package + (name "r-rlang") + (version "0.1.1") + (source (origin + (method url-fetch) + (uri (cran-uri "rlang" version)) + (sha256 + (base32 + "0grwqy3zkvz96mvpwfbfyqid4jkfrqh3ldy2n6dpv2kjd1fzj0ar")))) + (build-system r-build-system) + (home-page "http://rlang.tidyverse.org") + (synopsis "Functions for base types, core R and Tidyverse features") + (description "This package provides a toolbox for working with base types, +core R features like the condition system, and core @code{Tidyverse} features +like tidy evaluation.") + (license license:gpl3))) + (define-public r-tibble (package (name "r-tibble") - (version "1.3.0") + (version "1.3.3") (source (origin (method url-fetch) (uri (cran-uri "tibble" version)) (sha256 (base32 - "1q25i1cv3qms6d3lw7jd3z142w188znkcbyam460gn9si8l8g2bk")))) + "1bhq4pm56l7l6s1k44ajrcr7hz56h37m9ck4zji9f8xfdqschbl0")))) (build-system r-build-system) (propagated-inputs - `(("r-lazyeval" ,r-lazyeval) + `(("r-rlang" ,r-rlang) ("r-rcpp" ,r-rcpp))) (home-page "https://github.com/hadley/tibble") (synopsis "Simple data frames") @@ -1529,20 +1523,23 @@ and printing capabilities than traditional data frames.") (define-public r-dplyr (package (name "r-dplyr") - (version "0.5.0") + (version "0.7.2") (source (origin (method url-fetch) (uri (cran-uri "dplyr" version)) (sha256 (base32 - "0ks5cklb03laqf5ygcw986g1lv7wk1ipvypjlha8xly2y4lvilwk")))) + "0jpb32ca1c0mr660igna4yw4fmzydzfhxshd0g8wgmggkynx2qi2")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) ("r-r6" ,r-r6) ("r-magrittr" ,r-magrittr) - ("r-lazyeval" ,r-lazyeval) - ("r-dbi" ,r-dbi) + ("r-rlang" ,r-rlang) + ("r-plogr" ,r-plogr) + ("r-glue" ,r-glue) + ("r-pkgconfig" ,r-pkgconfig) + ("r-bindrcpp" ,r-bindrcpp) ("r-tibble" ,r-tibble))) (native-inputs `(("r-rcpp" ,r-rcpp) @@ -1605,14 +1602,14 @@ Groups in Data\".") (define-public r-formula (package (name "r-formula") - (version "1.2-1") + (version "1.2-2") (source (origin (method url-fetch) (uri (cran-uri "Formula" version)) (sha256 (base32 - "02in5325zzrqbhlygx6s0dinj6ymw845q70y56frqacv25ayzcax")))) + "0ad49bzip1zqmpj1d8jajwl4bd81fm3k6dq8p26x6mvlzc04dvwd")))) (properties `((upstream-name . "Formula"))) (build-system r-build-system) (home-page "http://cran.r-project.org/web/packages/Formula") @@ -1937,14 +1934,14 @@ limited to R.") (define-public r-backports (package (name "r-backports") - (version "1.0.5") + (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "backports" version)) (sha256 (base32 - "1pn1ii8vbkgxcqvx52kzsbwf9gkn9fp33388087zky2hmdzdirn0")))) + "1kcz6j82by28cjk5wi2j6dfqdin1kib4y7d2r4h3zabcxmk6jly5")))) (build-system r-build-system) (home-page "http://cran.r-project.org/web/packages/backports") (synopsis "Reimplementations of functions introduced since R 3.0.0") @@ -1960,14 +1957,14 @@ R version.") (define-public r-checkmate (package (name "r-checkmate") - (version "1.8.2") + (version "1.8.3") (source (origin (method url-fetch) (uri (cran-uri "checkmate" version)) (sha256 (base32 - "1zqcggl9m7slvc0q6zyhssdypb7jzf3l9byl5vxh1qdwjiw2y64g")))) + "04rxabzamhv6ybynx627sxk02qvq8znkv0y10vmq67xx6pxhqvla")))) (build-system r-build-system) (propagated-inputs `(("r-backports" ,r-backports))) @@ -2076,14 +2073,14 @@ module, Java Server Pages, and Python's psp module.") (define-public r-desc (package (name "r-desc") - (version "1.1.0") + (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "desc" version)) (sha256 (base32 - "0mc1jmiwqyj7s6gzxz6fyamzjpmdn3rpfpllby2fq11ml30c6jpr")))) + "0k07qighac1xzmm8k988zi7i88a0yfvia3gk5hbz0fyvb2v9kzrj")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) @@ -2210,13 +2207,13 @@ functions make it easy to control additional request components.") (define-public r-git2r (package (name "r-git2r") - (version "0.18.0") + (version "0.19.0") (source (origin (method url-fetch) (uri (cran-uri "git2r" version)) (sha256 (base32 - "0bgzdsdi9n6l8pchivs6a2g4ksa56qs8hygpyv2c0ndqmx4jxcwi")))) + "0ws6fbndmaafk2am4dwnz24qizxhld0yh54hgx0z6lzv3p1j209q")))) (build-system r-build-system) ;; This R package contains modified sources of libgit2. This modified ;; version of libgit2 is built as the package is built. Hence libgit2 is @@ -2254,25 +2251,21 @@ informative error messages when it's not available.") (define-public r-devtools (package (name "r-devtools") - (version "1.13.2") + (version "1.13.3") (source (origin (method url-fetch) (uri (cran-uri "devtools" version)) (sha256 (base32 - "08ajsr12wd31lsx3jv5l9mq4063dc5fpr9lcnzra6kl59vi5pa7v")))) + "146wb09cmfh10vhn1ps2nmzx104zldb3nj9qv2ic0gbcikbbryp6")))) (build-system r-build-system) (propagated-inputs - `(("r-curl" ,r-curl) - ("r-digest" ,r-digest) - ("r-evaluate" ,r-evaluate) + `(("r-digest" ,r-digest) ("r-git2r" ,r-git2r) ("r-httr" ,r-httr) ("r-jsonlite" ,r-jsonlite) ("r-memoise" ,r-memoise) - ("r-roxygen2" ,r-roxygen2) ("r-rstudioapi" ,r-rstudioapi) - ("r-rversions" ,r-rversions) ("r-whisker" ,r-whisker) ("r-withr" ,r-withr))) (home-page "https://github.com/hadley/devtools") @@ -2284,13 +2277,13 @@ tools to simplify the devolpment of R packages.") (define-public r-withr (package (name "r-withr") - (version "1.0.2") + (version "2.0.0") (source (origin (method url-fetch) (uri (cran-uri "withr" version)) (sha256 (base32 - "042z8nmqqilgrvhmbqrjc05qys3gzwq1rqy2wxp2bi5d41859493")))) + "0ncq9ygx33rx7aazn53p0a0vbr5xv0r6wbkzcwbhbwyd8k55bgin")))) (build-system r-build-system) (home-page "https://github.com/jimhester/withr") (synopsis "Run code with temporarily modified global state") @@ -2322,13 +2315,13 @@ time-of-day values, based on the @code{difftime} class.") (define-public r-readr (package (name "r-readr") - (version "1.1.0") + (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "readr" version)) (sha256 (base32 - "1g7g3gdmvq7nj8asw6fi13k38c420sy9696nqgkrhlvv5h13yqs7")))) + "1cvw5wdcqk88cp5fyv678mnmp66l3whcd2yh33p2qvx0168bja8s")))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp) @@ -2346,13 +2339,13 @@ disk (or a connection).") (define-public r-plotrix (package (name "r-plotrix") - (version "3.6-4") + (version "3.6-5") (source (origin (method url-fetch) (uri (cran-uri "plotrix" version)) (sha256 (base32 - "1wxzjnzvkl3aga51ad2xhv4s7v46kvnp4z0nz4cb9cn10057sfw8")))) + "01655y3qzy0283ppc85bi0g42g20zrqzcl0qb30cl6rcbflhymlb")))) (build-system r-build-system) (home-page "http://cran.r-project.org/web/packages/plotrix") (synopsis "Various plotting functions") @@ -2405,13 +2398,13 @@ well as additional utilities such as panel and axis annotation functions.") (define-public r-rcpparmadillo (package (name "r-rcpparmadillo") - (version "0.7.800.2.0") + (version "0.7.900.2.0") (source (origin (method url-fetch) (uri (cran-uri "RcppArmadillo" version)) (sha256 (base32 - "025lh504nw7ir1f2xsqnvfkq9rg0rb2xzfn3a2s0b2a9snqdzzwr")))) + "01qsff2p1fp5i9lq7rsykrskgr6smz24ddspbl5ad9a8rkmczwyv")))) (properties `((upstream-name . "RcppArmadillo"))) (build-system r-build-system) (propagated-inputs @@ -2497,14 +2490,14 @@ certain criterion, e.g., it contains a certain regular file.") (define-public r-rmarkdown (package (name "r-rmarkdown") - (version "1.4") + (version "1.6") (source (origin (method url-fetch) (uri (cran-uri "rmarkdown" version)) (sha256 (base32 - "1dvs9cq88g61wfimifagq6y98yxavxzjan39jvpdsg98mafckq9g")))) + "0p8ph5z5pifk1nxc1bppkfs1ir5gjc6ap9n64b4255m2fdaqfrc7")))) (properties `((upstream-name . "rmarkdown"))) (build-system r-build-system) (propagated-inputs @@ -2567,36 +2560,55 @@ variety of formats.") and draw tables.") (license license:gpl2+))) -(define-public r-plogr +(define-public r-pkgconfig (package - (name "r-plogr") - (version "0.1-1") - (source - (origin - (method url-fetch) - (uri (cran-uri "plogr" version)) - (sha256 - (base32 - "13zliqlbkl8b04k9ga0sx5jsh7k867gracgl84l2a9kcqy9mqx92")))) + (name "r-pkgconfig") + (version "2.0.1") + (source (origin + (method url-fetch) + (uri (cran-uri "pkgconfig" version)) + (sha256 + (base32 + "0h2sp93fqqjbfqgq82a3i94ybnndx6ghaal8pbf99firnsjb40mb")))) (build-system r-build-system) - (home-page "https://github.com/krlmlr/plogr") - (synopsis "R bindings for the plog C++ logging library") - (description - "This package provides the header files for a stripped-down version of -the plog header-only C++ logging library, and a method to log to R's standard -error stream.") + (home-page "https://github.com/gaborcsardi/pkgconfig") + (synopsis "Private configuration for R packages") + (description "This package provides the functionality to set configuration +options on a per-package basis. Options set by a given package only apply to +that package, other packages are unaffected.") (license license:expat))) +(define-public r-blob + (package + (name "r-blob") + (version "1.1.0") + (source (origin + (method url-fetch) + (uri (cran-uri "blob" version)) + (sha256 + (base32 + "05pazzcyz3c3vd2l70zq9cf172cgjff4dnf419zigfnxycyn1mhn")))) + (build-system r-build-system) + (propagated-inputs + `(("r-tibble" ,r-tibble))) + (home-page "https://github.com/hadley/blob") + (synopsis "Simple S3 Class for representing vectors of binary data") + (description "Raw vectors in R are useful for storing a single binary +object. What if you want to put a vector of them in a data frame? The blob +package provides the blob object, a list of raw vectors, suitable for use as +a column in data frame.") + (license license:gpl3+))) + (define-public r-rsqlite (package (name "r-rsqlite") - (version "1.1-2") + (version "2.0") (source (origin (method url-fetch) (uri (cran-uri "RSQLite" version)) (sha256 (base32 - "0mg9yhdvny3vjn72agai5ghqxd3vk8cd4x1lsc0gzc2b2dm2w0p4")))) + "1xpg1i1jkzkzv44k512k90c2vvl960pl2d4a3spwcha6yclyc3vz")))) (properties `((upstream-name . "RSQLite"))) (build-system r-build-system) (propagated-inputs @@ -2604,13 +2616,16 @@ error stream.") ("r-bh" ,r-bh) ("r-memoise" ,r-memoise) ("r-plogr" ,r-plogr) - ("r-rcpp" ,r-rcpp))) + ("r-rcpp" ,r-rcpp) + ("r-bit64" ,r-bit64) + ("r-blob" ,r-blob) + ("r-pkgconfig" ,r-pkgconfig))) (home-page "https://github.com/rstats-db/RSQLite") (synopsis "SQLite interface for R") (description "This package embeds the SQLite database engine in R and provides an interface compliant with the DBI package. The source for the SQLite -engine (version 3.8.6) is included.") +engine (version 3.8.8.2) is included.") (license license:lgpl2.0+))) (define-public r-rcurl @@ -2647,13 +2662,13 @@ ldap, and also supports cookies, redirects, authentication, etc.") (define-public r-xml (package (name "r-xml") - (version "3.98-1.6") + (version "3.98-1.9") (source (origin (method url-fetch) (uri (cran-uri "XML" version)) (sha256 (base32 - "1amxx7fpik162nimrr7m5lvv6rhx9cwdyg44fxp1i5wm3y4skwnz")))) + "1hzkdkgs0nzmfg9wm7kyh1j9i0i2g7925whzlihqvg9grdlh3dx3")))) (properties `((upstream-name . "XML"))) (build-system r-build-system) @@ -2765,14 +2780,14 @@ statements.") (define-public r-segmented (package (name "r-segmented") - (version "0.5-1.4") + (version "0.5-2.1") (source (origin (method url-fetch) (uri (cran-uri "segmented" version)) (sha256 (base32 - "1740cvx2q4v23g4q0zkvg50s5bv8jcrlzzhm7fac4xn0riwmzp5i")))) + "1i576xksc761nyv2dmq86nwbgqvp0plz6bjcn69nkdwq2wbizmw8")))) (build-system r-build-system) (home-page "http://cran.r-project.org/web/packages/segmented") (synopsis "Regression models with breakpoints estimation") @@ -2806,13 +2821,13 @@ worker processes and collect and return the results on the master.") (define-public r-sparsem (package (name "r-sparsem") - (version "1.76") + (version "1.77") (source (origin (method url-fetch) (uri (cran-uri "SparseM" version)) (sha256 (base32 - "16xnl9cacim35aawq6bmd2y6rrhnh1kg6dwsy3k5yslkfr1y9j62")))) + "0p6ljma2h12cq1xmy0cxb48ih8dhxxbnwkqzvx3cckxf2kprycm9")))) (properties `((upstream-name . "SparseM"))) (inputs @@ -2993,14 +3008,14 @@ flexible than the orphaned \"base64\" package.") (define-public r-irlba (package (name "r-irlba") - (version "2.1.2") + (version "2.2.1") (source (origin (method url-fetch) (uri (cran-uri "irlba" version)) (sha256 (base32 - "1qbcn0ix85pmk296jhpi419kvh06vxm5cq24yk013ps3g7fyi0si")))) + "0zfb7x1701n6gask0f8y2yq0vmb82xkxf6limp43ivx551hx600s")))) (build-system r-build-system) (propagated-inputs `(("r-matrix" ,r-matrix))) @@ -3015,14 +3030,14 @@ analysis of large sparse or dense matrices.") (define-public r-glmnet (package (name "r-glmnet") - (version "2.0-5") + (version "2.0-10") (source (origin (method url-fetch) (uri (cran-uri "glmnet" version)) (sha256 (base32 - "1cbpzmbv837fvq88rgn6mgzgr9f1wqp9fg8gh2kkmngvr1957a9c")))) + "07n2hz4fvjyv0siai8z8wqwfj8d58i8n1vzf1ckdfzp4kxa3z08d")))) (build-system r-build-system) (inputs `(("gfortran" ,gfortran))) @@ -3268,14 +3283,14 @@ performing parallel computations on multicore machines.") (define-public r-igraph (package (name "r-igraph") - (version "1.0.1") + (version "1.1.2") (source (origin (method url-fetch) (uri (cran-uri "igraph" version)) (sha256 (base32 - "00jnm8v3kvxpxav5klld2z2nnkcpj4sdwv4ksipddy5mp04ysr6w")))) + "1v26wyk52snh8z6m5p7yqwcd9dbqifhm57j112i9x53ppi0npcc9")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) @@ -3285,7 +3300,8 @@ performing parallel computations on multicore machines.") (propagated-inputs `(("r-irlba" ,r-irlba) ("r-magrittr" ,r-magrittr) - ("r-nmf" ,r-nmf))) + ("r-matrix" ,r-matrix) + ("r-pkgconfig" ,r-pkgconfig))) (home-page "http://igraph.org") (synopsis "Network analysis and visualization") (description @@ -3519,14 +3535,14 @@ the 'lite' version of the more complete @code{viridis} package.") (define-public r-tidyr (package (name "r-tidyr") - (version "0.6.1") + (version "0.6.3") (source (origin (method url-fetch) (uri (cran-uri "tidyr" version)) (sha256 (base32 - "11hs3gqpbaw3w281as4m7j9n594ix5axfpwbyjsd0l62pwnzj217")))) + "14s57zrjm2phiy600z9ivq4az71z0ggmp6nj0js7yrybxf0dlah6")))) (build-system r-build-system) (propagated-inputs `(("r-dplyr" ,r-dplyr) @@ -3575,21 +3591,19 @@ It uses and relies on grid graphics and formal (S4) classes and methods.") (define-public r-purrr (package (name "r-purrr") - (version "0.2.2") + (version "0.2.3") (source (origin (method url-fetch) (uri (cran-uri "purrr" version)) (sha256 (base32 - "0lss8q733nv7s154wargm6vnxq55qygnxakib8xdj4jv0y86sxc3")))) + "0j1y0nbvljcis9hgic4wbbzslcsidhpw0wzs7d2hx7a2ygi6mkma")))) (build-system r-build-system) (propagated-inputs - `(("r-bh" ,r-bh) - ("r-dplyr" ,r-dplyr) - ("r-lazyeval" ,r-lazyeval) + `(("r-tibble" ,r-tibble) ("r-magrittr" ,r-magrittr) - ("r-rcpp" ,r-rcpp))) + ("r-rlang" ,r-rlang))) (home-page "https://github.com/hadley/purrr") (synopsis "Functional programming tools") (description @@ -3600,26 +3614,30 @@ features present in other programming languages.") (define-public r-plotly (package (name "r-plotly") - (version "4.5.6") + (version "4.7.1") (source (origin (method url-fetch) (uri (cran-uri "plotly" version)) (sha256 (base32 - "09yw977yxlcxv57kni3q899zrxyxa6pznr06cylr9lqkyr7llfhx")))) + "0wj9lw7w28z8w9ip9vadv6sydjhqyg65kfiai9m3bndzz50b1m3w")))) (build-system r-build-system) (propagated-inputs `(("r-base64enc" ,r-base64enc) + ("r-crosstalk" ,r-crosstalk) ("r-digest" ,r-digest) + ("r-data-table" ,r-data-table) ("r-dplyr" ,r-dplyr) ("r-ggplot2" ,r-ggplot2) ("r-hexbin" ,r-hexbin) + ("r-htmltools" ,r-htmltools) ("r-htmlwidgets" ,r-htmlwidgets) ("r-httr" ,r-httr) ("r-jsonlite" ,r-jsonlite) ("r-lazyeval" ,r-lazyeval) ("r-magrittr" ,r-magrittr) ("r-purrr" ,r-purrr) + ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-scales" ,r-scales) ("r-tibble" ,r-tibble) ("r-tidyr" ,r-tidyr) @@ -3701,14 +3719,14 @@ character vector.") (define-public r-googlesheets (package (name "r-googlesheets") - (version "0.2.1") + (version "0.2.2") (source (origin (method url-fetch) (uri (cran-uri "googlesheets" version)) (sha256 (base32 - "0ps13h1cv7fj5dh8s4nvwi64wnnyqdsadcaa4iizq1c5s615cwk3")))) + "18q0xmxn09b52rmky7gr5flp0awndcnsgb7zcvkzvkrkvmwad52b")))) (build-system r-build-system) (propagated-inputs `(("r-cellranger" ,r-cellranger) @@ -3795,21 +3813,20 @@ package instead.") (define-public r-hmisc (package (name "r-hmisc") - (version "4.0-2") + (version "4.0-3") (source (origin (method url-fetch) (uri (cran-uri "Hmisc" version)) (sha256 (base32 - "1lg9k0kj803wsm3h0a991q9l2lrgsqryzfv2z79b88kjbfapqpqr")))) + "1a7i7azag6pldgala85d8hh7wnx1shamyiriy4jfc65nxrr2lq8w")))) (properties `((upstream-name . "Hmisc"))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) (propagated-inputs `(("r-acepack" ,r-acepack) - ("r-base64" ,r-base64) ("r-base64enc" ,r-base64enc) ("r-cluster" ,r-cluster) ("r-data-table" ,r-data-table) @@ -3926,14 +3943,14 @@ existing packages provide.") (define-public r-sfsmisc (package (name "r-sfsmisc") - (version "1.1-0") + (version "1.1-1") (source (origin (method url-fetch) (uri (cran-uri "sfsmisc" version)) (sha256 (base32 - "0580piv4n1nispl3pa8nfjjfnb8iwaqky2dzdy0aqnxrxgrhqhvz")))) + "0jzmbywlyzfxs7hlmyd0iynghfc9qp5sa5lnhr73y8r360yv1ahf")))) (build-system r-build-system) (home-page "http://cran.r-project.org/web/packages/sfsmisc") (synopsis "Utilities from \"Seminar fuer Statistik\" ETH Zurich") @@ -3967,14 +3984,14 @@ tests for whether a value is missing, empty or contains only @code{NA} and (define-public r-gdata (package (name "r-gdata") - (version "2.17.0") + (version "2.18.0") (source (origin (method url-fetch) (uri (cran-uri "gdata" version)) (sha256 (base32 - "0kiy3jbcszlpmarg311spdsfi5pn89wgy742dxsbzxk8907fr5w0")))) + "0zwdj7lscgxr8r62ii8hbdh4mb7sa9w4f5nv32zzrxdvymcpya2b")))) (build-system r-build-system) (inputs `(("perl" ,perl))) @@ -4248,13 +4265,13 @@ Wall Street Journal, among others. This package also provides (define-public r-statmod (package (name "r-statmod") - (version "1.4.29") + (version "1.4.30") (source (origin (method url-fetch) (uri (cran-uri "statmod" version)) (sha256 (base32 - "1fgzkwriba39d7946lq892f0si2fjdy37pvxki6ix8xyj8qgnci4")))) + "07v4x8af60alcw6vbiwf5fp25bhra61kvxz9kqx64lszm0i1fb4x")))) (build-system r-build-system) (home-page "http://cran.r-project.org/web/packages/statmod") (native-inputs @@ -4274,13 +4291,13 @@ dispersion modeling and Tweedie power-law families.") (define-public r-rann (package (name "r-rann") - (version "2.5") + (version "2.5.1") (source (origin (method url-fetch) (uri (cran-uri "RANN" version)) (sha256 (base32 - "007cgqg9bybg2zlljbv5m6cmlm3r6i251018rpgjcn0xnm9sjsj7")))) + "0il5i99vbcagnxvb15af5n37g04a4q1x96bz73zh3jhki9fpw9vm")))) (properties `((upstream-name . "RANN"))) (build-system r-build-system) @@ -4343,14 +4360,14 @@ Farebrother's algorithm or Liu et al.'s algorithm.") (define-public r-cowplot (package (name "r-cowplot") - (version "0.7.0") + (version "0.8.0") (source (origin (method url-fetch) (uri (cran-uri "cowplot" version)) (sha256 (base32 - "03iimcsh1pk7iqzjdlfcj43b8khijdk4hg00j4jdllv19xsfb0hx")))) + "03bh0r6ynr95gk4lc8asfi3kpmskm59vfzwn417pdziha3igs5x6")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) @@ -4416,14 +4433,14 @@ regression.") (define-public r-fastica (package (name "r-fastica") - (version "1.2-0") + (version "1.2-1") (source (origin (method url-fetch) (uri (cran-uri "fastICA" version)) (sha256 (base32 - "0ykk78fsk5da2g16i4wji85bvji7nayjvkfp07hyaxq9d15jmf0r")))) + "108z2ymby5y4h8l4l2krqwm28rya93gq09yylgilnm3afvfrfabg")))) (properties `((upstream-name . "fastICA"))) (build-system r-build-system) (home-page "http://cran.r-project.org/web/packages/fastICA") @@ -4499,14 +4516,14 @@ to change in the future.") (define-public r-flexmix (package (name "r-flexmix") - (version "2.3-13") + (version "2.3-14") (source (origin (method url-fetch) (uri (cran-uri "flexmix" version)) (sha256 (base32 - "1i205yw3kkxs27gqcs6zx0c2mh16p332a2p06wq6fdzb20bazg3z")))) + "0sl4zxh1sb2sr5q7svjw9ihrm219jzn82yrc9d43q6r1b8bpyz43")))) (build-system r-build-system) (propagated-inputs `(("r-lattice" ,r-lattice) @@ -4525,14 +4542,14 @@ models, generalized linear models and model-based clustering.") (define-public r-mclust (package (name "r-mclust") - (version "5.2.3") + (version "5.3") (source (origin (method url-fetch) (uri (cran-uri "mclust" version)) (sha256 (base32 - "0045msdw1xndfmlylbnm1ss716iiqzqwj454a97gmcq5kph86qzz")))) + "0h5syvpg3azrz5d10z2afilaa27jb4azi38idzlv05mfcs16s6rb")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) @@ -4672,14 +4689,14 @@ groupings.") (define-public r-vgam (package (name "r-vgam") - (version "1.0-3") + (version "1.0-4") (source (origin (method url-fetch) (uri (cran-uri "VGAM" version)) (sha256 (base32 - "0wr6szcpj8r4a1rlzgd6iym7khin69fmvxcf37iyvs8mms86dfr3")))) + "0r59hyp3afmvms890b3v2yyckf8v0qkjf2w11rnqd2zgg1gri0g5")))) (properties `((upstream-name . "VGAM"))) (build-system r-build-system) (inputs @@ -4697,14 +4714,14 @@ VGLMs can be loosely thought of as multivariate generalised linear models.") (define-public r-pbapply (package (name "r-pbapply") - (version "1.3-2") + (version "1.3-3") (source (origin (method url-fetch) (uri (cran-uri "pbapply" version)) (sha256 (base32 - "1sdmjlnwxb99f95g5v8k8mirrkzw99yig377v0qi9lzwjgd6fqqr")))) + "0iqhymf65jffh00qf056h1p76xf92bfmij6aymlmgnvn24fv4ybk")))) (build-system r-build-system) (home-page "https://github.com/psolymos/pbapply") (synopsis "Adding progress bar to apply functions") @@ -4761,14 +4778,14 @@ based on an interface to Fortran implementations by M. J. D. Powell.") (define-public r-rcppeigen (package (name "r-rcppeigen") - (version "0.3.2.9.1") + (version "0.3.3.3.0") (source (origin (method url-fetch) (uri (cran-uri "RcppEigen" version)) (sha256 (base32 - "1ih940yjbc530cmpl6kx1jic7pz2ps1w5vrvy32qizh6m5s3lk7x")))) + "0zz9v0f8nnlvhhqv91lkyfblvjnmav84l89mr6vmbqjc2hzqd3n8")))) (properties `((upstream-name . "RcppEigen"))) (build-system r-build-system) (propagated-inputs @@ -4939,14 +4956,14 @@ bootstrap test for generalized linear mixed models.") (define-public r-car (package (name "r-car") - (version "2.1-4") + (version "2.1-5") (source (origin (method url-fetch) (uri (cran-uri "car" version)) (sha256 (base32 - "0a6v7rsd1xsdyapnfqy37m7c4kx9wslkzsizc9k0lmnba0bwyfgx")))) + "1bm0ks9ga60z3izgq0d4kvirr9v4yf1820d1wznkihnbb55bc3m6")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass) @@ -5083,14 +5100,14 @@ multivariate case.") (define-public r-tclust (package (name "r-tclust") - (version "1.2-3") + (version "1.2-7") (source (origin (method url-fetch) (uri (cran-uri "tclust" version)) (sha256 (base32 - "0a1b7yp4l9wf6ic5czizyl2cnxrc1virj0icr8i6m1vv23jd8jfp")))) + "1mvqr280c6kwpg98byd0r1y0qf238xn2x15y8npqch6lpcszlb3x")))) (build-system r-build-system) (propagated-inputs `(("r-cluster" ,r-cluster) @@ -5108,17 +5125,19 @@ diagnostic tools (@code{ctlcurves} and @code{DiscrFact}).") (define-public r-ranger (package (name "r-ranger") - (version "0.7.0") + (version "0.8.0") (source (origin (method url-fetch) (uri (cran-uri "ranger" version)) (sha256 (base32 - "0g1rnpk4c06lmy0r5n0j7i2xna190kqalmxp42d9gnk3drnb1x43")))) + "1fdbm879wx3hlng8s4c4f8f2x5yxz57llakcqnpa0lymybidw3vz")))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp))) + `(("r-rcpp" ,r-rcpp) + ("r-matrix" ,r-matrix) + ("r-rcppeigen" ,r-rcppeigen))) (home-page "https://github.com/imbs-hl/ranger") (synopsis "Fast implementation of random forests") (description diff --git a/gnu/packages/tls.scm b/gnu/packages/tls.scm index 7ee341e99b..9d3e9d9e97 100644 --- a/gnu/packages/tls.scm +++ b/gnu/packages/tls.scm @@ -486,13 +486,13 @@ netcat implementation that supports TLS.") (package (name "python-acme") ;; Remember to update the hash of certbot when updating python-acme. - (version "0.16.0") + (version "0.17.0") (source (origin (method url-fetch) (uri (pypi-uri "acme" version)) (sha256 (base32 - "1kg9bnwywsr18hgvqyhxqqi90l2qa7449f41q3fdq2y59h9nk2sk")))) + "0vmnv7qhdhl9qhq03v6zrcj1lsmpmpjb94s0xsc7piwqxfmf9jrw")))) (build-system python-build-system) (arguments `(#:phases @@ -543,7 +543,7 @@ netcat implementation that supports TLS.") (uri (pypi-uri name version)) (sha256 (base32 - "11p1vsps5rbpha3k5jnmf9i6rcp6299h9b34wdh21cq6dgyh2n3r")))) + "173619jkq4bg88f6i837z3pcjkrfabrvv8vrpyx18k9i7xnb5xa3")))) (build-system python-build-system) (arguments `(,@(substitute-keyword-arguments (package-arguments python-acme) diff --git a/gnu/packages/tor.scm b/gnu/packages/tor.scm index 1d5a1f1612..64acb44490 100644 --- a/gnu/packages/tor.scm +++ b/gnu/packages/tor.scm @@ -44,14 +44,14 @@ (define-public tor (package (name "tor") - (version "0.3.0.9") + (version "0.3.0.10") (source (origin (method url-fetch) (uri (string-append "https://dist.torproject.org/tor-" version ".tar.gz")) (sha256 (base32 - "0hhyb1wil8japynqnm07r1f67w3wdnafdg9amzlrrcfcyq5qim28")))) + "1cas30wk4bhcivi6l9dj7wwlz6pc2jj883x1vijax3b8l54nx3ls")))) (build-system gnu-build-system) (arguments `(#:configure-flags (list "--enable-gcc-hardening" diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm index 9274a93f6a..729746aed3 100644 --- a/gnu/packages/version-control.scm +++ b/gnu/packages/version-control.scm @@ -15,6 +15,7 @@ ;;; Copyright © 2017 Vasile Dumitrascu <va511e@yahoo.com> ;;; Copyright © 2017 Clément Lassieur <clement@lassieur.org> ;;; Copyright © 2017 André <eu@euandre.org> +;;; Copyright © 2017 Marius Bakke <mbakke@fastmail.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -120,14 +121,14 @@ as well as the classic centralized workflow.") (define-public git (package (name "git") - (version "2.13.4") + (version "2.14.0") (source (origin (method url-fetch) (uri (string-append "mirror://kernel.org/software/scm/git/git-" version ".tar.xz")) (sha256 (base32 - "1nmg0n9l5ix876iqhcyhdnmiy7ihv0ybdijf1lssch6ja8m5j6ip")))) + "0xarcp0m7jbncic0g3ahz8l2d6b27h0g9ndgrhy9abkx61m6wgpr")))) (build-system gnu-build-system) (native-inputs `(("native-perl" ,perl) @@ -140,7 +141,7 @@ as well as the classic centralized workflow.") version ".tar.xz")) (sha256 (base32 - "0ljxkfi7ski9bgpdb8xpikl1xgjjk7bdzmzzkbj93jybk6iajkv7")))))) + "0kc2n6b1lrbr0wc8lk3xnrljn4fgzgab82icv658gdvyl9l3qrbx")))))) (inputs `(("curl" ,curl) ("expat" ,expat) @@ -176,7 +177,6 @@ as well as the classic centralized workflow.") ;; nars; see <https://bugs.gnu.org/21949>. "NO_INSTALL_HARDLINKS=indeed") #:test-target "test" - #:tests? #f ; FIXME: Many tests are failing ;; The explicit --with-tcltk forces the build system to hardcode the ;; absolute file name to 'wish'. @@ -203,6 +203,37 @@ as well as the classic centralized workflow.") ;; Add the "PM.stamp" to avoid "no rule to make target". (call-with-output-file "perl/PM.stamp" (const #t)) #t)) + (add-before 'check 'patch-tests + (lambda _ + ;; These files contain some funny bytes that Guile is unable + ;; to decode for shebang patching. Just delete them. + (for-each delete-file '("t/t4201-shortlog.sh" + "t/t7813-grep-icase-iso.sh")) + ;; Many tests contain inline shell scripts (hooks etc). + (substitute* (find-files "t" "\\.sh$") + (("#!/bin/sh") (string-append "#!" (which "sh")))) + ;; Un-do shebang patching here to prevent checksum mismatch. + (substitute* '("t/t4034/perl/pre" "t/t4034/perl/post") + (("^#!.*/bin/perl") "#!/usr/bin/perl")) + (substitute* "t/t5003-archive-zip.sh" + (("cp /bin/sh") (string-append "cp " (which "sh")))) + (substitute* "t/t6030-bisect-porcelain.sh" + (("\"/bin/sh\"") (string-append "\"" (which "sh") "\""))) + ;; FIXME: This test runs `git commit` with a bogus EDITOR + ;; and empty commit message, but does not fail the way it's + ;; expected to. The test passes when invoked interactively. + (substitute* "t/t7508-status.sh" + (("\tcommit_template_commented") "\ttrue")) + ;; More checksum mismatches due to odd shebangs. + (substitute* "t/t9100-git-svn-basic.sh" + (("\"#!/gnu.*/bin/sh") "\"#!/bin/sh")) + (substitute* "t/t9300-fast-import.sh" + (("\t#!/gnu.*/bin/sh") "\t#!/bin/sh") + (("'#!/gnu.*/bin/sh") "'#!/bin/sh")) + ;; FIXME: Some hooks fail with "basename: command not found". + ;; See 't/trash directory.t9164.../svn-hook.log'. + (delete-file "t/t9164-git-svn-dcommit-concurrent.sh") + #t)) (add-after 'install 'install-shell-completion (lambda* (#:key outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index 0a551c74f4..1152cdf0a0 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -1121,7 +1121,7 @@ access to mpv's powerful playback capabilities.") (define-public youtube-dl (package (name "youtube-dl") - (version "2017.07.23") + (version "2017.07.30.1") (source (origin (method url-fetch) (uri (string-append "https://yt-dl.org/downloads/" @@ -1129,7 +1129,7 @@ access to mpv's powerful playback capabilities.") version ".tar.gz")) (sha256 (base32 - "0h8jim7qx7b97wg7s8izz3and1xp70b9clqwpxl33xls9linh04m")))) + "1m1n5d06xh8hnild6kssiv9yaq2sm7vy0c8h506v3nff7i9wf0a7")))) (build-system python-build-system) (arguments ;; The problem here is that the directory for the man page and completion diff --git a/gnu/packages/virtualization.scm b/gnu/packages/virtualization.scm index 0ac76a72d9..628396e52c 100644 --- a/gnu/packages/virtualization.scm +++ b/gnu/packages/virtualization.scm @@ -317,14 +317,14 @@ manage system or application containers.") (define-public libvirt (package (name "libvirt") - (version "3.5.0") + (version "3.6.0") (source (origin (method url-fetch) - (uri (string-append "http://libvirt.org/sources/libvirt-" + (uri (string-append "https://libvirt.org/sources/libvirt-" version ".tar.xz")) (sha256 (base32 - "05mm4xdw6g960rwvc9189nhxpm1vrilnmpl4h4m1lha11pivlqr9")))) + "0gcyql5dp6j370kvik9hjhxirrg89m7l1q52yq0g75h7jpv9fb1s")))) (build-system gnu-build-system) (arguments `(;; FAIL: virshtest @@ -334,7 +334,7 @@ manage system or application containers.") ;; FAIL: networkxml2firewalltest ;; FAIL: nwfilterebiptablestest ;; FAIL: nwfilterxml2firewalltest - ;; Times out after PASS: virsh-vcpupin + ;; Times while running commandest. #:tests? #f #:configure-flags (list "--with-polkit" @@ -381,7 +381,7 @@ manage system or application containers.") ("iptables" ,iptables))) (native-inputs `(("pkg-config" ,pkg-config))) - (home-page "http://libvirt.org") + (home-page "https://libvirt.org") (synopsis "Simple API for virtualization") (description "Libvirt is a C toolkit to interact with the virtualization capabilities of recent versions of Linux. The library aims at providing long diff --git a/gnu/packages/vpn.scm b/gnu/packages/vpn.scm index aec8c1807d..61ebf0d5fa 100644 --- a/gnu/packages/vpn.scm +++ b/gnu/packages/vpn.scm @@ -239,14 +239,14 @@ DNS domain name queries.") (define-public sshoot (package (name "sshoot") - (version "1.2.5") + (version "1.2.6") (source (origin (method url-fetch) (uri (pypi-uri name version)) (sha256 (base32 - "0a92lk8790dpp9j64vb6p4sazax0x3nby01lnfll7mxs1hx6n27q")))) + "1ccgh0hjyxrwkgy3hnxz3hgbjbs0lmfs25d5l5jam0xbpcpj63h0")))) (build-system python-build-system) (arguments '(#:phases @@ -265,7 +265,7 @@ DNS domain name queries.") `(("python-fixtures" ,python-fixtures) ("python-pbr" ,python-pbr) ("python-testtools" ,python-testtools))) - (home-page "https://bitbucket.org/ack/sshoot") + (home-page "https://github.com/albertodonato/sshoot") (synopsis "sshuttle VPN session manager") (description "sshoot provides a command-line interface to manage multiple @command{sshuttle} virtual private networks. It supports flexible profiles diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 096d05c167..54fd410df7 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -54,6 +54,7 @@ #:use-module (gnu packages) #:use-module (gnu packages apr) #:use-module (gnu packages check) + #:use-module (gnu packages cran) #:use-module (gnu packages documentation) #:use-module (gnu packages docbook) #:use-module (gnu packages autotools) @@ -72,6 +73,7 @@ #:use-module (gnu packages gnuzilla) #:use-module (gnu packages gperf) #:use-module (gnu packages gtk) + #:use-module (gnu packages javascript) #:use-module (gnu packages image) #:use-module (gnu packages libidn) #:use-module (gnu packages libunistring) @@ -3380,13 +3382,13 @@ CDF, Atom 0.3, and Atom 1.0 feeds.") (define-public r-httpuv (package (name "r-httpuv") - (version "1.3.3") + (version "1.3.5") (source (origin (method url-fetch) (uri (cran-uri "httpuv" version)) (sha256 (base32 - "0aibs0hf38n8f6xxx4g2i2lzd6l5h92m5pscx2z834sdvhnladxv")))) + "1sg4f223zfyd265b28rlhsn3b6mqflcpnmya98cjmjncmy9vjdj3")))) (build-system r-build-system) (native-inputs `(("r-rcpp" ,r-rcpp))) (home-page "https://github.com/rstudio/httpuv") @@ -3404,13 +3406,13 @@ particularly easy to create complete web applications using httpuv alone.") (define-public r-jsonlite (package (name "r-jsonlite") - (version "1.4") + (version "1.5") (source (origin (method url-fetch) (uri (cran-uri "jsonlite" version)) (sha256 (base32 - "11rgkjp5qir79niad0aizjxvjzyvkl6l9nsrv3ikv446vllmrasn")))) + "00lfg464jhf7k01bal9pcjvbdf5cxk6xi2h46hccp1x3h883g434")))) (build-system r-build-system) (home-page "http://arxiv.org/abs/1403.2805") (synopsis "Robust, high performance JSON parser and generator for R") @@ -3428,13 +3430,13 @@ in systems and applications.") (define-public r-servr (package (name "r-servr") - (version "0.5") + (version "0.6") (source (origin (method url-fetch) (uri (cran-uri "servr" version)) (sha256 (base32 - "1ixcl9xjc1k9zvl6v6bsw4kpramr1h53b4s46qg8kahkqy6kqd8a")))) + "0sqz3wssxa19g9mpmf9s4gx2a5rvzl8nrd11qkgpz5v3iqsc6ysr")))) (build-system r-build-system) (propagated-inputs `(("r-httpuv" ,r-httpuv) @@ -3453,13 +3455,13 @@ directory.") (define-public r-htmltools (package (name "r-htmltools") - (version "0.3.5") + (version "0.3.6") (source (origin (method url-fetch) (uri (cran-uri "htmltools" version)) (sha256 (base32 - "0j9bf80grd6gwh7116m575pycv87c0wcwkxsz3gzzfs4aw3pxyr9")))) + "18k8r1s8sz1jy7dkz35n69wj20xhmllr53xmwb4pdzf2z61gpbs4")))) (build-system r-build-system) (arguments `(#:phases @@ -3487,13 +3489,13 @@ directory.") (define-public r-htmlwidgets (package (name "r-htmlwidgets") - (version "0.8") + (version "0.9") (source (origin (method url-fetch) (uri (cran-uri "htmlwidgets" version)) (sha256 (base32 - "1df3pwl34rvdbr9sgr5h27q9bmqpckvpwq4frl3d1v614y3vfclj")))) + "0plqkfqys1ca3ki7sb7yc6gwjpi7yy4g3mzh7hfy8s6qri0vam0i")))) (build-system r-build-system) (propagated-inputs `(("r-htmltools" ,r-htmltools) @@ -3541,13 +3543,13 @@ LaTeX.") (define-public r-curl (package (name "r-curl") - (version "2.5") + (version "2.8.1") (source (origin (method url-fetch) (uri (cran-uri "curl" version)) (sha256 (base32 - "09p86i5f88gx1i7cidm1ka56g0jjkghqfam96p1jhwlh2fv6nrks")))) + "0dgfl7wn4r8inv55xnk4ybf1y2x4qmi4cbr6phr3lfi1dnjm4hsm")))) (build-system r-build-system) (arguments `(#:phases @@ -4781,3 +4783,133 @@ internetarchive python module for programatic access to archive.org.") (define-public python2-internetarchive (package-with-python2 (strip-python2-variant python-internetarchive))) + +(define-public r-shiny + (package + (name "r-shiny") + (version "1.0.3") + (source + (origin + (method url-fetch) + (uri (string-append "https://github.com/rstudio/shiny/" + "archive/v" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0z2v2s4hd44mvzjn7r70549kdzkrrch9nxhp27r6x2cy6micizm3")))) + (build-system r-build-system) + (arguments + `(#:modules ((guix build r-build-system) + (guix build minify-build-system) + (guix build utils) + (ice-9 match)) + #:imported-modules (,@%r-build-system-modules + (guix build minify-build-system)) + #:phases + (modify-phases (@ (guix build r-build-system) %standard-phases) + (add-after 'unpack 'replace-bundled-minified-JavaScript + (lambda* (#:key inputs #:allow-other-keys) + (let ((replace-file (lambda (old new) + (format #t "replacing ~a with ~a\n" old new) + (delete-file old) + (symlink new old)))) + ;; NOTE: Files in ./inst/www/shared/datepicker/js/locales/ + ;; contain just data. They are not minified code, so we don't + ;; replace them. + (with-directory-excursion "inst/www/shared" + (replace-file "bootstrap/shim/respond.min.js" + (string-append (assoc-ref inputs "js-respond") + "/share/javascript/respond.min.js")) + (replace-file "bootstrap/shim/html5shiv.min.js" + (string-append (assoc-ref inputs "js-html5shiv") + "/share/javascript/html5shiv.min.js")) + (replace-file "json2-min.js" + (string-append (assoc-ref inputs "js-json2") + "/share/javascript/json2.min.js")) + (replace-file "strftime/strftime-min.js" + (string-append (assoc-ref inputs "js-strftime") + "/share/javascript/strftime.min.js")) + (replace-file "highlight/highlight.pack.js" + (string-append (assoc-ref inputs "js-highlight") + "/share/javascript/highlight.min.js")) + (replace-file "datatables/js/jquery.dataTables.min.js" + (string-append (assoc-ref inputs "js-datatables") + "/share/javascript/jquery.dataTables.min.js")) + (replace-file "selectize/js/selectize.min.js" + (string-append (assoc-ref inputs "js-selectize") + "/share/javascript/selectize.min.js")) + (replace-file "selectize/js/es5-shim.min.js" + (string-append (assoc-ref inputs "js-es5-shim") + "/share/javascript/es5-shim.min.js")) + (for-each (match-lambda + ((source . target) + (delete-file target) + (minify source #:target target))) + '(("jqueryui/jquery-ui.js" . + "jqueryui/jquery-ui.min.js") + ("showdown/src/showdown.js" . + "showdown/compressed/showdown.js") + ("datepicker/js/bootstrap-datepicker.js" . + "datepicker/js/bootstrap-datepicker.min.js") + ("ionrangeslider/js/ion.rangeSlider.js" . + "ionrangeslider/js/ion.rangeSlider.min.js") + ("bootstrap/js/bootstrap.js" . + "bootstrap/js/bootstrap.min.js") + ("shiny.js" . + "shiny.min.js") + ("jquery.js" . + "jquery.min.js"))))) + #t))))) + (propagated-inputs + `(("r-httpuv" ,r-httpuv) + ("r-mime" ,r-mime) + ("r-jsonlite" ,r-jsonlite) + ("r-xtable" ,r-xtable) + ("r-digest" ,r-digest) + ("r-htmltools" ,r-htmltools) + ("r-r6" ,r-r6) + ("r-sourcetools" ,r-sourcetools))) + (inputs + `(("js-datatables" ,js-datatables) + ("js-html5shiv" ,js-html5shiv) + ("js-json2" ,js-json2) + ("js-respond" ,js-respond) + ("js-selectize" ,js-selectize) + ("js-strftime" ,js-strftime) + ("js-highlight" ,js-highlight) + ("js-es5-shim" ,js-es5-shim))) + (home-page "http://shiny.rstudio.com") + (synopsis "Easy interactive web applications with R") + (description + "Makes it incredibly easy to build interactive web applications +with R. Automatic \"reactive\" binding between inputs and outputs and +extensive prebuilt widgets make it possible to build beautiful, +responsive, and powerful applications with minimal effort.") + (license l:artistic2.0))) + +(define-public r-crosstalk + (package + (name "r-crosstalk") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "crosstalk" version)) + (sha256 + (base32 + "0lfa89vhrzi7a1rghmygcjr8gzddw35sinb3jx6g49mc9jias7mk")))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-htmltools" ,r-htmltools) + ("r-jsonlite" ,r-jsonlite) + ("r-lazyeval" ,r-lazyeval) + ("r-r6" ,r-r6) + ("r-shiny" ,r-shiny))) + (home-page "https://rstudio.github.io/crosstalk/") + (synopsis "Inter-widget interactivity for HTML widgets") + (description + "This package provides building blocks for allowing HTML widgets to +communicate with each other, with Shiny or without (i.e. static @code{.html} +files). It currently supports linked brushing and filtering.") + (license l:expat))) diff --git a/gnu/system/vm.scm b/gnu/system/vm.scm index 90d29b0783..4494af0031 100644 --- a/gnu/system/vm.scm +++ b/gnu/system/vm.scm @@ -49,6 +49,7 @@ #:use-module (gnu packages admin) #:use-module (gnu bootloader) + #:use-module ((gnu bootloader grub) #:select (grub-mkrescue-bootloader)) #:use-module (gnu system shadow) #:use-module (gnu system pam) #:use-module (gnu system linux-initrd) @@ -369,6 +370,12 @@ to USB sticks meant to be read-only." #:volatile-root? #t rest))) + (bootloader (if (string=? "iso9660" file-system-type) + (bootloader-configuration + (inherit (operating-system-bootloader os)) + (bootloader grub-mkrescue-bootloader)) + (operating-system-bootloader os))) + ;; Force our own root file system. (file-systems (cons (file-system (mount-point "/") |