Merge branch 'master' into core-updates

diff --combined gnu/packages/bioinformatics.scm
index a482881,122d6a7..57e2f00
--- 1/gnu/packages/bioinformatics.scm
--- 2/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@@ -295,10 -295,9 +295,10 @@@ BAM files."
                 (base32
                  "1vgw2mwngq20c530zim52zvgmw1lci8rzl33pvh44xqk3xlzvjsa"))
                (modules '((guix build utils)))
 -              (snippet
 -               ;; Delete bundled htslib.
 -               '(delete-file-recursively "htslib-1.8"))))
 +              (snippet '(begin
 +                          ;; Delete bundled htslib.
 +                          (delete-file-recursively "htslib-1.8")
 +                          #t))))
      (build-system gnu-build-system)
      (arguments
       `(#:test-target "test"
@@@ -1195,12 -1194,10 +1195,12 @@@ errors at the end of reads."
                  "0hwa5r9qbglppb7sz5z79rlmmddr3n51n468jb3wh8rwjgn3yr90"))
                (modules '((guix build utils)))
                (snippet
 -               '(substitute* "Makefile"
 -                  ;; replace BUILD_HOST and BUILD_TIME for deterministic build
 -                  (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"")
 -                  (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\"")))))
 +               '(begin
 +                  (substitute* "Makefile"
 +                    ;; replace BUILD_HOST and BUILD_TIME for deterministic build
 +                    (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"")
 +                    (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\""))
 +                  #t))))
      (build-system gnu-build-system)
      (inputs
       `(("perl" ,perl)
@@@ -1394,12 -1391,10 +1394,12 @@@ well as many of the command line option
                  "15z2w3bvnc0n4qmb9bd6d8ylc2h2nj883x2w9iixf4x3vki9b22i"))
                (modules '((guix build utils)))
                (snippet
 -               '(substitute* "setup.py"
 -                  ;; remove dependency on outdated "distribute" module
 -                  (("^from distribute_setup import use_setuptools") "")
 -                  (("^use_setuptools\\(\\)") "")))))
 +               '(begin
 +                  (substitute* "setup.py"
 +                    ;; remove dependency on outdated "distribute" module
 +                    (("^from distribute_setup import use_setuptools") "")
 +                    (("^use_setuptools\\(\\)") ""))
 +                  #t))))
      (build-system python-build-system)
      (arguments
       `(#:tests? #f ;tests fail because test data are not included
@@@ -1431,11 -1426,9 +1431,11 @@@ multiple sequence alignments."
                 (base32
                  "0dzap2axin9cbbl0d825w294bpn00zagfm1sigamm4v2pm5bj9lp"))
                (modules '((guix build utils)))
 -              (snippet
 -               ;; Drop bundled htslib. TODO: Also remove samtools and bcftools.
 -               '(delete-file-recursively "htslib"))))
 +              (snippet '(begin
 +                          ;; Drop bundled htslib. TODO: Also remove samtools
 +                          ;; and bcftools.
 +                          (delete-file-recursively "htslib")
 +                          #t))))
      (build-system python-build-system)
      (arguments
       `(#:modules ((ice-9 ftw)
@@@ -1807,10 -1800,9 +1807,10 @@@ time."
                ;; for download from Sourceforge, but it has not been merged.
                (patches (search-patches "crossmap-allow-system-pysam.patch"))
                (modules '((guix build utils)))
 -              ;; remove bundled copy of pysam
 -              (snippet
 -               '(delete-file-recursively "lib/pysam"))))
 +              (snippet '(begin
 +                          ;; remove bundled copy of pysam
 +                          (delete-file-recursively "lib/pysam")
 +                          #t))))
      (build-system python-build-system)
      (arguments
       `(#:python ,python-2
@@@ -1919,8 -1911,7 +1919,8 @@@ files."
                (snippet
                 '(begin
                    ;; Delete bundled libBigWig sources
 -                  (delete-file-recursively "libBigWig")))))
 +                  (delete-file-recursively "libBigWig")
 +                  #t))))
      (build-system python-build-system)
      (arguments
       `(#:phases
@@@ -3879,11 -3870,9 +3879,11 @@@ sequences)."
                  "00fx14vpmgsijwxd1xql3if934l82v8ckqgjjyyhnr36qb9qrskv"))
                (modules '((guix build utils)))
                (snippet
 -               ;; Delete bundled kseq.
 -               ;; TODO: Also delete bundled murmurhash and open bloom filter.
 -               '(delete-file "src/mash/kseq.h"))))
 +               '(begin
 +                  ;; Delete bundled kseq.
 +                  ;; TODO: Also delete bundled murmurhash and open bloom filter.
 +                  (delete-file "src/mash/kseq.h")
 +                  #t))))
      (build-system gnu-build-system)
      (arguments
       `(#:tests? #f ; No tests.
@@@ -4063,19 -4052,18 +4063,19 @@@ assembled metagenomic sequence."
                 (base32
                  "1z3x0vd8ma7pdrnywj7i3kgwl89sdkwrrn62zl7r5calqaq2hyip"))
                (modules '((guix build utils)))
 -              (snippet
 -               '(substitute* "setup.py"
 -                  ;; Use setuptools, or else the executables are not
 -                  ;; installed.
 -                  (("distutils.core") "setuptools")
 -                  ;; use "gcc" instead of "cc" for compilation
 -                  (("^defines")
 -                   "cc.set_executables(
 +              (snippet '(begin
 +                          (substitute* "setup.py"
 +                            ;; Use setuptools, or else the executables are not
 +                            ;; installed.
 +                            (("distutils.core") "setuptools")
 +                            ;; use "gcc" instead of "cc" for compilation
 +                            (("^defines")
 +                             "cc.set_executables(
  compiler='gcc',
  compiler_so='gcc',
  linker_exe='gcc',
 -linker_so='gcc -shared'); defines")))))
 +linker_so='gcc -shared'); defines"))
 +                          #t))))
      (build-system python-build-system)
      (arguments
       `(#:python ,python-2 ; only Python 2 is supported
@@@ -4876,8 -4864,7 +4876,8 @@@ BAM and Wiggle files in both transcript
               (("^from distribute_setup import use_setuptools") "")
               (("^use_setuptools\\(\\)") "")
               ;; do not use bundled copy of pysam
 -             (("^have_pysam = False") "have_pysam = True"))))))
 +             (("^have_pysam = False") "have_pysam = True"))
 +           #t))))
      (build-system python-build-system)
      (arguments `(#:python ,python-2))
      (inputs
@@@ -4928,9 -4915,9 +4928,9 @@@ distribution, coverage uniformity, stra
                         "Data2DB"
                         "PCL2Bin")))
             (modify-phases %standard-phases
 -             (add-before 'configure 'bootstrap
 +             (replace 'bootstrap
                 (lambda _
 -                 (zero? (system* "bash" "gen_auto"))))
 +                 (invoke "bash" "gen_auto")))
               (add-after 'build 'build-additional-tools
                 (lambda* (#:key make-flags #:allow-other-keys)
                   (every (lambda (dir)
@@@ -5433,10 -5420,9 +5433,10 @@@ structures, classes for genomic regions
                (sha256
                 (base32 "08r684l50pnxjpvmhzjgqq56yv9rfw90k8vx0nsrnrzk8mf9hsdq"))
                (modules '((guix build utils)))
 -              (snippet
 -               ;; Remove bundled samtools.
 -               '(delete-file-recursively "samtools"))))
 +              (snippet '(begin
 +                          ;; Remove bundled samtools.
 +                          (delete-file-recursively "samtools")
 +                          #t))))
      (build-system gnu-build-system)
      (arguments
       `(#:tests? #f ;no "check" target
@@@ -5641,11 -5627,10 +5641,11 @@@ writing files into the .sra format."
                 (out  (assoc-ref %outputs "out"))
                 (doc  (assoc-ref %outputs "doc")))
             (setenv "PATH" (string-append tar "/bin:" bzip "/bin"))
 -           (system* "tar" "xvf" (assoc-ref %build-inputs "source"))
 +           (invoke "tar" "xvf" (assoc-ref %build-inputs "source"))
             (chdir (string-append "seqan-library-" ,version))
             (copy-recursively "include" (string-append out "/include"))
 -           (copy-recursively "share"  (string-append doc "/share"))))))
 +           (copy-recursively "share"  (string-append doc "/share"))
 +           #t))))
      (native-inputs
       `(("source" ,source)
         ("tar" ,tar)
@@@ -7675,13 -7660,13 +7675,13 @@@ alignments."
  (define-public r-rtracklayer
    (package
      (name "r-rtracklayer")
-     (version "1.40.2")
+     (version "1.40.3")
      (source (origin
                (method url-fetch)
                (uri (bioconductor-uri "rtracklayer" version))
                (sha256
                 (base32
-                 "0l90jn4df3akxl0n1i9wvnbjqrzjc0d15r8vqr7b15q2117mrn5r"))))
+                 "0kvsjdaypn1jnxbnsxpycildwdyxwnjkigfq8qm8mlyfc4ahdgy3"))))
      (build-system r-build-system)
      (arguments
       `(#:phases
@@@ -8492,14 -8477,14 +8492,14 @@@ of other R packages who wish to make us
  (define-public r-bamsignals
    (package
      (name "r-bamsignals")
-     (version "1.12.0")
+     (version "1.12.1")
      (source
       (origin
         (method url-fetch)
         (uri (bioconductor-uri "bamsignals" version))
         (sha256
          (base32
-          "09l4v414ijkjpkvcv2580v13v18ky196f0lv27ldblpa8bddvmns"))))
+          "141q3p4lzwiqk1mfxi8q1q84axjl0gyiqg59xd3sp4viny4jqmgv"))))
      (build-system r-build-system)
      (propagated-inputs
       `(("r-biocgenerics" ,r-biocgenerics)
@@@ -9234,13 -9219,13 +9234,13 @@@ number detection tools."
  (define-public r-methylkit
    (package
      (name "r-methylkit")
-     (version "1.6.0")
+     (version "1.6.1")
      (source (origin
                (method url-fetch)
                (uri (bioconductor-uri "methylKit" version))
                (sha256
                 (base32
-                 "01qmndm5z21p78w7xfp8ynan6jpfg54rnkpj8b86rc081qh0sgjj"))))
+                 "1hr2czi5ybdf7hdmqsv39d17f3mvmw94wa38bc14zzm9mgy9gfy7"))))
      (properties `((upstream-name . "methylKit")))
      (build-system r-build-system)
      (propagated-inputs
@@@ -11049,6 -11034,11 +11049,6 @@@ droplet sequencing.  It has been partic
           (sha256
            (base32
             "0g38g8s3npr0gjm9fahlbhiskyfws9l5i0x1ml3rakzj7az5l9c9"))))
 -      (arguments
 -       `(#:phases
 -         (modify-phases  %standard-phases
 -           (add-after 'unpack 'bootstrap
 -             (lambda _ (invoke "autoreconf" "-vif"))))))
        (native-inputs
         `(("autoconf" ,autoconf)
           ("automake" ,automake)
@@@ -11962,8 -11952,7 +11962,8 @@@ bytes of memory space, where n is the l
                      (snippet
                       '(begin (delete-file-recursively "include/spdlog")
                               (for-each delete-file '("include/xxhash.h"
 -                                                     "src/xxhash.c"))))))
 +                                                     "src/xxhash.c"))
 +                             #t))))
         ("libdivsufsort" ,libdivsufsort)
         ("libgff" ,libgff)
         ("tbb" ,tbb)
@@@ -12688,8 -12677,7 +12688,8 @@@ contain
         (snippet
          '(begin
             (for-each delete-file (find-files "jar/lib" "\\.jar$"))
 -           (delete-file-recursively "3rdParty")))))
 +           (delete-file-recursively "3rdParty")
 +           #t))))
      (build-system ant-build-system)
      (arguments
       `(#:tests? #f                      ; test data are not included

diff --combined gnu/packages/statistics.scm
index 3996eb9,f39cbb5..3eba723
--- 1/gnu/packages/statistics.scm
--- 2/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@@ -638,7 -638,7 +638,7 @@@ curves, Cox models, and parametric acce
      (name "r")
      (source #f)
      (build-system trivial-build-system)
 -    (arguments '(#:builder (mkdir %output)))
 +    (arguments '(#:builder (begin (mkdir %output) #t)))
      (propagated-inputs
       `(("r-minimal" ,r-minimal)
         ("r-boot" ,r-boot)
@@@ -5344,14 -5344,14 +5344,14 @@@ diagnostic tools (@code{ctlcurves} and 
  (define-public r-ranger
    (package
      (name "r-ranger")
-     (version "0.10.0")
+     (version "0.10.1")
      (source
       (origin
         (method url-fetch)
         (uri (cran-uri "ranger" version))
         (sha256
          (base32
-          "1yl833cm2jpfy9j7zchkq4mm5x1av70w89zrhpwdn8nq2npxxzf0"))))
+          "12z67xkgdmr5cflpd6cln0mn5xxajanqbfwlckv6cfma0gvf2z1j"))))
      (build-system r-build-system)
      (propagated-inputs
       `(("r-rcpp" ,r-rcpp)