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| author | Ben J. Woodcroft <donttrustben near gmail.com> | 2017-03-10 20:25:00 +1000 |
|---|---|---|
| committer | Ben Woodcroft <donttrustben@gmail.com> | 2017-03-10 20:31:30 +1000 |
| commit | 79f09fa2394c5de06668406222a655eac39c36f6 (patch) | |
| tree | 26227903f0410b2fabd93e66271b7c9576a89535 | |
| parent | 5ded35d89d33a58294956c4a6c86cfb2fc7c7924 (diff) | |
| download | patches-79f09fa2394c5de06668406222a655eac39c36f6.tar patches-79f09fa2394c5de06668406222a655eac39c36f6.tar.gz | |
gnu: hmmer: Build reproducibly.
* gnu/packages/patches/hmmer-remove-cpu-specificity.patch: New file.
* gnu/packages/bioinformatics.scm (hmmer): Use it.
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 20 | ||||
| -rw-r--r-- | gnu/packages/patches/hmmer-remove-cpu-specificity.patch | 22 |
2 files changed, 33 insertions, 9 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b6f753ef0a..866900d40b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2839,15 +2839,17 @@ indexing scheme is called a @dfn{Hierarchical Graph FM index} (HGFM).") (package (name "hmmer") (version "3.1b2") - (source (origin - (method url-fetch) - (uri (string-append - "http://eddylab.org/software/hmmer" - (version-prefix version 1) "/" - version "/hmmer-" version ".tar.gz")) - (sha256 - (base32 - "0djmgc0pfli0jilfx8hql1axhwhqxqb8rxg2r5rg07aw73sfs5nx")))) + (source + (origin + (method url-fetch) + (uri (string-append + "http://eddylab.org/software/hmmer" + (version-prefix version 1) "/" + version "/hmmer-" version ".tar.gz")) + (sha256 + (base32 + "0djmgc0pfli0jilfx8hql1axhwhqxqb8rxg2r5rg07aw73sfs5nx")) + (patches (search-patches "hmmer-remove-cpu-specificity.patch")))) (build-system gnu-build-system) (native-inputs `(("perl" ,perl))) (home-page "http://hmmer.org/") diff --git a/gnu/packages/patches/hmmer-remove-cpu-specificity.patch b/gnu/packages/patches/hmmer-remove-cpu-specificity.patch new file mode 100644 index 0000000000..ba98db4d0e --- /dev/null +++ b/gnu/packages/patches/hmmer-remove-cpu-specificity.patch @@ -0,0 +1,22 @@ +This patch removes compilation flags which make the build for the machine +where compilation takes place, rendering the build not reproducible. + +diff --git a/configure b/configure +index 8b6aaef..49a6afc 100755 +--- a/configure ++++ b/configure +@@ -6125,14 +6125,6 @@ fi # guess arch + + if test "x$ax_gcc_arch" != x -a "x$ax_gcc_arch" != xno; then + for arch in $ax_gcc_arch; do +- if test "x$acx_maxopt_portable" = xyes; then # if we require portable code +- flags="-mtune=$arch" +- # -mcpu=$arch and m$arch generate nonportable code on every arch except +- # x86. And some other arches (e.g. Alpha) don't accept -mtune. Grrr. +- case $host_cpu in i*86|x86_64*) flags="$flags -mcpu=$arch -m$arch";; esac +- else +- flags="-march=$arch -mcpu=$arch -m$arch" +- fi + for flag in $flags; do + as_CACHEVAR=`$as_echo "ax_cv_check_cflags__$flag" | $as_tr_sh` + { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether C compiler accepts $flag" >&5 |