From 4617cc7fd509cc73703e5b273c634f995bb69a5d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 7 Dec 2020 16:44:23 +0100
Subject: [PATCH] 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 5f524f310c..5a3d638434 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1726,8 +1726,6 @@ (define-public r-diffbind
          "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 @@ (define-public r-quasr
          "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 @@ (define-public r-cytolib
                (("\\(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 @@ (define-public r-ncdfflow
                (("\\(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 @@ (define-public r-flowworkspace
                (("\\{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 @@ (define-public r-seqbias
      `(("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 9cf5c0acab..9edf75a82c 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7980,8 +7980,6 @@ (define-public r-variantannotation
                 "1sl0l6v05lfglj281nszma0h5k234md7rn2pdah8vs2d4iq3kimw"))))
     (properties
      `((upstream-name . "VariantAnnotation")))
-    (inputs
-     `(("zlib" ,zlib)))
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
        ("r-biobase" ,r-biobase)
@@ -8260,8 +8258,6 @@ (define-public r-rsamtools
              (substitute* "NAMESPACE"
                (("import\\(zlibbioc\\)") ""))
              #t)))))
-    (inputs
-     `(("zlib" ,zlib)))
     (propagated-inputs
      `(("r-biocgenerics" ,r-biocgenerics)
        ("r-biocparallel" ,r-biocparallel)
@@ -8794,9 +8790,8 @@ (define-public r-rhtslib
     (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 @@ (define-public r-bamsignals
        ("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 @@ (define-public r-rhdf5
     (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 @@ (define-public r-methylkit
        ("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")