Configure blocks indefinitely waiting on input from STDIN, which then fails when one presses "enter" on the blocked emerge process. Error log contains: * perl Build.PL --installdirs=vendor --libdoc= --destdir=/var/tmp/portage/dev-perl/Bio-SamTools-1.430.0/image/ --create_packlist=1 This module requires samtools 0.1.10 or higher (samtools.sourceforge.net). Can't find libbam-0.1-legacy.so and/or bam-0.1-legacy/bam.h! If you haven't done so already, please compile samtools 0.1.10 or higher from http://samtools.sourceforge.net and set the SAMTOOLS environment variable to point to a samtools distribution directory containing the compiled libbam-0.1-legacy.so and bam-0.1-legacy/bam.h files. * ERROR: dev-perl/Bio-SamTools-1.430.0::gentoo failed (configure phase): * Unable to build! Dependency graph of installed packages prior to this message are as follows: [ebuild N ~] dev-perl/Bio-SamTools-1.430.0 0 KiB [ebuild N ] sci-biology/bioperl-1.6.9 USE="db minimal network run -graphviz -sqlite" 0 KiB [ebuild N ] dev-perl/libwww-perl-6.150.0 USE="ssl" 0 KiB [ebuild N ] dev-perl/HTTP-Cookies-6.40.0 USE="{-test}" 0 KiB [ebuild N ] dev-perl/WWW-RobotRules-6.20.0 0 KiB [ebuild N ] dev-perl/File-Listing-6.40.0-r1 0 KiB [ebuild N ] dev-perl/Net-HTTP-6.90.0 USE="minimal" 0 KiB [ebuild N ] dev-perl/LWP-Protocol-https-6.60.0 0 KiB [ebuild N ] dev-perl/HTML-Parser-3.720.0 USE="{-test}" 0 KiB [ebuild N ] dev-perl/HTML-Tagset-3.200.0-r1 0 KiB [ebuild N #] virtual/perl-XSLoader-0.300.0 0 KiB [ebuild N ] dev-perl/HTTP-Negotiate-6.10.0-r1 0 KiB [ebuild N ] sci-biology/bioperl-db-1.6.9 USE="{-test}" 0 KiB [ebuild N ] dev-perl/DBD-mysql-4.44.0 USE="ssl {-test}" 0 KiB [ebuild N ] virtual/libmysqlclient-18:0/18 USE="-static-libs" 0 KiB [ebuild N ] dev-db/mysql-connector-c-6.1.11-r1:0/18 USE="ssl -libressl -static-libs" 0 KiB [ebuild N ] dev-util/cmake-3.9.6 USE="ncurses -doc -emacs -qt5 -server -system-jsoncpp {-test}" 0 KiB [ebuild N ] app-crypt/rhash-1.3.5 USE="nls ssl -debug -libressl -static-libs" 0 KiB [ebuild N ] app-arch/libarchive-3.3.1:0/13 USE="acl bzip2 e2fsprogs iconv lzma threads xattr zlib -expat -libressl -lz4 -lzo -nettle -static-libs" 0 KiB [ebuild N ] dev-perl/DBI-1.637.0 USE="-examples {-test}" 0 KiB [ebuild N ] dev-perl/PlRPC-0.202.0-r2 0 KiB [ebuild N ] dev-perl/Net-Daemon-0.480.0-r2 0 KiB [ebuild N ~] virtual/perl-Sys-Syslog-0.350.0-r1 0 KiB [ebuild N ] sci-biology/biosql-1.0.1-r1 USE="-mysql -postgres" 0 KiB [ebuild N ] sci-biology/bioperl-network-1.6.9 USE="{-test}" 0 KiB [ebuild N ] dev-perl/Graph-0.970.400 0 KiB [ebuild N ] sci-biology/bioperl-run-1.6.9 USE="minimal {-test}" 0 KiB [ebuild N ~] sci-biology/samtools-0.1.20-r3:0.1-legacy USE="-examples" PYTHON_TARGETS="python2_7" 0 KiB Install target is perl 5.28
Created attachment 621008 [details, diff] adds support for lib64
The bug has been referenced in the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=1442f328453dc90ea24b64ec3abd4e661504f408 commit 1442f328453dc90ea24b64ec3abd4e661504f408 Author: Kent Fredric <kentnl@gentoo.org> AuthorDate: 2020-05-20 17:00:14 +0000 Commit: Kent Fredric <kentnl@gentoo.org> CommitDate: 2020-05-20 17:01:20 +0000 dev-perl/Bio-SamTools: Add fixed version for bug #661112 - Reworked patches so the autodetection stuff is nixed, because its really silly and doesn't work. - Paths now computed in ebuild and passed explicitly - Fix handling of libdir for lib64 re bug #661112, but in a different way than proposed by Sławomir Nizio, mostly because I didn't see that suggestion until after I'd done all my changes (but also because relying on a hardcoded path in the code is also fragile) - Converted to EAPI7 - Removed unused empty variable assignments Bug: https://bugs.gentoo.org/661112 Package-Manager: Portage-2.3.99, Repoman-2.3.22 Signed-off-by: Kent Fredric <kentnl@gentoo.org> .../Bio-SamTools/Bio-SamTools-1.430.0-r1.ebuild | 38 +++++++ .../files/Bio-SamTools-1.430.0-legacy-r1.patch | 110 +++++++++++++++++++++ 2 files changed, 148 insertions(+)
Your solution is obviously better, thanks!
The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=2a866fb9126e4c0a780620e041598cc6d3726ad3 commit 2a866fb9126e4c0a780620e041598cc6d3726ad3 Author: Kent Fredric <kentnl@gentoo.org> AuthorDate: 2020-06-20 04:28:41 +0000 Commit: Kent Fredric <kentnl@gentoo.org> CommitDate: 2020-06-20 04:28:41 +0000 dev-perl/Bio-SamTools: Cleanup old 1.430.0 - Unstable(~) eclipsed by 1.430.0-r1 for ~1 month Closes: https://bugs.gentoo.org/661112 Package-Manager: Portage-2.3.100, Repoman-2.3.22 Signed-off-by: Kent Fredric <kentnl@gentoo.org> dev-perl/Bio-SamTools/Bio-SamTools-1.430.0.ebuild | 33 -------- .../files/Bio-SamTools-1.430.0-legacy.patch | 88 ---------------------- 2 files changed, 121 deletions(-)
