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-rw-r--r--gnu/packages/admin.scm22
-rw-r--r--gnu/packages/base.scm10
-rw-r--r--gnu/packages/bioinformatics.scm135
-rw-r--r--gnu/packages/bootloaders.scm33
-rw-r--r--gnu/packages/compression.scm9
-rw-r--r--gnu/packages/cran.scm106
-rw-r--r--gnu/packages/ebook.scm3
-rw-r--r--gnu/packages/emacs.scm10
-rw-r--r--gnu/packages/ftp.scm4
-rw-r--r--gnu/packages/gcc.scm7
-rw-r--r--gnu/packages/gnupg.scm4
-rw-r--r--gnu/packages/graphics.scm6
-rw-r--r--gnu/packages/image.scm44
-rw-r--r--gnu/packages/javascript.scm191
-rw-r--r--gnu/packages/lego.scm61
-rw-r--r--gnu/packages/linux.scm42
-rw-r--r--gnu/packages/machine-learning.scm1
-rw-r--r--gnu/packages/markup.scm4
-rw-r--r--gnu/packages/maths.scm54
-rw-r--r--gnu/packages/mp3.scm13
-rw-r--r--gnu/packages/package-management.scm9
-rw-r--r--gnu/packages/patches/fabric-tests.patch15
-rw-r--r--gnu/packages/patches/gd-CVE-2017-7890.patch30
-rw-r--r--gnu/packages/patches/glibc-CVE-2015-5180.patch311
-rw-r--r--gnu/packages/patches/glibc-CVE-2015-7547.patch590
-rw-r--r--gnu/packages/patches/glibc-CVE-2016-3075.patch43
-rw-r--r--gnu/packages/patches/glibc-CVE-2016-3706.patch188
-rw-r--r--gnu/packages/patches/glibc-CVE-2016-4429.patch58
-rw-r--r--gnu/packages/php.scm17
-rw-r--r--gnu/packages/python.scm28
-rw-r--r--gnu/packages/rdesktop.scm22
-rw-r--r--gnu/packages/shells.scm4
-rw-r--r--gnu/packages/statistics.scm333
-rw-r--r--gnu/packages/tls.scm6
-rw-r--r--gnu/packages/tor.scm4
-rw-r--r--gnu/packages/version-control.scm39
-rw-r--r--gnu/packages/video.scm4
-rw-r--r--gnu/packages/virtualization.scm10
-rw-r--r--gnu/packages/vpn.scm6
-rw-r--r--gnu/packages/web.scm156
40 files changed, 2260 insertions, 372 deletions
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)))