Bug 728018 – sci-biology/samtools-1.9-r1 calls "ar" directly ( make: ar: No such file or directory w/ binutils-config[-native-symlinks] )

• Product: Gentoo Linux
• Status: RESOLVED FIXED

[Description Kent Fredric (IRC: kent\n) (RETIRED) 2020-06-12 07:35:02 UTC]

Context:

x86_64-pc-linux-gnu-gcc -O2 -pipe -mtune=native -march=native -I.  -I./lz4  -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.c
x86_64-pc-linux-gnu-gcc -O2 -pipe -mtune=native -march=native -I.  -I./lz4  -c -o test/test.o test/test.c
x86_64-pc-linux-gnu-gcc -O2 -pipe -mtune=native -march=native -I.  -I./lz4  -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c
x86_64-pc-linux-gnu-gcc -O2 -pipe -mtune=native -march=native -I.  -I./lz4  -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c
x86_64-pc-linux-gnu-gcc -O2 -pipe -mtune=native -march=native -I.  -I./lz4  -c -o test/split/test_count_rg.o test/split/test_count_rg.c
x86_64-pc-linux-gnu-gcc -O2 -pipe -mtune=native -march=native -I.  -I./lz4  -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c
x86_64-pc-linux-gnu-gcc -O2 -pipe -mtune=native -march=native -I.  -I./lz4  -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c
x86_64-pc-linux-gnu-gcc -O2 -pipe -mtune=native -march=native -I.  -I./lz4  -c -o test/split/test_parse_args.o test/split/test_parse_args.c
x86_64-pc-linux-gnu-gcc -O2 -pipe -mtune=native -march=native -I.  -I./lz4  -c -o test/vcf-miniview.o test/vcf-miniview.c
x86_64-pc-linux-gnu-gcc -O2 -pipe -mtune=native -march=native -I.  -I./lz4  -c -o bamtk.o bamtk.c
ar -csru libbam.a bam_aux.o bam.o bam_import.o sam.o sam_header.o bam_plbuf.o
make: ar: No such file or directory
make: *** [Makefile:141: libbam.a] Error 127
make: *** Waiting for unfinished jobs....
 * ERROR: sci-biology/samtools-1.9-r1::gentoo failed (compile phase):
 *   emake failed
 * 


 * Package:    sci-biology/samtools-1.9-r1
 * Repository: gentoo
 * Maintainer: [e-mail]
 * USE:        abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU
 * FEATURES:   ccache compressdebug network-sandbox preserve-libs sandbox splitdebug userpriv usersandbox


Makefile:

AR       = ar
	$(AR) -csru $@ $(LOBJS)
	$(AR) -rcs $@ $(LIBST_OBJS)



Conclusion:

Seems like doing:

src_compile() {
   emake AR="$(tc-getAR)"
}

would be enough to make this work.

[Comment 1 Kent Fredric (IRC: kent\n) (RETIRED) 2020-06-12 07:37:29 UTC]

Created attachment 644462 [details]
samtools-1.9-r1:20200612-072612.log.gz

[Comment 2 Larry the Git Cow 2020-08-03 16:56:01 UTC]

The bug has been referenced in the following commit(s):

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=90c55f4b6812ba59ca61467380f0a153f3ff2edf

commit 90c55f4b6812ba59ca61467380f0a153f3ff2edf
Author:     David Seifert <[e-mail]>
AuthorDate: 2020-08-03 16:54:23 +0000
Commit:     David Seifert <[e-mail]>
CommitDate: 2020-08-03 16:54:23 +0000

    sci-biology/samtools: Bump to version 1.10
    
    Bug: https://bugs.gentoo.org/728018
    Package-Manager: Portage-3.0.1, Repoman-2.3.23
    Signed-off-by: David Seifert <[e-mail]>

 sci-biology/samtools/Manifest             |  1 +
 sci-biology/samtools/samtools-1.10.ebuild | 56 +++++++++++++++++++++++++++++++
 2 files changed, 57 insertions(+)

[Comment 3 Larry the Git Cow 2020-08-03 21:11:44 UTC]

The bug has been closed via the following commit(s):

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=b6948f3ed9612bc6f11b4ccab40ac4d80f73e397

commit b6948f3ed9612bc6f11b4ccab40ac4d80f73e397
Author:     David Seifert <[e-mail]>
AuthorDate: 2020-08-03 21:11:18 +0000
Commit:     David Seifert <[e-mail]>
CommitDate: 2020-08-03 21:11:18 +0000

    sci-biology/samtools: Remove old
    
    Closes: https://bugs.gentoo.org/728018
    Package-Manager: Portage-3.0.1, Repoman-2.3.23
    Signed-off-by: David Seifert <[e-mail]>

 sci-biology/samtools/Manifest                      |   2 -
 .../samtools/files/samtools-1.5-buildsystem.patch  | 413 ---------------------
 sci-biology/samtools/samtools-1.5.ebuild           |  61 ---
 sci-biology/samtools/samtools-1.9-r1.ebuild        |  49 ---
 4 files changed, 525 deletions(-)