Merge branch 'master' into core-updates

18 files changed, 774 insertions, 378 deletions

diff --git a/gnu/local.mk b/gnu/local.mk
index 90dbe94025..545a7d173f 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -813,6 +813,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/higan-remove-march-native-flag.patch	\
   %D%/packages/patches/hubbub-sort-entities.patch		\
   %D%/packages/patches/hurd-fix-eth-multiplexer-dependency.patch        \
+  %D%/packages/patches/hplip-remove-imageprocessor.patch	\
   %D%/packages/patches/hydra-disable-darcs-test.patch		\
   %D%/packages/patches/icecat-avoid-bundled-libraries.patch	\
   %D%/packages/patches/icecat-CVE-2018-12383.patch		\
@@ -1230,7 +1231,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/wpa-supplicant-fix-zeroed-keys.patch	\
   %D%/packages/patches/wpa-supplicant-fix-nonce-reuse.patch	\
   %D%/packages/patches/wpa-supplicant-krack-followups.patch	\
-  %D%/packages/patches/wxmaxima-do-not-use-old-gnuplot-parameters.patch	\
   %D%/packages/patches/x265-detect512-all-arches.patch		\
   %D%/packages/patches/xboing-CVE-2004-0149.patch		\
   %D%/packages/patches/xf86-video-ark-remove-mibstore.patch	\
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 1fac960eff..8820ba0d8e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -753,15 +753,15 @@ e.g. microbiome samples, genomes, metagenomes.")
     (package
       (inherit base)
       (arguments
-       `(#:phases
-         (modify-phases %standard-phases
-           ;; Do not require the unmaintained pyqi library.
-           (add-after 'unpack 'remove-pyqi
-             (lambda _
-               (substitute* "setup.py"
-                 (("install_requires.append\\(\"pyqi\"\\)") "pass"))
-               #t)))
-         ,@(package-arguments base))))))
+       (substitute-keyword-arguments (package-arguments base)
+         ((#:phases phases)
+          `(modify-phases ,phases
+             ;; Do not require the unmaintained pyqi library.
+             (add-after 'unpack 'remove-pyqi
+               (lambda _
+                 (substitute* "setup.py"
+                   (("install_requires.append\\(\"pyqi\"\\)") "pass"))
+                 #t)))))))))
 
 (define-public bioperl-minimal
   (let* ((inputs `(("perl-module-build" ,perl-module-build)
@@ -2716,8 +2716,10 @@ Illumina, Roche 454, and the SOLiD platform.")
                   (string-append "  strcpy(train_dir, \"" share "/train/\");"))))
              #t))
          (replace 'build
-           (lambda _ (and (zero? (system* "make" "clean"))
-                          (zero? (system* "make" "fgs")))))
+           (lambda _
+             (invoke "make" "clean")
+             (invoke "make" "fgs")
+             #t))
          (replace 'install
            (lambda* (#:key outputs #:allow-other-keys)
              (let* ((out (string-append (assoc-ref outputs "out")))
@@ -2734,21 +2736,24 @@ Illumina, Roche 454, and the SOLiD platform.")
              (let* ((out (string-append (assoc-ref outputs "out")))
                     (bin (string-append out "/bin/"))
                     (frag (string-append bin "run_FragGeneScan.pl")))
-               (and (zero? (system* frag ; Test complete genome.
-                             "-genome=./example/NC_000913.fna"
-                             "-out=./test2"
-                             "-complete=1"
-                             "-train=complete"))
-                    (file-exists? "test2.faa")
-                    (file-exists? "test2.ffn")
-                    (file-exists? "test2.gff")
-                    (file-exists? "test2.out")
-                    (zero? (system* ; Test incomplete sequences.
-                            frag
-                            "-genome=./example/NC_000913-fgs.ffn"
-                            "-out=out"
-                            "-complete=0"
-                            "-train=454_30")))))))))
+               ;; Test complete genome.
+               (invoke frag
+                       "-genome=./example/NC_000913.fna"
+                       "-out=./test2"
+                       "-complete=1"
+                       "-train=complete")
+               (unless (and (file-exists? "test2.faa")
+                            (file-exists? "test2.ffn")
+                            (file-exists? "test2.gff")
+                            (file-exists? "test2.out"))
+                 (error "Expected files do not exist."))
+               ;; Test incomplete sequences.
+               (invoke frag
+                       "-genome=./example/NC_000913-fgs.ffn"
+                       "-out=out"
+                       "-complete=0"
+                       "-train=454_30")
+               #t))))))
     (inputs
      `(("perl" ,perl)
        ("python" ,python-2))) ;not compatible with python 3.
@@ -3471,26 +3476,28 @@ VCF.")
            (lambda* (#:key inputs #:allow-other-keys)
              (mkdir-p "lib/jni")
              (mkdir-p "jdk-src")
-             (and (zero? (system* "tar" "--strip-components=1" "-C" "jdk-src"
-                                  "-xf" (assoc-ref inputs "jdk-src")))
-                  (zero? (system* "javah" "-jni"
-                                  "-classpath" "classes"
-                                  "-d" "lib/"
-                                  "net.sf.samtools.util.zip.IntelDeflater"))
-                  (with-directory-excursion "src/c/inteldeflater"
-                    (zero? (system* "gcc" "-I../../../lib" "-I."
-                                    (string-append "-I" (assoc-ref inputs "jdk")
-                                                   "/include/linux")
-                                    "-I../../../jdk-src/src/share/native/common/"
-                                    "-I../../../jdk-src/src/solaris/native/common/"
-                                    "-c" "-O3" "-fPIC" "IntelDeflater.c"))
-                    (zero? (system* "gcc" "-shared"
-                                    "-o" "../../../lib/jni/libIntelDeflater.so"
-                                    "IntelDeflater.o" "-lz" "-lstdc++"))))))
+             (invoke "tar" "--strip-components=1" "-C" "jdk-src"
+                     "-xf" (assoc-ref inputs "jdk-src"))
+             (invoke "javah" "-jni"
+                     "-classpath" "classes"
+                     "-d" "lib/"
+                     "net.sf.samtools.util.zip.IntelDeflater")
+             (with-directory-excursion "src/c/inteldeflater"
+               (invoke "gcc" "-I../../../lib" "-I."
+                       (string-append "-I" (assoc-ref inputs "jdk")
+                                      "/include/linux")
+                       "-I../../../jdk-src/src/share/native/common/"
+                       "-I../../../jdk-src/src/solaris/native/common/"
+                       "-c" "-O3" "-fPIC" "IntelDeflater.c")
+               (invoke "gcc" "-shared"
+                       "-o" "../../../lib/jni/libIntelDeflater.so"
+                       "IntelDeflater.o" "-lz" "-lstdc++"))
+             #t))
          ;; We can only build everything else after building the JNI library.
          (add-after 'build-jni 'build-rest
            (lambda* (#:key make-flags #:allow-other-keys)
-             (zero? (apply system* `("ant" "all" ,@make-flags)))))
+             (apply invoke `("ant" "all" ,@make-flags))
+             #t))
          (add-before 'build 'set-JAVA6_HOME
            (lambda _
              (setenv "JAVA6_HOME" (getenv "JAVA_HOME"))
@@ -3977,16 +3984,16 @@ sequences).")
 (define-public mash
   (package
     (name "mash")
-    (version "2.0")
+    (version "2.1")
     (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/marbl/mash/archive/v"
-                    version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/marbl/mash.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "00fx14vpmgsijwxd1xql3if934l82v8ckqgjjyyhnr36qb9qrskv"))
+                "049hwcc059p2fd9vwndn63laifvvsi0wmv84i6y1fr79k15dxwy6"))
               (modules '((guix build utils)))
               (snippet
                '(begin
@@ -4011,9 +4018,7 @@ sequences).")
                             "src/mash/CommandScreen.cpp")
                (("^#include \"kseq\\.h\"")
                 "#include \"htslib/kseq.h\""))
-             #t))
-         (add-after 'fix-includes 'autoconf
-           (lambda _ (zero? (system* "autoconf")))))))
+             #t)))))
     (native-inputs
      `(("autoconf" ,autoconf)
        ;; Capnproto and htslib are statically embedded in the final
@@ -4040,13 +4045,14 @@ form of assemblies or reads.")
     (version "2.12.1")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append "https://bitbucket.org/berkeleylab/metabat/get/v"
-                           version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://bitbucket.org/berkeleylab/metabat.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "1hmvdalz3zj5sqqklg0l4npjdv37cv2hsdi1al9iby2ndxjs1b73"))
+         "0hyg2smw1nz69mfvjpk45xyyychmda92c80a0cv7baji84ri4iyn"))
        (patches (search-patches "metabat-fix-compilation.patch"))))
     (build-system scons-build-system)
     (arguments
@@ -4109,16 +4115,16 @@ probabilistic distances of genome abundance and tetranucleotide frequency.")
 (define-public minced
   (package
     (name "minced")
-    (version "0.2.0")
+    (version "0.3.2")
     (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/ctSkennerton/minced/archive/"
-                    version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/ctSkennerton/minced.git")
+                    (commit version)))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "0wxmlsapxfpxfd3ps9636h7i2xy6la8i42mwh0j2lsky63h63jp1"))))
+                "1f5h9him0gd355cnx7p6pnxpknhckd4g0v62mg8zyhfbx9as25fv"))))
     (build-system gnu-build-system)
     (arguments
      `(#:test-target "test"
@@ -4230,12 +4236,13 @@ that a read originated from a particular isoform.")
          (delete 'configure)
          (replace 'check
            ;; There are no tests, so just test if it runs.
-           (lambda _ (zero? (system* "./muscle" "-version"))))
+           (lambda _ (invoke "./muscle" "-version") #t))
          (replace 'install
            (lambda* (#:key outputs #:allow-other-keys)
              (let* ((out (assoc-ref outputs "out"))
                     (bin (string-append out "/bin")))
-               (install-file "muscle" bin)))))))
+               (install-file "muscle" bin)
+               #t))))))
     (home-page "http://www.drive5.com/muscle")
     (synopsis "Multiple sequence alignment program")
     (description
@@ -4260,11 +4267,6 @@ program for nucleotide and protein sequences.")
                  (base32
                   "1hkw21rq1mwf7xp0rmbb2gqc0i6p11108m69i7mr7xcjl268pxnb"))))
     (build-system gnu-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'autoconf
-           (lambda _ (zero? (system* "autoreconf" "-vif")))))))
     (inputs
      ;; XXX: TODO: Enable Lua and Guile bindings.
      ;; https://github.com/tjunier/newick_utils/issues/13
@@ -4309,19 +4311,20 @@ interrupted by stop codons.  OrfM finds and prints these ORFs.")
     (license license:lgpl3+)))
 
 (define-public pplacer
-  (let ((commit "g807f6f3"))
+  (let ((commit "807f6f3"))
     (package
       (name "pplacer")
       ;; The commit should be updated with each version change.
       (version "1.1.alpha19")
       (source
        (origin
-         (method url-fetch)
-         (uri (string-append "https://github.com/matsen/pplacer/archive/v"
-                             version ".tar.gz"))
-         (file-name (string-append name "-" version ".tar.gz"))
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/matsen/pplacer.git")
+               (commit (string-append "v" version))))
+         (file-name (git-file-name name version))
          (sha256
-          (base32 "0z1lnd2s8sh6kpzg106wzbh2szw7h0hvq8syd5a6wv4rmyyz6x0f"))))
+          (base32 "11ppbbbx20p2g9wj3ff64dhnarb12q79v7qh4rk0gj6lkbz4n7cn"))))
       (build-system ocaml-build-system)
       (arguments
        `(#:ocaml ,ocaml-4.01
@@ -4338,11 +4341,12 @@ interrupted by stop codons.  OrfM finds and prints these ORFs.")
                       (local-dir "cddlib_guix"))
                  (mkdir local-dir)
                  (with-directory-excursion local-dir
-                   (system* "tar" "xvf" cddlib-src))
+                   (invoke "tar" "xvf" cddlib-src))
                  (let ((cddlib-src-folder
                         (string-append local-dir "/"
                                        (list-ref (scandir local-dir) 2)
                                        "/lib-src")))
+                   (for-each make-file-writable (find-files "cdd_src" ".*"))
                    (for-each
                     (lambda (file)
                       (copy-file file
@@ -4406,8 +4410,7 @@ downstream analysis.")
          (add-after 'unpack 'enter-scripts-dir
            (lambda _ (chdir "scripts")))
          (replace 'check
-           (lambda _
-             (zero? (system* "python" "-m" "unittest" "discover" "-v"))))
+           (lambda _ (invoke "python" "-m" "unittest" "discover" "-v") #t))
          (add-after 'install 'wrap-executables
            (lambda* (#:key inputs outputs #:allow-other-keys)
              (let* ((out (assoc-ref outputs "out"))
@@ -4667,13 +4670,14 @@ large-scale data and can be applied to hundreds of species at once.")
     (version "2.0.7")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append "https://bitbucket.org/regulatorygenomicsupf/"
-                           "pyicoteo/get/v" version ".tar.bz2"))
-       (file-name (string-append name "-" version ".tar.bz2"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://bitbucket.org/regulatorygenomicsupf/pyicoteo.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "0d6087f29xp8wxwlj111c3sylli98n0l8ry58c51ixzq0zfm50wa"))))
+         "0hz5g8d25lbjy1wpscr490l0lmyvaix893hhax4fxnh1h9w34w8p"))))
     (build-system python-build-system)
     (arguments
      `(#:python ,python-2 ; does not work with Python 3
@@ -4757,10 +4761,11 @@ partial genes, and identifies translation initiation sites.")
                                            (getenv "PATH")))
              (setenv "PERL5LIB" (string-append (getcwd) "/lib" ":"
                                                (getenv "PERL5LIB")))
-             (zero? (length (filter (lambda (file)
-                                      (display file)(display "\n")
-                                      (not (zero? (system* "perl" file))))
-                                    (find-files "t" ".*\\.t$"))))))
+             (for-each (lambda (file)
+                         (display file)(display "\n")
+                         (invoke "perl" file))
+                       (find-files "t" ".*\\.t$"))
+             #t))
          (replace 'install
            ;; There is no 'install' target in the Makefile.
            (lambda* (#:key outputs #:allow-other-keys)
@@ -4849,18 +4854,17 @@ extremely diverse sets of genomes.")
 (define-public raxml
   (package
     (name "raxml")
-    (version "8.2.10")
+    (version "8.2.12")
     (source
      (origin
-       (method url-fetch)
-       (uri
-        (string-append
-         "https://github.com/stamatak/standard-RAxML/archive/v"
-         version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/stamatak/standard-RAxML.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "13s7aspfdcfr6asynwdg1x6vznys6pzap5f8wsffbnnwpkkg9ya8"))))
+         "1jqjzhch0rips0vp04prvb8vmc20c5pdmsqn8knadcf91yy859fh"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f ; There are no tests.
@@ -5053,21 +5057,24 @@ distribution, coverage uniformity, strand specificity, etc.")
            (modify-phases %standard-phases
              (replace 'bootstrap
                (lambda _
-                 (invoke "bash" "gen_auto")))
+                 (substitute* "gen_tools_am"
+                   (("/usr/bin/env.*") (which "perl")))
+                 (invoke "bash" "gen_auto")
+                 #t))
              (add-after 'build 'build-additional-tools
                (lambda* (#:key make-flags #:allow-other-keys)
-                 (every (lambda (dir)
-                          (with-directory-excursion (string-append "tools/" dir)
-                            (zero? (apply system* "make" make-flags))))
-                        dirs)))
+                 (for-each (lambda (dir)
+                             (with-directory-excursion (string-append "tools/" dir)
+                               (apply invoke "make" make-flags)))
+                           dirs)
+                 #t))
              (add-after 'install 'install-additional-tools
                (lambda* (#:key make-flags #:allow-other-keys)
-                 (fold (lambda (dir result)
-                         (with-directory-excursion (string-append "tools/" dir)
-                           (and result
-                                (zero? (apply system*
-                                              `("make" ,@make-flags "install"))))))
-                       #t dirs)))))))
+                 (for-each (lambda (dir)
+                             (with-directory-excursion (string-append "tools/" dir)
+                               (apply invoke `("make" ,@make-flags "install"))))
+                           dirs)
+                 #t))))))
       (inputs
        `(("gsl" ,gsl)
          ("boost" ,boost)
@@ -5233,17 +5240,16 @@ Roche 454, Ion Torrent and Pacific BioSciences SMRT.")
 (define-public ngs-sdk
   (package
     (name "ngs-sdk")
-    (version "1.3.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri
-        (string-append "https://github.com/ncbi/ngs/archive/"
-                       version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
-       (sha256
-        (base32
-         "1wiyf4c6nm2j87pv015cbi0qny5byf3pbvcw3likifz5dl56ag40"))))
+    (version "2.9.3")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/ncbi/ngs.git")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "17c0v1nah3g3d2ib5bbi0vhma1ghd6vb9xycavqsh64lhp840rk3"))))
     (build-system gnu-build-system)
     (arguments
      `(#:parallel-build? #f ; not supported
@@ -5259,9 +5265,10 @@ Roche 454, Ion Torrent and Pacific BioSciences SMRT.")
 
                ;; The 'configure' script doesn't recognize things like
                ;; '--enable-fast-install'.
-               (zero? (system* "./configure"
-                               (string-append "--build-prefix=" (getcwd) "/build")
-                               (string-append "--prefix=" out))))))
+               (invoke "./configure"
+                       (string-append "--build-prefix=" (getcwd) "/build")
+                       (string-append "--prefix=" out))
+               #t)))
          (add-after 'unpack 'enter-dir
            (lambda _ (chdir "ngs-sdk") #t)))))
     (native-inputs `(("perl" ,perl)))
@@ -5299,23 +5306,24 @@ simultaneously.")
 (define-public ncbi-vdb
   (package
     (name "ncbi-vdb")
-    (version "2.8.2")
-    (source
-     (origin
-       (method url-fetch)
-       (uri
-        (string-append "https://github.com/ncbi/ncbi-vdb/archive/"
-                       version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
-       (sha256
-        (base32
-         "1acn4bv81mfl137qnbn9995mjjhwd36pm0b7qli1iw5skrxa9j8m"))))
+    (version "2.9.3")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/ncbi/ncbi-vdb.git")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1l4ny67nxwv1lagk9wwjbrgm7ln7adci6dnpc7k1yaln6shj0qpm"))))
     (build-system gnu-build-system)
     (arguments
      `(#:parallel-build? #f ; not supported
        #:tests? #f ; no "check" target
        #:phases
        (modify-phases %standard-phases
+         (add-after 'unpack 'make-files-writable
+           (lambda _ (for-each make-file-writable (find-files "." ".*")) #t))
          (add-before 'configure 'set-perl-search-path
            (lambda _
              ;; Work around "dotless @INC" build failure.
@@ -5349,8 +5357,7 @@ simultaneously.")
 
                ;; The 'configure' script doesn't recognize things like
                ;; '--enable-fast-install'.
-               (zero? (system*
-                       "./configure"
+               (invoke "./configure"
                        (string-append "--build-prefix=" (getcwd) "/build")
                        (string-append "--prefix=" (assoc-ref outputs "out"))
                        (string-append "--debug")
@@ -5359,7 +5366,8 @@ simultaneously.")
                        (string-append "--with-ngs-sdk-prefix="
                                       (assoc-ref inputs "ngs-sdk"))
                        (string-append "--with-hdf5-prefix="
-                                      (assoc-ref inputs "hdf5")))))))
+                                      (assoc-ref inputs "hdf5")))
+               #t)))
          (add-after 'install 'install-interfaces
            (lambda* (#:key outputs #:allow-other-keys)
              ;; Install interface libraries.  On i686 the interface libraries
@@ -5464,12 +5472,13 @@ subsequent visualization, annotation and storage of results.")
     (version "1.90b4")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append "https://github.com/chrchang/plink-ng/archive/v"
-                           version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/chrchang/plink-ng.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
-        (base32 "09ixrds009aczjswxr2alcb774mksq5g0v78dgjjn1h4dky0kf9a"))))
+        (base32 "02npdwgkpfkdnhw819rhj5kw02a5k5m90b14zq9zzya4hyg929c0"))))
     (build-system gnu-build-system)
     (arguments
      '(#:tests? #f ;no "check" target
@@ -5551,14 +5560,14 @@ structures, classes for genomic regions, mapped sequencing reads, etc.")
 (define-public preseq
   (package
     (name "preseq")
-    (version "2.0")
+    (version "2.0.3")
     (source (origin
               (method url-fetch)
-              (uri (string-append "https://github.com/smithlabcode/"
-                                  "preseq/archive/v" version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (uri (string-append "https://github.com/smithlabcode/preseq/"
+                                  "releases/download/v" version
+                                  "/preseq_v" version ".tar.bz2"))
               (sha256
-               (base32 "08r684l50pnxjpvmhzjgqq56yv9rfw90k8vx0nsrnrzk8mf9hsdq"))
+               (base32 "149x9xmk1wy1gff85325yfzqc0qk4sgp1w6gbyj9cnji4x1dszbl"))
               (modules '((guix build utils)))
               (snippet '(begin
                           ;; Remove bundled samtools.
@@ -5648,17 +5657,17 @@ sequence itself can be retrieved from these databases.")
 (define-public sra-tools
   (package
     (name "sra-tools")
-    (version "2.8.2-1")
+    (version "2.9.3")
     (source
      (origin
-       (method url-fetch)
-       (uri
-        (string-append "https://github.com/ncbi/sra-tools/archive/"
-                       version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/ncbi/sra-tools.git")
+             (commit version)))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "1camsijmvv2s45mb4iyf44ghl4gkd4rl0viphpcgl3ccchy32a0g"))))
+         "0663gcdxkziwsmlznjxysb00621rllpbz6jwsfifq7z3dj3lwm8b"))))
     (build-system gnu-build-system)
     (arguments
      `(#:parallel-build? #f ; not supported
@@ -5708,8 +5717,7 @@ sequence itself can be retrieved from these databases.")
 
              ;; The 'configure' script doesn't recognize things like
              ;; '--enable-fast-install'.
-             (zero? (system*
-                     "./configure"
+             (invoke "./configure"
                      (string-append "--build-prefix=" (getcwd) "/build")
                      (string-append "--prefix=" (assoc-ref outputs "out"))
                      (string-append "--debug")
@@ -5727,18 +5735,7 @@ sequence itself can be retrieved from these databases.")
                      (string-append "--with-ngs-sdk-prefix="
                                     (assoc-ref inputs "ngs-sdk"))
                      (string-append "--with-hdf5-prefix="
-                                    (assoc-ref inputs "hdf5"))))))
-         ;; This version of sra-tools fails to build with glibc because of a
-         ;; naming conflict.  glibc-2.25/include/bits/mathcalls.h already
-         ;; contains a definition of "canonicalize", so we rename it.
-         ;;
-         ;; See upstream bug report:
-         ;; https://github.com/ncbi/sra-tools/issues/67
-         (add-after 'unpack 'patch-away-glibc-conflict
-           (lambda _
-             (substitute* "tools/bam-loader/bam.c"
-               (("canonicalize\\(" line)
-                (string-append "sra_tools_" line)))
+                                    (assoc-ref inputs "hdf5")))
              #t)))))
     (native-inputs `(("perl" ,perl)))
     (inputs
@@ -5865,24 +5862,16 @@ is one that takes arguments.")
 (define-public seqtk
   (package
     (name "seqtk")
-    (version "1.2")
+    (version "1.3")
     (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/lh3/seqtk/archive/v"
-                    version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/lh3/seqtk.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "0ywdyzpmfiz2wp6ampbzqg4y8bj450nfgqarpamg045b8mk32lxx"))
-                            (modules '((guix build utils)))
-              (snippet
-               '(begin
-                  ;; Remove extraneous header files, as is done in the seqtk
-                  ;; master branch.
-                  (for-each (lambda (file) (delete-file file))
-                            (list "ksort.h" "kstring.h" "kvec.h"))
-                  #t))))
+                "1bfzlqa84b5s1qi22blmmw2s8xdyp9h9ydcq22pfjhh5gab3yz6l"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases
@@ -5890,11 +5879,12 @@ is one that takes arguments.")
          (delete 'configure)
          (replace 'check
            ;; There are no tests, so we just run a sanity check.
-           (lambda _ (zero? (system* "./seqtk" "seq"))))
+           (lambda _ (invoke "./seqtk" "seq") #t))
          (replace 'install
            (lambda* (#:key outputs #:allow-other-keys)
              (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
-               (install-file "seqtk" bin)))))))
+               (install-file "seqtk" bin)
+               #t))))))
     (inputs
      `(("zlib" ,zlib)))
     (home-page "https://github.com/lh3/seqtk")
@@ -5910,20 +5900,20 @@ optionally compressed by gzip.")
     (name "snap-aligner")
     (version "1.0beta.18")
     (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/amplab/snap/archive/v"
-                    version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/amplab/snap.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "1vnsjwv007k1fl1q7d681kbwn6bc66cgw6h16hym6gvyy71qv2ly"))))
+                "01w3qq4wm07z73vky0cfwlmrbf50n3w722cxrlzxfi99mnb808d8"))))
     (build-system gnu-build-system)
     (arguments
      '(#:phases
        (modify-phases %standard-phases
          (delete 'configure)
-         (replace 'check (lambda _ (zero? (system* "./unit_tests"))))
+         (replace 'check (lambda _ (invoke "./unit_tests") #t))
          (replace 'install
            (lambda* (#:key outputs #:allow-other-keys)
              (let* ((out (assoc-ref outputs "out"))
@@ -5952,14 +5942,14 @@ of these reads to align data quickly through a hash-based indexing scheme.")
     (version "2.1b")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append
-             "https://github.com/biocore/sortmerna/archive/"
-             version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/biocore/sortmerna.git")
+             (commit version)))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "1ghaghvd82af9j5adavxh77g7hm247d1r69m3fbi6f1jdivj5ldk"))))
+         "0j3mbz4n25738yijmjbr5r4fyvkgm8v5vn3sshyfvmyqf5q9byqf"))))
     (build-system gnu-build-system)
     (outputs '("out"      ;for binaries
                "db"))     ;for sequence databases
@@ -6205,8 +6195,7 @@ Cuffdiff or Ballgown programs.")
        #:phases
        (modify-phases %standard-phases
          (replace 'check
-           (lambda _
-             (zero? (system* "python" "-m" "unittest" "discover" "-v")))))))
+           (lambda _ (invoke "python" "-m" "unittest" "discover" "-v") #t)))))
     (propagated-inputs
      `(("python-sqlalchemy" ,python2-sqlalchemy)
        ("python-decorator" ,python2-decorator)
@@ -6839,17 +6828,17 @@ SELECT or UPDATE queries to an end-point.")
 (define-public vsearch
   (package
     (name "vsearch")
-    (version "2.8.0")
+    (version "2.9.1")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append
-             "https://github.com/torognes/vsearch/archive/v"
-             version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/torognes/vsearch.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "15pbirgzhvflj4pi5n82vybbzjy9mlb0lv5l3qhrmdkfzpbyahw3"))
+         "0vhrpjfdf75ba04b24xknp41790cvcgwl0vgpy7qbzj5xh2521ss"))
        (patches (search-patches "vsearch-unbundle-cityhash.patch"))
        (snippet
         '(begin
@@ -6860,11 +6849,6 @@ SELECT or UPDATE queries to an end-point.")
            (delete-file "src/city.cc")
            #t))))
     (build-system gnu-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'autogen
-           (lambda _ (zero? (system* "autoreconf" "-vif")))))))
     (inputs
      `(("zlib" ,zlib)
        ("bzip2" ,bzip2)
@@ -8874,13 +8858,14 @@ Sequences.")
     (version "1.1.4")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append "https://github.com/ManuSetty/SeqGL/"
-                           "archive/" version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/ManuSetty/SeqGL.git")
+             (commit version)))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "0pnk1p3sci5yipyc8xnb6jbmydpl80fld927xgnbcv104hy8h8yh"))))
+         "1r6ywvhxl3ffv48lgj7sbd582mcc6dha3ksgc2qjlvjrnkbj3799"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biostrings" ,r-biostrings)
@@ -9042,7 +9027,7 @@ AM_CONDITIONAL(AMPNG, true)"))
                (("\\$\\(bindir\\)/embossupdate") ""))
              #t))
          (add-after 'disable-update-check 'autogen
-           (lambda _ (zero? (system* "autoreconf" "-vif")))))))
+           (lambda _ (invoke "autoreconf" "-vif") #t)))))
     (inputs
      `(("perl" ,perl)
        ("libpng" ,libpng)
@@ -9215,12 +9200,14 @@ group or two ChIP groups run under different conditions.")
       (name "filevercmp")
       (version (string-append "0-1." (string-take commit 7)))
       (source (origin
-        (method url-fetch)
-        (uri (string-append "https://github.com/ekg/filevercmp/archive/"
-                            commit ".tar.gz"))
-        (file-name (string-append name "-" version ".tar.gz"))
-        (sha256
-         (base32 "0yp5jswf5j2pqc6517x277s4s6h1ss99v57kxw9gy0jkfl3yh450"))))
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/ekg/filevercmp.git")
+                      (commit commit)))
+                (file-name (git-file-name name commit))
+                (sha256
+                 (base32
+                  "1j9vxsy0y050v59h0q1d6501fcw1kjvj0d18l1xk2zyg0jzj247c"))))
       (build-system gnu-build-system)
       (arguments
        `(#:tests? #f ; There are no tests to run.
@@ -9230,7 +9217,8 @@ group or two ChIP groups run under different conditions.")
            (replace 'install
              (lambda* (#:key outputs #:allow-other-keys)
                (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
-                 (install-file "filevercmp" bin)))))))
+                 (install-file "filevercmp" bin)
+                 #t))))))
       (home-page "https://github.com/ekg/filevercmp")
       (synopsis "This program compares version strings")
       (description "This program compares version strings.  It intends to be a
@@ -11259,16 +11247,16 @@ sort, markdup, and depth.")
 (define-public ritornello
   (package
     (name "ritornello")
-    (version "1.0.0")
+    (version "2.0.1")
     (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/KlugerLab/"
-                                  "Ritornello/archive/v"
-                                  version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/KlugerLab/Ritornello.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "02nik86gq9ljjriv6pamwlmqnfky3ads1fpklx6mc3hx6k40pg38"))))
+                "1xahvq215qld7x1w8vpa5zbrsj6p9crb9shqa2x89sb0aaxa02jk"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f                      ; there are no tests
@@ -11277,7 +11265,7 @@ sort, markdup, and depth.")
          (add-after 'unpack 'patch-samtools-references
            (lambda* (#:key inputs #:allow-other-keys)
              (substitute* '("src/SamStream.h"
-                            "src/BufferedGenomeReader.h")
+                            "src/FLD.cpp")
                (("<sam.h>") "<samtools/sam.h>"))
              #t))
          (delete 'configure)
@@ -11503,15 +11491,16 @@ applications for tackling some common problems in a user-friendly way.")
 (define-public tadbit
   (package
     (name "tadbit")
-    (version "0.2")
+    (version "0.2.0")
     (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/3DGenomes/TADbit/"
-                                  "archive/v" version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/3DGenomes/TADbit.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "1cnfqrl4685zar4nnw94j94nhvl2h29jm448nadqi1h05z6fdk4f"))))
+                "07g3aj648prmsvxp9caz5yl41k0y0647vxh0f5p3w8376mfiljd0"))))
     (build-system python-build-system)
     (arguments
      `(;; Tests are included and must be run after installation, but
@@ -11566,13 +11555,14 @@ models.  TADbit is complemented by TADkit for visualizing 3D models.")
     (version "302.0.0")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append "https://github.com/ENCODE-DCC/kentUtils/"
-                           "archive/v" version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/ENCODE-DCC/kentUtils.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "134aja3k1cj32kbk1nnw0q9gxjb2krr15q6sga8qldzvc0585rmm"))
+         "0n1wbyjpzii2b9qhyp9r1q76j623cggpg3y8fmw78ld3z4y7ivha"))
        (modules '((guix build utils)
                   (srfi srfi-26)
                   (ice-9 ftw)))
@@ -11623,6 +11613,8 @@ models.  TADbit is complemented by TADkit for visualizing 3D models.")
        #:tests? #f
        #:phases
        (modify-phases %standard-phases
+         (add-after 'unpack 'fix-permissions
+           (lambda _ (make-file-writable "src/inc/localEnvironment.mk") #t))
          (add-after 'unpack 'fix-paths
            (lambda _
              (substitute* "Makefile"
@@ -11918,14 +11910,14 @@ accurate as existing quantification tools.")
     (name "libgff")
     (version "1.0")
     (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/Kingsford-Group/"
-                    "libgff/archive/v" version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/Kingsford-Group/libgff.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "0vc4nxyhlm6g9vvmx5l4lfs5pnvixsv1hiiy4kddf2y3p6jna8ls"))))
+                "0n6vfjnq7a2mianipscbshrvbncss8z4zkgkbjw754p9043nfkps"))))
     (build-system cmake-build-system)
     (arguments `(#:tests? #f))          ; no tests included
     (home-page "https://github.com/Kingsford-Group/libgff")
@@ -11970,14 +11962,14 @@ bytes of memory space, where n is the length of the string.")
     (name "sailfish")
     (version "0.10.1")
     (source (origin
-              (method url-fetch)
-              (uri
-               (string-append "https://github.com/kingsfordgroup/"
-                              "sailfish/archive/v" version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/kingsfordgroup/sailfish.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "1inn60dxiwsz8g9w7kvfhjxj4bwfb0r12dyhpzzhfbig712dkmm0"))
+                "1amcc5hqvsl42hg4x19bi9vy47cl874s0lw1fmi0hwsdk9i8c03v"))
               (modules '((guix build utils)))
               (snippet
                '(begin
@@ -12025,10 +12017,10 @@ bytes of memory space, where n is the length of the string.")
                    (include "external/install/include/rapmap/")
                    (rapmap (assoc-ref inputs "rapmap")))
                (mkdir-p "/tmp/rapmap")
-               (system* "tar" "xf"
-                        (assoc-ref inputs "rapmap")
-                        "-C" "/tmp/rapmap"
-                        "--strip-components=1")
+               (invoke "tar" "xf"
+                       (assoc-ref inputs "rapmap")
+                       "-C" "/tmp/rapmap"
+                       "--strip-components=1")
                (mkdir-p src)
                (mkdir-p include)
                (for-each (lambda (file)
diff --git a/gnu/packages/c.scm b/gnu/packages/c.scm
index 83268e871c..d89b6ea00d 100644
--- a/gnu/packages/c.scm
+++ b/gnu/packages/c.scm
@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2016, 2018 Ludovic Courtès <ludo@gnu.org>
-;;; Copyright © 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz>
 ;;;
@@ -160,8 +160,7 @@ standard.")
      `(#:phases
        (modify-phases %standard-phases
          (replace 'check
-           (lambda _
-             (zero? (system* "make" "-C" "cc/cpp" "test")))))))
+           (lambda _ (invoke "make" "-C" "cc/cpp" "test") #t)))))
     (native-inputs
      `(("bison" ,bison)
        ("flex" ,flex)))
diff --git a/gnu/packages/cups.scm b/gnu/packages/cups.scm
index d7db5dd1fa..4343910d59 100644
--- a/gnu/packages/cups.scm
+++ b/gnu/packages/cups.scm
@@ -391,9 +391,13 @@ device-specific programs to convert and print many types of files.")
                (base32
                 "0g3q5mm2crjyc1z4z6gv4lam6sc5d3diz704djrnpqadk4q3h290"))
               (modules '((guix build utils)))
+              (patches (search-patches "hplip-remove-imageprocessor.patch"))
               (snippet
-               ;; Fix type mismatch.
                '(begin
+                  ;; Delete non-free blobs
+                  (for-each delete-file (find-files "." "\\.so$"))
+                  (delete-file "prnt/hpcups/ImageProcessor.h")
+                  ;; Fix type mismatch.
                   (substitute* "prnt/hpcups/genPCLm.cpp"
                     (("boolean") "bool"))
                   #t))))
diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 5fc3607b76..d4a1d35d95 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -848,14 +848,14 @@ pictures, sounds, or video.")
   (package
     (inherit postgresql)
     (name "postgresql")
-    (version "9.6.9")
+    (version "9.6.11")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://ftp.postgresql.org/pub/source/v"
                                   version "/postgresql-" version ".tar.bz2"))
               (sha256
                (base32
-                "0biy8j69dbvdmrag55pdszpc0702agzqhhcwdx21xp02mzim4ydr"))))))
+                "0c55akrkzqd6p6a8hr0338wk246hl76r9j16p4zn3s51d7f0l99q"))))))
 
 (define-public python-pymysql
   (package
diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index 4821c18f6e..c6008e6a94 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -12463,3 +12463,78 @@ correctly.")
 @item helm-slime-repl-history: Select an input from the SLIME REPL history and insert it.
 @end itemize\n")
       (license license:gpl3+))))
+
+(define-public emacs-clang-format
+  (let ((commit "5556c31528af2661bed3011bd63ffc0ed44e18a0"))
+    (package
+      (name "emacs-clang-format")
+      (version (git-version "0.0.0" "1" commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/emacsorphanage/clang-format")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "0ynvnp3vrcpngmwakb23xv4xn7jbkg43s196q7pg9nkl13x4n2nq"))))
+      (build-system emacs-build-system)
+      (inputs
+       `(("clang" ,clang)))
+      (arguments
+       `(#:phases
+         (modify-phases %standard-phases
+           (add-after 'unpack 'configure
+             (lambda* (#:key inputs #:allow-other-keys)
+               (let ((clang (assoc-ref inputs "clang")))
+                 ;; Repo is read-only.
+                 (chmod "clang-format.el" #o644)
+                 (emacs-substitute-variables "clang-format.el"
+                   ("clang-format-executable"
+                    (string-append clang "/bin/clang-format"))))
+               #t)))))
+      (home-page "https://github.com/emacsorphanage/clang-format")
+      (synopsis "Format code using clang-format")
+      (description "This package allows to filter code through clang-format to
+fix its formatting.  @command{clang-format} is a tool that formats C/C++/Obj-C
+code according to a set of style options, see
+@url{http://clang.llvm.org/docs/ClangFormatStyleOptions.html}.")
+      (license license:gpl3+))))
+
+(define-public emacs-gtk-look
+  (package
+    (name "emacs-gtk-look")
+    (version "29")
+    (source (origin
+              (method url-fetch)
+              (uri "https://download.tuxfamily.org/user42/gtk-look.el")
+              (sha256
+               (base32
+                "14p2nwrd51cr1v06fxbjjn6jdrkf9d6vcxhmscm0kl677s25ypsp"))))
+    (build-system emacs-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'configure
+           (lambda _
+             ;; File is read-only.
+             (chmod "gtk-look.el" #o644)
+             (emacs-substitute-variables "gtk-look.el"
+               ("gtk-lookup-devhelp-indices"
+                '(list (expand-file-name "~/.guix-profile/share/gtk-doc/html/*/*.devhelp*"))))
+             #t)))))
+    (home-page "http://user42.tuxfamily.org/gtk-look/index.html")
+    (synopsis "Find and display HTML documentation for GTK, GNOME and Glib")
+    (description "@command{gtk-look} finds and displays HTML documentation for
+GTK, GNOME and Glib functions and variables in Emacs, similar to what
+info-lookup-symbol does for info files (C-h S).  The documentation is expected
+to be devhelp indexes with HTML files.  The location of the indexes can be
+customized.  In addition to C code development @command{gtk-look} is good for
+
+@itemize
+@item @command{perl-gtk2}, recognising class funcs like
+@command{Gtk2::Label->new} and bare method names like @command{set_text}.
+@item @command{guile-gnome}, recognising methods like @command{set-text} and
+classes like @command{<gtk-window>}.
+@end itemize\n")
+    (license license:gpl3+)))
diff --git a/gnu/packages/gtk.scm b/gnu/packages/gtk.scm
index b553fa19cd..66456ab1e2 100644
--- a/gnu/packages/gtk.scm
+++ b/gnu/packages/gtk.scm
@@ -1632,6 +1632,33 @@ it does not deal with windowing system surfaces, drawing, scene graphs, or
 input.")
     (license license:expat)))
 
+(define-public spread-sheet-widget
+  (package
+    (name "spread-sheet-widget")
+    (version "0.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://alpha.gnu.org/gnu/ssw/"
+                           name "-" version ".tar.gz"))
+       (sha256
+        (base32 "1h93yyh2by6yrmkwqg38nd5knids05k5nqzcihc1hdwgzg3c4b8y"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("glib" ,glib "bin") ; for glib-genmarshal, etc.
+       ("pkg-config" ,pkg-config)))
+    ;; In 'Requires' of spread-sheet-widget.pc.
+    (propagated-inputs
+     `(("glib" ,glib)
+       ("gtk+" ,gtk+)))
+    (home-page "https://www.gnu.org/software/ssw/")
+    (synopsis "Gtk+ widget for dealing with 2-D tabular data")
+    (description
+     "GNU Spread Sheet Widget is a library for Gtk+ which provides a widget for
+viewing and manipulating 2 dimensional tabular data in a manner similar to many
+popular spread sheet programs.")
+    (license license:gpl3+)))
+
 (define-public yad
   (package
     (name "yad")
diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm
index 0c65f0e78d..a77cacffe1 100644
--- a/gnu/packages/guile.scm
+++ b/gnu/packages/guile.scm
@@ -2246,8 +2246,8 @@ tracker's SOAP service, such as @url{https://bugs.gnu.org}.")
 
 ;; There has not been any release yet.
 (define-public guile-newt
-  (let ((commit "596ad760bee1be419d71271732f0f30eaee55143")
-        (revision "0"))
+  (let ((commit "4eaa3cf84b9b426cc0ff7bec48b76cca6ca3ec83")
+        (revision "1"))
     (package
       (name "guile-newt")
       (version (string-append "0-" revision "." (string-take commit 9)))
@@ -2259,7 +2259,7 @@ tracker's SOAP service, such as @url{https://bugs.gnu.org}.")
                 (file-name (string-append name "-" version "-checkout"))
                 (sha256
                  (base32
-                  "18qqbi0bc7vp2vlrhib3p3wwgn7wrlv5728dn0avirhw4fxxivnf"))))
+                  "0ww7jbdsmjlsxm60ym6cb5s5kc4ljz8bn4y2lvcqnap0aihqfk10"))))
       (build-system gnu-build-system)
       (arguments
        '(#:make-flags
diff --git a/gnu/packages/kodi.scm b/gnu/packages/kodi.scm
index 6729f1f322..fe7f93fa53 100644
--- a/gnu/packages/kodi.scm
+++ b/gnu/packages/kodi.scm
@@ -3,6 +3,7 @@
 ;;; Copyright © 2017 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2017 Oleg Pykhalov <go.wigust@gmail.com>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -48,6 +49,7 @@
   #:use-module (gnu packages gl)
   #:use-module (gnu packages glib)
   #:use-module (gnu packages gperf)
+  #:use-module (gnu packages groff)
   #:use-module (gnu packages gnunet)
   #:use-module (gnu packages gnupg)
   #:use-module (gnu packages image)
@@ -62,6 +64,7 @@
   #:use-module (gnu packages python)
   #:use-module (gnu packages samba)
   #:use-module (gnu packages sdl)
+  #:use-module (gnu packages serialization)
   #:use-module (gnu packages ssh)
   #:use-module (gnu packages swig)
   #:use-module (gnu packages textutils)
@@ -75,11 +78,12 @@
   #:use-module (gnu packages assembly))
 
 (define-public crossguid
-  (let ((commit "8f399e8bd4252be9952f3dfa8199924cc8487ca4"))
+  (let ((commit "fef89a4174a7bf8cd99fa9154864ce9e8e3bf989")
+        (revision "2"))
     (package
       (name "crossguid")
-      (version (string-append "0.0-1." (string-take commit 7)))
-      ;; There's no official release.  Just a Git repository.
+      (version (string-append "0.0-" revision "." (string-take commit 7)))
+      ;; This is the commit that Kodi wants.
       (source (origin
                 (method git-fetch)
                 (uri (git-reference
@@ -88,13 +92,12 @@
                 (file-name (string-append name "-" version "-checkout"))
                 (sha256
                  (base32
-                  "1i29y207qqddvaxbn39pk2fbh3gx8zvdprfp35wasj9rw2wjk3s9"))))
+                  "1blrkc7zcqrqcr5msvhyhm98s2jvm9hr0isqs4288q2r4mdnrfq0"))))
       (build-system gnu-build-system)
       (arguments
        '(#:phases
          (modify-phases %standard-phases
            (delete 'configure)          ; no configure script
-           ;; There's no build system here, so we have to do it ourselves.
            (replace 'build
              (lambda _
                (invoke "g++" "-c" "guid.cpp" "-o" "guid.o"
@@ -129,7 +132,7 @@ generator library for C++.")
 ;; of the standard build process. To make things easier, we bootstrap
 ;; and patch shebangs here, so we don't have to worry about it later.
 (define libdvdnav/kodi
-  (let ((commit "6.0.0-Leia-Alpha-1"))
+  (let ((commit "6.0.0-Leia-Alpha-3"))
     (package
       (name "libdvdnav-bootstrapped")
       (version commit)
@@ -141,7 +144,7 @@ generator library for C++.")
                 (file-name (string-append name "-" version "-checkout"))
                 (sha256
                  (base32
-                  "1xiyfgf8v8aknlxlzsvk6pbzkhclz0hbh3s1b0w6ivkng2k310j9"))))
+                  "0qwlf4lgahxqxk1r2pzl866mi03pbp7l1fc0rk522sc0ak2s9jhb"))))
       (build-system gnu-build-system)
       (arguments
        '(#:tests? #f
@@ -164,7 +167,7 @@ generator library for C++.")
       (license license:gpl2+))))
 
 (define libdvdread/kodi
-  (let ((commit "6.0.0-Leia-Alpha-1"))
+  (let ((commit "6.0.0-Leia-Alpha-3"))
     (package
       (name "libdvdread-bootstrapped")
       (version commit)
@@ -176,7 +179,7 @@ generator library for C++.")
                 (file-name (string-append name "-" version "-checkout"))
                 (sha256
                  (base32
-                  "1c3g18n2vwhgcfz3dka1pmw58bnv2ram7xjvizfiykb3sgi9zfwp"))))
+                  "1xxn01mhkdnp10cqdr357wx77vyzfb5glqpqyg8m0skyi75aii59"))))
       (build-system gnu-build-system)
       (arguments
        '(#:tests? #f
@@ -199,7 +202,7 @@ generator library for C++.")
       (license (list license:gpl2+ license:lgpl2.1+)))))
 
 (define libdvdcss/kodi
-  (let ((commit "1.4.1-Leia-Alpha-1"))
+  (let ((commit "1.4.2-Leia-Beta-5"))
     (package
       (name "libdvdcss-bootstrapped")
       (version commit)
@@ -211,7 +214,7 @@ generator library for C++.")
                 (file-name (string-append name "-" version "-checkout"))
                 (sha256
                  (base32
-                  "0adafwsawxssj3nilkql447v0l4a2584rdpmy5rfjmznh91lykgh"))))
+                  "0j41ydzx0imaix069s3z07xqw9q95k7llh06fc27dcn6f7b8ydyl"))))
       (build-system gnu-build-system)
       (arguments
        '(#:tests? #f
@@ -233,28 +236,53 @@ generator library for C++.")
       (description (package-description libdvdcss))
       (license license:gpl2+))))
 
+(define-public fstrcmp
+  (package
+    (name "fstrcmp")
+    (version "0.7.D001")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (string-append "http://fstrcmp.sourceforge.net/fstrcmp-"
+                            version ".tar.gz"))
+        (sha256
+         (base32
+          "0xilghiy3mz78bjmfldi39qyy7jvw5b6wafsx370lw401y2qw0g4"))))
+    (build-system gnu-build-system)
+    (home-page "http://fstrcmp.sourceforge.net/")
+    (arguments
+     '(#:configure-flags '("SH=sh")))
+    (native-inputs
+     `(("ghostscript" ,ghostscript) ; ps2pdf
+       ("groff" ,groff)
+       ("libtool" ,libtool)
+       ("which" ,which)))
+    (synopsis "fuzzy comparison of strings")
+    (description
+     "The fstrcmp project provides a library that is used to make fuzzy
+comparisons of strings and byte arrays, including multi-byte character strings.
+This can be useful in error messages, enabling the suggestion of likely valid
+alternatives. In compilers, this can reduce the cascade of secondary errors.")
+    (license license:gpl3+)))
+
 (define-public kodi
-  ;; We package the git version because the current released
-  ;; version was cut while the cmake transition was in turmoil.
-  (let ((commit "ec16dbca4dcf2923f53f819695a6d47c52e68d74")
-        (revision "8"))
   (package
     (name "kodi")
-    (version (git-version "18.0_alpha" revision commit))
+    (version "18.0b5")
     (source (origin
               (method git-fetch)
               (uri (git-reference
                     (url "https://github.com/xbmc/xbmc.git")
-                    (commit commit)))
+                    (commit (string-append version "-Leia"))))
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1rxg752cl59124cfpfwmyjldn6qpq5jginxddpzvgagfadf10i4d"))
+                "042qzvhys3sajby6ywgmrsymhji37qk0iqgppznrvm53vrizwsam"))
               (snippet
                '(begin
                   (use-modules (guix build utils))
                   (for-each delete-file-recursively
-                            '("project/BuildDependencies/bin/"
+                            '("project/BuildDependencies/"
                               ;; TODO: Purge these jars.
                               ;;"tools/codegenerator/groovy"
                               ;; And these sources:
@@ -370,10 +398,12 @@ generator library for C++.")
        ("eudev" ,eudev)
        ("ffmpeg" ,ffmpeg)
        ("flac" ,flac)
+       ("flatbuffers" ,flatbuffers)
        ("fmt" ,fmt)
        ("fontconfig" ,fontconfig)
        ("freetype" ,freetype)
        ("fribidi" ,fribidi)
+       ("fstrcmp" ,fstrcmp)
        ("giflib" ,giflib)
        ("glew" ,glew)
        ("gnutls" ,gnutls)
@@ -427,7 +457,7 @@ plug-in system.")
                    license:expat                  ;cpluff, dbwrappers
                    license:public-domain          ;cpluff/examples
                    license:bsd-3                  ;misc, gtest
-                   license:bsd-2)))))             ;xbmc/freebsd
+                   license:bsd-2))))              ;xbmc/freebsd
 
 (define-public kodi-cli
   (let ((commit "104dc23b2a993c8e6db8c46f4f8bec24b146549b") ; Add support for
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 2f5798c055..3e1fe7c2c1 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -2763,18 +2763,16 @@ point numbers.")
 (define-public wxmaxima
   (package
     (name "wxmaxima")
-    (version "18.02.0")
+    (version "18.10.1")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "https://github.com/andrejv/" name "/archive"
-                           "/Version-" version ".tar.gz"))
+       (uri (string-append "https://github.com/wxMaxima-developers/" name
+                           "/archive/Version-" version ".tar.gz"))
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "03kr2rgfp4hcf3is8m8d8f9hj660c3xgrc50vrrfpixx4syh6wvj"))
-       (patches
-        (search-patches "wxmaxima-do-not-use-old-gnuplot-parameters.patch"))))
+         "0c2blq65r0am509p3rjqpwqk6vl5r2yg1p9nh2jczf80vhi3ldas"))))
     (build-system cmake-build-system)
     (native-inputs
      `(("gettext" ,gettext-minimal)))
diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index fdbfab796c..89ef58e80c 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -309,29 +309,27 @@ playing your music.")
     (name "cmus")
     (version "2.7.1")
     (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/" name "/" name "/archive/v"
-                    version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/cmus/cmus.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "0raixgjavkm7hxppzsc5zqbfbh2bhjcmbiplhnsxsmyj8flafyc1"))))
+                "0xd96py21bl869qlv1353zw7xsgq6v5s8szr0ldr63zj5fgc2ps5"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f ; cmus does not include tests
        #:phases
        (modify-phases %standard-phases
-         (replace
-          'configure
-          (lambda* (#:key outputs #:allow-other-keys)
-            (let ((out (assoc-ref outputs "out")))
-
-              ;; It's an idiosyncratic configure script that doesn't
-              ;; understand --prefix=..; it wants prefix=.. instead.
-              (zero?
-               (system* "./configure"
-                        (string-append "prefix=" out)))))))))
+         (replace 'configure
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out")))
+               ;; It's an idiosyncratic configure script that doesn't
+               ;; understand --prefix=..; it wants prefix=.. instead.
+               (invoke "./configure"
+                       (string-append "prefix=" out))
+               #t))))))
     ;; TODO: cmus optionally supports the following formats, which haven't yet
     ;; been added to Guix:
     ;;
@@ -1144,14 +1142,14 @@ your own lessons.")
     (name "powertabeditor")
     (version "2.0.0-alpha10")
     (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/powertab/powertabeditor/archive/"
-                    version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/powertab/powertabeditor.git")
+                    (commit version)))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "1fr14ql0yhlqvh6y08yaanszm2nvca5i50rqym396kfvga3ky18x"))
+                "1z4fhdp71ck9synr12rg1p6365xnypd8ih40c5icj4si36khvksk"))
               (modules '((guix build utils)))
               (snippet
                '(begin
@@ -1185,14 +1183,14 @@ add_library( rapidjson INTERFACE IMPORTED )"))
        (modify-phases %standard-phases
          (replace 'check
            (lambda _
-             (zero? (system* "bin/pte_tests"
-                             ;; FIXME: these tests fail
-                             "exclude:Actions/EditStaff"
-                             "exclude:Formats/PowerTabOldImport/MergeMultiBarRests"
-                             "exclude:Score/ViewFilter/FilterRule"
-                             "exclude:Score/ViewFilter/ViewFilter"
-                             "exclude:Formats/PowerTabOldImport/Directions"
-                             ))))
+             (invoke "bin/pte_tests"
+                     ;; FIXME: these tests fail
+                     "exclude:Actions/EditStaff"
+                     "exclude:Formats/PowerTabOldImport/MergeMultiBarRests"
+                     "exclude:Score/ViewFilter/FilterRule"
+                     "exclude:Score/ViewFilter/ViewFilter"
+                     "exclude:Formats/PowerTabOldImport/Directions")
+             #t))
          ;; FIXME: This bug has been fixed upstream, but no release has been
          ;; made yet.  See https://github.com/powertab/powertabeditor/issues/257
          (add-after 'unpack 'fix-boost-bug
@@ -1751,9 +1749,7 @@ export.")
            (lambda _
              (substitute* "tcl/pd-gui.tcl"
                (("exec wish ") (string-append "exec " (which "wish8.6") " ")))
-             #t))
-         (add-after 'unpack 'autoconf
-           (lambda _ (zero? (system* "bash" "./autogen.sh")))))))
+             #t)))))
     (native-inputs
      `(("autoconf" ,autoconf)
        ("automake" ,automake)
@@ -4071,14 +4067,15 @@ ISRCs and the MCN (=UPC/EAN) from disc.")
         (base32
          "0ikb9igyyk28jm34raxfzkw2qyn4nzzwsymdyprp7cmvi6g2ajb7"))))
     (build-system cmake-build-system)
-    (arguments `(#:phases
-                 (modify-phases %standard-phases
-                   (replace 'check
-                     (lambda _
-                       (and
-                        ;; requires network connections
-                        ;; (zero? (system* "tests/mbtest"))
-                        (zero? (system* "tests/ctest"))))))))
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (replace 'check
+           (lambda _
+             ;; requires network connections
+             ;; (invoke "tests/mbtest")
+             (invoke "tests/ctest")
+             #t)))))
     (inputs `(("neon" ,neon)
               ("libxml2" ,libxml2)))
     (native-inputs `(("pkg-config" ,pkg-config)))
diff --git a/gnu/packages/patches/hplip-remove-imageprocessor.patch b/gnu/packages/patches/hplip-remove-imageprocessor.patch
new file mode 100644
index 0000000000..cde3ecba2d
--- /dev/null
+++ b/gnu/packages/patches/hplip-remove-imageprocessor.patch
@@ -0,0 +1,232 @@
+This patch is based heavily on the Debian patch.
+
+https://salsa.debian.org/printing-team/hplip/raw/debian/3.18.10+dfsg0-1/debian/patches/0025-Remove-all-ImageProcessor-functionality-which-is-clo.patch
+
+---
+ Makefile.am                  | 22 +++-------------------
+ Makefile.in                  | 33 +++++----------------------------
+ prnt/hpcups/HPCupsFilter.cpp | 21 ---------------------
+ 3 files changed, 8 insertions(+), 68 deletions(-)
+
+diff --git a/Makefile.am b/Makefile.am
+index ef6480f..ecada5c 100644
+--- a/Makefile.am
++++ b/Makefile.am
+@@ -166,7 +166,7 @@ if !HPLIP_CLASS_DRIVER
+ dist_hplip_SCRIPTS = hpssd.py __init__.py hpdio.py
+ endif #HPLIP_CLASS_DRIVER
+ 
+-dist_noinst_DATA += prnt/drv/hpijs.drv.in.template prnt/drv/hpcups.drv.in.template prnt/hpcups/libImageProcessor-x86_64.so prnt/hpcups/libImageProcessor-x86_32.so
++dist_noinst_DATA += prnt/drv/hpijs.drv.in.template prnt/drv/hpcups.drv.in.template
+ dist_noinst_SCRIPTS += dat2drv.py install.py  hplip-install init-suse-firewall init-iptables-firewall class_rpm_build.sh hplipclassdriver.spec createPPD.sh Makefile_dat2drv hpijs-drv
+ 
+ if !HPLIP_CLASS_DRIVER
+@@ -590,11 +590,10 @@ hpcups_SOURCES = prnt/hpcups/HPCupsFilter.cpp prnt/hpcups/HPCupsFilter.h prnt/hp
+ 	prnt/hpcups/flate_colorspace.h prnt/hpcups/RunLenEncoding.h prnt/hpcups/common_defines.h \
+ 	prnt/hpcups/genPCLm.h \
+ 	common/utils.c common/utils.h prnt/hpcups/Hbpl1_Wrapper.cpp prnt/hpcups/genPCLm.cpp \
+-	prnt/hpcups/genJPEGStrips.cpp prnt/hpcups/RunLenEncoding.cpp \
+-	prnt/hpcups/ImageProcessor.h
++	prnt/hpcups/genJPEGStrips.cpp prnt/hpcups/RunLenEncoding.cpp
+ 
+ hpcups_CXXFLAGS = $(APDK_ENDIAN_FLAG) $(DBUS_CFLAGS)
+-hpcups_LDADD = -L./prnt/hpcups/ -ljpeg -ldl -lImageProcessor -lcups -lcupsimage -lz $(DBUS_LIBS)
++hpcups_LDADD = -L./prnt/hpcups/ -ljpeg -ldl -lcups -lcupsimage -lz $(DBUS_LIBS)
+ #else
+ #hpcupsdir = $(cupsfilterdir)
+ #hpcups_PROGRAMS = hpcups
+@@ -679,21 +678,10 @@ printpluginsdir=$(cupsfilterdir)
+ 
+ 
+ dist_filter_DATA = hpcups hpps dat2drv
+-dist_printplugins_DATA = prnt/plugins/hbpl1-arm32.so prnt/plugins/hbpl1-arm64.so prnt/plugins/hbpl1-x86_32.so prnt/plugins/hbpl1-x86_64.so prnt/plugins/lj-arm32.so prnt/plugins/lj-arm64.so prnt/plugins/lj-x86_32.so prnt/plugins/lj-x86_64.so
+ endif #HPLIP_CLASS_DRIVER
+ 
+ install-data-hook:
+ if HPLIP_BUILD
+-	if [ \( "$(UNAME)" = "x86_64" -a  -d "$(libdir)/" \) ]; then \
+-		cp prnt/hpcups/libImageProcessor-x86_64.so $(libdir)/ ; \
+-		chmod 775 $(libdir)/libImageProcessor-x86_64.so ; \
+-		ln -sf $(libdir)/libImageProcessor-x86_64.so $(libdir)/libImageProcessor.so ; \
+-	fi; \
+-	if [ \( \( "$(UNAME)" = "i686" -o "$(UNAME)" = "i386" \) -a -d "$(libdir)/" \) ]; then \
+-		cp prnt/hpcups/libImageProcessor-x86_32.so $(libdir)/ ; \
+-		chmod 775 $(libdir)/libImageProcessor-x86_32.so ; \
+-		ln -sf $(libdir)/libImageProcessor-x86_32.so $(libdir)/libImageProcessor.so ; \
+-	fi
+ if !HPLIP_CLASS_DRIVER
+ #	   If scanner build, add hpaio entry to sane dll.conf.
+ 	if [ "$(scan_build)" = "yes" ]; then \
+@@ -874,10 +862,6 @@ if HPLIP_CLASS_DRIVER
+ 	rm -rf $(distdir)/setup.py
+ 	rm -rf $(distdir)/systray.py
+ 	rm -rf $(distdir)/timedate.py
+-	rm -rf $(distdir)/prnt/plugins/lj-arm32.so
+-	rm -rf $(distdir)/prnt/plugins/lj-arm64.so
+-	rm -rf $(distdir)/prnt/plugins/lj-x86_32.so
+-	rm -rf $(distdir)/prnt/plugins/lj-x86_64.so
+ 	rm -rf $(distdir)/hpijs-drv
+ 	rm -rf $(distdir)/prnt/hpcups/
+ 	rm -rf $(distdir)/prnt/ps/
+diff --git a/Makefile.in b/Makefile.in
+index 910a268..cd44203 100644
+--- a/Makefile.in
++++ b/Makefile.in
+@@ -103,7 +103,7 @@ DIST_COMMON = $(am__configure_deps) \
+ 
+ # ip library
+ @HPLIP_BUILD_TRUE@am__append_12 = libhpip.la
+-@FULL_BUILD_TRUE@@HPLIP_BUILD_TRUE@am__append_13 = prnt/drv/hpijs.drv.in.template prnt/drv/hpcups.drv.in.template prnt/hpcups/libImageProcessor-x86_64.so prnt/hpcups/libImageProcessor-x86_32.so
++@FULL_BUILD_TRUE@@HPLIP_BUILD_TRUE@am__append_13 = prnt/drv/hpijs.drv.in.template prnt/drv/hpcups.drv.in.template
+ @FULL_BUILD_TRUE@@HPLIP_BUILD_TRUE@am__append_14 = dat2drv.py install.py  hplip-install init-suse-firewall init-iptables-firewall class_rpm_build.sh hplipclassdriver.spec createPPD.sh Makefile_dat2drv hpijs-drv
+ @FULL_BUILD_TRUE@@HPLIP_BUILD_TRUE@@HPLIP_CLASS_DRIVER_FALSE@am__append_15 = scan/sane/hpaio.desc \
+ @FULL_BUILD_TRUE@@HPLIP_BUILD_TRUE@@HPLIP_CLASS_DRIVER_FALSE@	installer/text_install.py \
+@@ -500,8 +500,7 @@ am__hpcups_SOURCES_DIST = prnt/hpcups/HPCupsFilter.cpp \
+ 	prnt/hpcups/RunLenEncoding.h prnt/hpcups/common_defines.h \
+ 	prnt/hpcups/genPCLm.h common/utils.c common/utils.h \
+ 	prnt/hpcups/Hbpl1_Wrapper.cpp prnt/hpcups/genPCLm.cpp \
+-	prnt/hpcups/genJPEGStrips.cpp prnt/hpcups/RunLenEncoding.cpp \
+-	prnt/hpcups/ImageProcessor.h
++	prnt/hpcups/genJPEGStrips.cpp prnt/hpcups/RunLenEncoding.cpp
+ @HPCUPS_INSTALL_TRUE@am_hpcups_OBJECTS =  \
+ @HPCUPS_INSTALL_TRUE@	hpcups-HPCupsFilter.$(OBJEXT) \
+ @HPCUPS_INSTALL_TRUE@	hpcups-dbuscomm.$(OBJEXT) \
+@@ -723,8 +722,7 @@ am__dist_locatedriver_DATA_DIST = locatedriver
+ am__dist_models_DATA_DIST = data/models/models.dat
+ am__dist_noinst_DATA_DIST = prnt/drv/hpijs.drv.in.template \
+ 	prnt/drv/hpcups.drv.in.template \
+-	prnt/hpcups/libImageProcessor-x86_64.so \
+-	prnt/hpcups/libImageProcessor-x86_32.so scan/sane/hpaio.desc \
++	scan/sane/hpaio.desc \
+ 	installer/text_install.py data/localization/hplip_de.ts \
+ 	data/localization/hplip_es.ts data/localization/hplip_fr.ts \
+ 	data/localization/hplip_it.ts data/localization/hplip_pt.ts \
+@@ -1932,11 +1930,6 @@ am__dist_ppd_DATA_DIST = prnt/ps/hp-designjet_z6810ps_42in-ps.ppd.gz \
+ 	ppd/classppd/ps/hp-postscript-inkjet.ppd.gz \
+ 	ppd/classppd/ps/hp-postscript-laserjet-pro.ppd.gz \
+ 	ppd/classppd/ps/hp-postscript-laserjet.ppd.gz
+-am__dist_printplugins_DATA_DIST = prnt/plugins/hbpl1-arm32.so \
+-	prnt/plugins/hbpl1-arm64.so prnt/plugins/hbpl1-x86_32.so \
+-	prnt/plugins/hbpl1-x86_64.so prnt/plugins/lj-arm32.so \
+-	prnt/plugins/lj-arm64.so prnt/plugins/lj-x86_32.so \
+-	prnt/plugins/lj-x86_64.so
+ am__dist_prnt_DATA_DIST = prnt/cups.py prnt/__init__.py prnt/ldl.py \
+ 	prnt/pcl.py prnt/colorcal.py
+ am__dist_rules_DATA_DIST = data/rules/56-hpmud.rules \
+@@ -4665,11 +4658,10 @@ libapdk_la_CFLAGS = $(libapdk_la_CXXFLAGS) -Iprnt/hpijs
+ @HPCUPS_INSTALL_TRUE@	prnt/hpcups/flate_colorspace.h prnt/hpcups/RunLenEncoding.h prnt/hpcups/common_defines.h \
+ @HPCUPS_INSTALL_TRUE@	prnt/hpcups/genPCLm.h \
+ @HPCUPS_INSTALL_TRUE@	common/utils.c common/utils.h prnt/hpcups/Hbpl1_Wrapper.cpp prnt/hpcups/genPCLm.cpp \
+-@HPCUPS_INSTALL_TRUE@	prnt/hpcups/genJPEGStrips.cpp prnt/hpcups/RunLenEncoding.cpp \
+-@HPCUPS_INSTALL_TRUE@	prnt/hpcups/ImageProcessor.h
++@HPCUPS_INSTALL_TRUE@	prnt/hpcups/genJPEGStrips.cpp prnt/hpcups/RunLenEncoding.cpp
+ 
+ @HPCUPS_INSTALL_TRUE@hpcups_CXXFLAGS = $(APDK_ENDIAN_FLAG) $(DBUS_CFLAGS)
+-@HPCUPS_INSTALL_TRUE@hpcups_LDADD = -L./prnt/hpcups/ -ljpeg -ldl -lImageProcessor -lcups -lcupsimage -lz $(DBUS_LIBS)
++@HPCUPS_INSTALL_TRUE@hpcups_LDADD = -L./prnt/hpcups/ -ljpeg -ldl -lcups -lcupsimage -lz $(DBUS_LIBS)
+ #else
+ #hpcupsdir = $(cupsfilterdir)
+ #hpcups_PROGRAMS = hpcups
+@@ -4717,7 +4709,6 @@ ppddir = $(hpppddir)
+ @HPLIP_CLASS_DRIVER_TRUE@filterdir = $(cupsfilterdir)
+ @HPLIP_CLASS_DRIVER_TRUE@printpluginsdir = $(cupsfilterdir)
+ @HPLIP_CLASS_DRIVER_TRUE@dist_filter_DATA = hpcups hpps dat2drv
+-@HPLIP_CLASS_DRIVER_TRUE@dist_printplugins_DATA = prnt/plugins/hbpl1-arm32.so prnt/plugins/hbpl1-arm64.so prnt/plugins/hbpl1-x86_32.so prnt/plugins/hbpl1-x86_64.so prnt/plugins/lj-arm32.so prnt/plugins/lj-arm64.so prnt/plugins/lj-x86_32.so prnt/plugins/lj-x86_64.so
+ all: all-am
+ 
+ .SUFFIXES:
+@@ -9380,16 +9371,6 @@ uninstall-am: uninstall-apparmor_abstractionDATA \
+ 
+ 
+ install-data-hook:
+-@HPLIP_BUILD_TRUE@	if [ \( "$(UNAME)" = "x86_64" -a  -d "$(libdir)/" \) ]; then \
+-@HPLIP_BUILD_TRUE@		cp prnt/hpcups/libImageProcessor-x86_64.so $(libdir)/ ; \
+-@HPLIP_BUILD_TRUE@		chmod 775 $(libdir)/libImageProcessor-x86_64.so ; \
+-@HPLIP_BUILD_TRUE@		ln -sf $(libdir)/libImageProcessor-x86_64.so $(libdir)/libImageProcessor.so ; \
+-@HPLIP_BUILD_TRUE@	fi; \
+-@HPLIP_BUILD_TRUE@	if [ \( \( "$(UNAME)" = "i686" -o "$(UNAME)" = "i386" \) -a -d "$(libdir)/" \) ]; then \
+-@HPLIP_BUILD_TRUE@		cp prnt/hpcups/libImageProcessor-x86_32.so $(libdir)/ ; \
+-@HPLIP_BUILD_TRUE@		chmod 775 $(libdir)/libImageProcessor-x86_32.so ; \
+-@HPLIP_BUILD_TRUE@		ln -sf $(libdir)/libImageProcessor-x86_32.so $(libdir)/libImageProcessor.so ; \
+-@HPLIP_BUILD_TRUE@	fi
+ #	   If scanner build, add hpaio entry to sane dll.conf.
+ @HPLIP_BUILD_TRUE@@HPLIP_CLASS_DRIVER_FALSE@	if [ "$(scan_build)" = "yes" ]; then \
+ @HPLIP_BUILD_TRUE@@HPLIP_CLASS_DRIVER_FALSE@	   $(mkinstalldirs) $(DESTDIR)/etc/sane.d; \
+@@ -9556,10 +9537,6 @@ dist-hook:
+ @HPLIP_CLASS_DRIVER_TRUE@	rm -rf $(distdir)/setup.py
+ @HPLIP_CLASS_DRIVER_TRUE@	rm -rf $(distdir)/systray.py
+ @HPLIP_CLASS_DRIVER_TRUE@	rm -rf $(distdir)/timedate.py
+-@HPLIP_CLASS_DRIVER_TRUE@	rm -rf $(distdir)/prnt/plugins/lj-arm32.so
+-@HPLIP_CLASS_DRIVER_TRUE@	rm -rf $(distdir)/prnt/plugins/lj-arm64.so
+-@HPLIP_CLASS_DRIVER_TRUE@	rm -rf $(distdir)/prnt/plugins/lj-x86_32.so
+-@HPLIP_CLASS_DRIVER_TRUE@	rm -rf $(distdir)/prnt/plugins/lj-x86_64.so
+ @HPLIP_CLASS_DRIVER_TRUE@	rm -rf $(distdir)/hpijs-drv
+ @HPLIP_CLASS_DRIVER_TRUE@	rm -rf $(distdir)/prnt/hpcups/
+ @HPLIP_CLASS_DRIVER_TRUE@	rm -rf $(distdir)/prnt/ps/
+diff --git a/prnt/hpcups/HPCupsFilter.cpp b/prnt/hpcups/HPCupsFilter.cpp
+index 5b282d8..0bacfaf 100644
+--- a/prnt/hpcups/HPCupsFilter.cpp
++++ b/prnt/hpcups/HPCupsFilter.cpp
+@@ -31,7 +31,6 @@
+ \*****************************************************************************/
+ 
+ #include "HPCupsFilter.h"
+-#include "ImageProcessor.h"
+ 
+ #include <signal.h>
+ #include <sys/wait.h>
+@@ -637,16 +636,10 @@ int HPCupsFilter::processRasterData(cups_raster_t *cups_raster)
+ 
+ 
+     sprintf(hpPreProcessedRasterFile, "%s/hp_%s_cups_SwapedPagesXXXXXX",CUPS_TMP_DIR, m_JA.user_name);
+-    image_processor_t* imageProcessor = imageProcessorCreate();
+ 
+     while (cupsRasterReadHeader2(cups_raster, &cups_header))
+     {
+ 
+-        IMAGE_PROCESSOR_ERROR result = imageProcessorStartPage(imageProcessor, &cups_header);
+-        if (result != IPE_SUCCESS){
+-            dbglog("DEBUG: imageProcessorStartPage failed result = %d\n", result);
+-        }
+-
+         current_page_number++;
+ 
+         if (current_page_number == 1) {
+@@ -745,12 +738,6 @@ int HPCupsFilter::processRasterData(cups_raster_t *cups_raster)
+             color_raster = rgbRaster;
+             black_raster = kRaster;
+ 
+-            result = imageProcessorProcessLine(imageProcessor, m_pPrinterBuffer, cups_header.cupsBytesPerLine);
+-            if (result != IPE_SUCCESS){
+-                dbglog("DEBUG: imageProcessorProcessLine failed result = %d\n", result);
+-            }
+-
+-
+             if ((y == 0) && !is_ljmono) {
+                 //For ljmono, make sure that first line is not a blankRaster line.Otherwise printer
+                 //may not skip blank lines before actual data
+@@ -780,12 +767,6 @@ int HPCupsFilter::processRasterData(cups_raster_t *cups_raster)
+             }
+         }  // for() loop end
+ 
+-        result = imageProcessorEndPage(imageProcessor);
+-        if (result != IPE_SUCCESS){
+-                dbglog("DEBUG: imageProcessorEndPage failed result = %d\n", result);
+-        }
+-
+-
+         m_Job.NewPage();
+         if (err != NO_ERROR) {
+             break;
+@@ -800,8 +781,6 @@ int HPCupsFilter::processRasterData(cups_raster_t *cups_raster)
+         rgbRaster = NULL;
+     }
+ 
+-    imageProcessorDestroy(imageProcessor);
+-
+     unlink(hpPreProcessedRasterFile);
+     return ret_status;
+ }
+-- 
+2.19.1
+
diff --git a/gnu/packages/patches/vsearch-unbundle-cityhash.patch b/gnu/packages/patches/vsearch-unbundle-cityhash.patch
index b1ecb1f063..2a2ab13a73 100644
--- a/gnu/packages/patches/vsearch-unbundle-cityhash.patch
+++ b/gnu/packages/patches/vsearch-unbundle-cityhash.patch
@@ -6,7 +6,7 @@ index e56a8a2..4adcc48 100644
  if TARGET_PPC
  AM_CXXFLAGS=-Wall -Wsign-compare -O3 -g -mcpu=power8
  else
--AM_CXXFLAGS=-Wall -Wsign-compare -O3 -g
+-AM_CXXFLAGS=-Wall -Wsign-compare -O3 -g -march=x86-64 -mtune=generic
 +AM_CXXFLAGS=-Wall -Wsign-compare -O3 -g -lcityhash
  endif
  
@@ -39,7 +39,7 @@ index e56a8a2..4adcc48 100644
 -
  if TARGET_WIN
  
--libcityhash_a_CXXFLAGS = -Wall -Wno-sign-compare -O3 -g -D_MSC_VER
+-libcityhash_a_CXXFLAGS = $(AM_CXXFLAGS) -Wno-sign-compare -D_MSC_VER
 -__top_builddir__bin_vsearch_LDFLAGS = -static
 -__top_builddir__bin_vsearch_LDADD = libregex.a libcityhash.a libcpu_ssse3.a libcpu_sse2.a
 +__top_builddir__bin_vsearch_LDFLAGS = -static -lcityhash
@@ -47,7 +47,7 @@ index e56a8a2..4adcc48 100644
  
  else
  
--libcityhash_a_CXXFLAGS = -Wall -Wno-sign-compare -O3 -g
+-libcityhash_a_CXXFLAGS = $(AM_CXXFLAGS) -Wno-sign-compare
 -
  if TARGET_PPC
 -__top_builddir__bin_vsearch_LDADD = libcityhash.a libcpu.a
diff --git a/gnu/packages/patches/wxmaxima-do-not-use-old-gnuplot-parameters.patch b/gnu/packages/patches/wxmaxima-do-not-use-old-gnuplot-parameters.patch
deleted file mode 100644
index 345101bd3a..0000000000
--- a/gnu/packages/patches/wxmaxima-do-not-use-old-gnuplot-parameters.patch
+++ /dev/null
@@ -1,26 +0,0 @@
-This fixes the wxplot2d plotting issue found at
-https://github.com/andrejv/wxmaxima/issues/973.
-
-From 5a0693c97ceaa4935b908f1e478126896952f399 Mon Sep 17 00:00:00 2001
-From: =?UTF-8?q?Gunter=20K=C3=B6nigsmann?= <gunter@peterpall.de>
-Date: Mon, 19 Feb 2018 05:37:35 +0100
-Subject: [PATCH] Seems I accidentally made wxMaxima to default to parameters
- for old gnuplots. Resolves #973
-
----
- data/wxmathml.lisp.in | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/data/wxmathml.lisp.in b/data/wxmathml.lisp.in
-index a32e3fc3..4e19acaf 100644
---- a/data/wxmathml.lisp.in
-+++ b/data/wxmathml.lisp.in
-@@ -43,7 +43,7 @@
- (defvar $wxsubscripts t
-   "Recognize TeX-style subscripts")
- (defvar $wxplot_pngcairo nil "Use gnuplot's pngcairo terminal for new plots?")
--(defmvar $wxplot_old_gnuplot t)
-+(defmvar $wxplot_old_gnuplot nil)
- 
- (defun $wxstatusbar (status)
-   (format t "<statusbar>~a</statusbar>~%" status))
diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 7704a19767..d90805071b 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -10530,6 +10530,31 @@ useful as a validator for JSON data.")
 (define-public python2-validictory
   (package-with-python2 python-validictory))
 
+(define-public python-pyelftools
+  (package
+    (name "python-pyelftools")
+    (version "0.25")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "pyelftools" version))
+       (sha256
+        (base32
+         "090vdksbz341f7ljvr0zswblw4lspa8qaiikzyjkf318arpxmil9"))))
+    (build-system python-build-system)
+    ;; Test suite requires python-setuptools
+    (native-inputs
+     `(("python-setuptools" ,python-setuptools)))
+    (home-page
+     "https://github.com/eliben/pyelftools")
+    (synopsis
+     "Analyze binary and library file information")
+    (description "This Python library provides interfaces for parsing and
+analyzing two binary and library file formats; the Executable and Linking
+Format (ELF), and debugging information in the Debugging With Attributed
+Record Format (DWARF).")
+    (license license:public-domain)))
+
 (define-public python-pyev
   (package
     (name "python-pyev")
@@ -14532,14 +14557,14 @@ run on top of the dynamic task schedulers. ")
 (define-public python-ilinkedlist
   (package
     (name "python-ilinkedlist")
-    (version "0.2.0")
+    (version "0.3.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "ilinkedlist" version))
        (sha256
         (base32
-         "0klb846q5vs62d8f89my7wan1sji4yjj6pjhjch9dha3p8vlncd2"))))
+         "04wpv7km8jggrngc4bjg3nm615czd3bjdvpsy2icg6c1c8162zyg"))))
     (build-system python-build-system)
     (native-inputs `(("python-pytest" ,python-pytest)))
     (inputs `(("python" ,python)))
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index bb942b4fea..9bfa4c5683 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -39,6 +39,7 @@
   #:use-module (guix build-system trivial)
   #:use-module (gnu packages)
   #:use-module (gnu packages algebra)
+  #:use-module (gnu packages autotools)
   #:use-module (gnu packages bash)
   #:use-module (gnu packages check)
   #:use-module (gnu packages compression)
@@ -75,7 +76,7 @@
 (define-public pspp
   (package
     (name "pspp")
-    (version "1.0.1")
+    (version "1.2.0")
     (source
      (origin
       (method url-fetch)
@@ -83,7 +84,7 @@
                           version ".tar.gz"))
       (sha256
        (base32
-        "1r8smr5057993h90nx0mdnff8nxw9x546zzh6qpy4h3xblp1la5s"))))
+        "07pp27zycrb5x927jwaj9r3q7hy915jh51xs85zxby6gfiwl63m5"))))
     (build-system gnu-build-system)
     (inputs
      `(("cairo" ,cairo)
@@ -94,11 +95,15 @@
        ("readline" ,readline)
        ("gtk" ,gtk+)
        ("gtksourceview" ,gtksourceview)
+       ("spread-sheet-widget" ,spread-sheet-widget)
        ("zlib" ,zlib)))
     (native-inputs
-     `(("glib" ,glib "bin")             ;for glib-genmarshal
+     `(("autoconf" ,autoconf)           ;for tests
+       ("glib" ,glib "bin")             ;for glib-genmarshal
        ("perl" ,perl)
-       ("pkg-config" ,pkg-config)))
+       ("pkg-config" ,pkg-config)
+       ("python" ,python-2)             ;for tests
+       ("texinfo" ,texinfo)))
     (home-page "https://www.gnu.org/software/pspp/")
     (synopsis "Statistical analysis")
     (description
@@ -116,7 +121,7 @@ be output in text, PostScript, PDF or HTML.")
 (define r-with-tests
   (package
     (name "r-with-tests")
-    (version "3.5.0")
+    (version "3.5.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://cran/src/base/R-"
@@ -124,7 +129,7 @@ be output in text, PostScript, PDF or HTML.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "0w38865laqg28cdhikxdxhx4rfp0kgcn72gakwypsy91br9ja5zx"))))
+                "1vap2k8kj5icy9naw61f9zyphf4rs0c9rxvil0zxkwx0xvsvyqq4"))))
     (build-system gnu-build-system)
     (arguments
      `(#:disallowed-references (,tzdata-for-tests)
diff --git a/gnu/packages/xml.scm b/gnu/packages/xml.scm
index e19d03588f..7f7ff6fc38 100644
--- a/gnu/packages/xml.scm
+++ b/gnu/packages/xml.scm
@@ -19,6 +19,7 @@
 ;;; Copyright © 2017 Alex Vong <alexvong1995@gmail.com>
 ;;; Copyright © 2017 Petter <petter@mykolab.ch>
 ;;; Copyright © 2017 Stefan Reichör <stefan@xsteve.at>
+;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -39,6 +40,7 @@
   #:use-module (gnu packages)
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages compression)
+  #:use-module (gnu packages curl)
   #:use-module (gnu packages gnupg)
   #:use-module (gnu packages java)
   #:use-module (gnu packages gnuzilla)
@@ -2111,3 +2113,39 @@ derivations of regular expressions.")
      "The Haskell XML Toolbox bases on the ideas of HaXml and HXML, but
 introduces a more general approach for processing XML with Haskell.")
     (license license:expat)))
+
+(define-public xmlrpc-c
+  (package
+    (name "xmlrpc-c")
+    (version "1.43.08")
+    (source (origin
+             (method url-fetch)
+             (uri (string-append "mirror://sourceforge/xmlrpc-c/Xmlrpc-c%20Super%20Stable/"
+                                 version "/xmlrpc-c-" version ".tgz"))
+             (sha256
+              (base32
+               "18zwbj6i2hpcn5riiyp8i6rml0sfv60dd7phw1x8g4r4lj2bbxf9"))))
+    (build-system gnu-build-system)
+    (inputs
+     `(("curl" ,curl)))
+    (native-inputs
+     `(;; For tools, if ever needed.
+       ("perl" ,perl)))
+    (arguments
+     `(#:make-flags ; Add $libdir to the RUNPATH of all the executables.
+       (list (string-append "LDFLAGS_PERSONAL=-Wl,-rpath=" %output "/lib"))
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'fix-/bin/sh-in-tests
+           (lambda _
+             (substitute* "GNUmakefile"
+               (("#! /bin/sh") (which "sh")))
+             #t)))))
+    (home-page "http://xmlrpc-c.sourceforge.net/")
+    (synopsis "Lightweight RPC library based on XML and HTTP")
+    (description
+     "XML-RPC is a quick-and-easy way to make procedure calls over the Internet.
+It converts the procedure call into an XML document, sends it to a remote
+server using HTTP, and gets back the response as XML.  This library provides a
+modular implementation of XML-RPC for C and C++.")
+    (license (list license:psfl license:expat))))
diff --git a/gnu/services/desktop.scm b/gnu/services/desktop.scm
index e038f97683..47d1096c6d 100644
--- a/gnu/services/desktop.scm
+++ b/gnu/services/desktop.scm
@@ -672,7 +672,7 @@ include the @command{udisksctl} command, part of UDisks, and GNOME Disks."
    ("KillUserProcesses" (yesno elogind-kill-user-processes?))
    ("KillOnlyUsers" (user-name-list elogind-kill-only-users))
    ("KillExcludeUsers" (user-name-list elogind-kill-exclude-users))
-   ("InhibitDelayMaxSecs" (non-negative-integer elogind-inhibit-delay-max-seconds))
+   ("InhibitDelayMaxSec" (non-negative-integer elogind-inhibit-delay-max-seconds))
    ("HandlePowerKey" (handle-action elogind-handle-power-key))
    ("HandleSuspendKey" (handle-action elogind-handle-suspend-key))
    ("HandleHibernateKey" (handle-action elogind-handle-hibernate-key))
@@ -682,16 +682,16 @@ include the @command{udisksctl} command, part of UDisks, and GNOME Disks."
    ("SuspendKeyIgnoreInhibited" (yesno elogind-suspend-key-ignore-inhibited?))
    ("HibernateKeyIgnoreInhibited" (yesno elogind-hibernate-key-ignore-inhibited?))
    ("LidSwitchIgnoreInhibited" (yesno elogind-lid-switch-ignore-inhibited?))
-   ("HoldoffTimeoutSecs" (non-negative-integer elogind-holdoff-timeout-seconds))
+   ("HoldoffTimeoutSec" (non-negative-integer elogind-holdoff-timeout-seconds))
    ("IdleAction" (handle-action elogind-idle-action))
-   ("IdleActionSeconds" (non-negative-integer elogind-idle-action-seconds))
+   ("IdleActionSec" (non-negative-integer elogind-idle-action-seconds))
    ("RuntimeDirectorySize"
     (identity
      (lambda (config)
        (match (elogind-runtime-directory-size-percent config)
          (#f (non-negative-integer (elogind-runtime-directory-size config)))
          (percent (string-append (non-negative-integer percent) "%"))))))
-   ("RemoveIpc" (yesno elogind-remove-ipc?))
+   ("RemoveIPC" (yesno elogind-remove-ipc?))
    "[Sleep]"
    ("SuspendState" (sleep-list elogind-suspend-state))
    ("SuspendMode" (sleep-list elogind-suspend-mode))