322/323: gnu: r-rhtslib: Propagate zlib.

[guix-commits]

rekado pushed a commit to branch wip-r
in repository guix.

commit abad6a9ad4474ae37e10dcbd5e4517561e98dd99
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Mon Dec 7 16:44:23 2020 +0100

    gnu: r-rhtslib: Propagate zlib.
    
    * gnu/packages/bioinformatics.scm (r-rhtslib)[inputs]: Move zlib from 
here...
    [propagated-inputs]: ...to here.
    (r-variantannotation, r-rsamtools, r-bamsignals, r-rhdf5,
    r-methylkit)[inputs]: Remove zlib.
    * gnu/packages/bioconductor.scm (r-diffbind, r-quasr, r-cytolib, r-ncdfflow,
    r-flowworkspace, r-seqbias)[inputs]: Remove zlib.
---
 gnu/packages/bioconductor.scm   | 12 ------------
 gnu/packages/bioinformatics.scm | 13 +------------
 2 files changed, 1 insertion(+), 24 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 5f524f3..5a3d638 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1726,8 +1726,6 @@ signal in the input, that lead to spurious peaks during 
peak calling.")
          "0irhqsi6rrkrkc7dhwmfpqfd0mnigs17027czcx8vgbrbra4lcvd"))))
     (properties `((upstream-name . "DiffBind")))
     (build-system r-build-system)
-    (inputs
-     `(("zlib" ,zlib)))
     (propagated-inputs
      `(("r-amap" ,r-amap)
        ("r-apeglm" ,r-apeglm)
@@ -5664,8 +5662,6 @@ index.")
          "032m01q34nnmvbhcb2g3pz2fqmgcw5464m74m1m0h7x9bl04a5k8"))))
     (properties `((upstream-name . "QuasR")))
     (build-system r-build-system)
-    (inputs
-     `(("zlib" ,zlib)))
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
        ("r-biobase" ,r-biobase)
@@ -6049,8 +6045,6 @@ cluster count and membership by stability evidence in 
unsupervised analysis.")
                (("\\(RHDF5_LIBS\\)" match)
                 (string-append match "/libhdf5.a")))
              #t)))))
-    (inputs
-     `(("zlib" ,zlib)))
     (native-inputs
      `(("r-knitr" ,r-knitr)
        ("pkg-config" ,pkg-config)))
@@ -6150,8 +6144,6 @@ change point detection.")
                (("\\(RHDF5_LIBS\\)" match)
                 (string-append match "/libhdf5.a")))
              #t)))))
-    (inputs
-     `(("zlib" ,zlib)))
     (propagated-inputs
      `(("r-bh" ,r-bh)
        ("r-biobase" ,r-biobase)
@@ -6332,8 +6324,6 @@ for other R packages to compile and link against.")
                (("\\{h5lib\\}" match)
                 (string-append match "/libhdf5.a")))
              #t)))))
-    (inputs
-     `(("zlib" ,zlib)))
     (propagated-inputs
      `(("r-aws-s3" ,r-aws-s3)
        ("r-aws-signature" ,r-aws-signature)
@@ -6997,8 +6987,6 @@ with multiple R processes supported by the package 
@code{parallel}.")
      `(("r-biostrings" ,r-biostrings)
        ("r-genomicranges" ,r-genomicranges)
        ("r-rhtslib" ,r-rhtslib)))
-    (inputs
-     `(("zlib" ,zlib))) ; This comes from rhtslib.
     (home-page "https://bioconductor.org/packages/seqbias/";)
     (synopsis "Estimation of per-position bias in high-throughput sequencing 
data")
     (description
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 1c1ef3e..0300306 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7980,8 +7980,6 @@ CAGE.")
                 "1sl0l6v05lfglj281nszma0h5k234md7rn2pdah8vs2d4iq3kimw"))))
     (properties
      `((upstream-name . "VariantAnnotation")))
-    (inputs
-     `(("zlib" ,zlib)))
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
        ("r-biobase" ,r-biobase)
@@ -8260,8 +8258,6 @@ biological sequences or sets of sequences.")
              (substitute* "NAMESPACE"
                (("import\\(zlibbioc\\)") ""))
              #t)))))
-    (inputs
-     `(("zlib" ,zlib)))
     (propagated-inputs
      `(("r-biocgenerics" ,r-biocgenerics)
        ("r-biocparallel" ,r-biocparallel)
@@ -8794,9 +8790,8 @@ secondary structure and comparative analysis in R.")
     (arguments '(#:configure-flags '("--no-staged-install")))
     (propagated-inputs
      `(("curl" ,curl)
+       ("zlib" ,zlib) ; packages using rhtslib need to link with zlib
        ("r-zlibbioc" ,r-zlibbioc)))
-    (inputs
-     `(("zlib" ,zlib)))
     (native-inputs
      `(("pkg-config" ,pkg-config)
        ("r-knitr" ,r-knitr)))
@@ -8827,8 +8822,6 @@ of other R packages who wish to make use of HTSlib.")
        ("r-rcpp" ,r-rcpp)
        ("r-rhtslib" ,r-rhtslib)
        ("r-zlibbioc" ,r-zlibbioc)))
-    (inputs
-     `(("zlib" ,zlib)))
     (native-inputs
      `(("r-knitr" ,r-knitr)))
     (home-page "https://bioconductor.org/packages/bamsignals";)
@@ -9127,8 +9120,6 @@ HDF5 datasets.")
     (propagated-inputs
      `(("r-rhdf5filters" ,r-rhdf5filters)
        ("r-rhdf5lib" ,r-rhdf5lib)))
-    (inputs
-     `(("zlib" ,zlib)))
     (native-inputs
      `(("r-knitr" ,r-knitr)))
     (home-page "https://bioconductor.org/packages/rhdf5";)
@@ -9616,8 +9607,6 @@ number detection tools.")
        ("r-zlibbioc" ,r-zlibbioc)))
     (native-inputs
      `(("r-knitr" ,r-knitr))) ; for vignettes
-    (inputs
-     `(("zlib" ,zlib)))
     (home-page "https://github.com/al2na/methylKit";)
     (synopsis
      "DNA methylation analysis from high-throughput bisulfite sequencing 
results")