Здравствуйте, я на самом деле пытаюсь установить пакет perl с именем HMMCleaner
Я выполнил для этого команду:
cpan Bio::MUST::Apps::HmmCleaner
, но в процессе я получил несколько сообщений говоря: Warning: prerequisite something 0 not found.
Вот заголовок вывода:
(/beegfs/data/me/myconda) me@pbil-deb:/beegfs/data/me/TOOLS/Bio-MUST-Apps-HmmCleaner-0.180750/bin$ cpan Test::Harness::Straps
Loading internal null logger. Install Log::Log4perl for logging messages
Reading '/beegfs/home/me/.cpan/Metadata'
Database was generated on Fri, 14 Feb 2020 09:41:03 GMT
Running install for module 'Test::Harness::Straps'
Fetching with LWP:
http://www.cpan.org/authors/id/M/MS/MSCHWERN/Test-Harness-Straps-0.30.tar.gz
Fetching with LWP:
http://www.cpan.org/authors/id/M/MS/MSCHWERN/CHECKSUMS
Checksum for /beegfs/home/me/.cpan/sources/authors/id/M/MS/MSCHWERN/Test-Harness-Straps-0.30.tar.gz ok
Configuring M/MS/MSCHWERN/Test-Harness-Straps-0.30.tar.gz with Build.PL
Test::Harness::Straps is provided for backwards compatibility only.
No further development is planned. No bugs will be fixed.
For customizable TAP parsing please use L<TAP::Parser> instead.
Created MYMETA.yml and MYMETA.json
Creating new 'Build' script for 'Test-Harness-Straps' version '0.30'
MSCHWERN/Test-Harness-Straps-0.30.tar.gz
/beegfs/data/me/myconda/bin/perl Build.PL --installdirs site -- OK
Running Build for M/MS/MSCHWERN/Test-Harness-Straps-0.30.tar.gz
Building Test-Harness-Straps
MSCHWERN/Test-Harness-Straps-0.30.tar.gz
./Build -- OK
Running Build test
t/00compile.t ...... 1/5 # Testing Test::Harness::Straps 0.30 under Perl 5.026002 and Test::More 1.302073
t/00compile.t ...... ok
t/callback.t ....... ok
t/point-parse.t .... ok
t/point.t .......... ok
t/strap-analyze.t .. ok
t/strap.t .......... ok
All tests successful.
Files=6, Tests=425, 9 wallclock secs ( 0.12 usr 0.04 sys + 0.98 cusr 0.67 csys = 1.81 CPU)
Result: PASS
MSCHWERN/Test-Harness-Straps-0.30.tar.gz
./Build test -- OK
Running Build install
Building Test-Harness-Straps
Installing /beegfs/home/me/perl5/lib/perl5/Test/Harness/Assert.pm
Installing /beegfs/home/me/perl5/lib/perl5/Test/Harness/Straps.pm
Installing /beegfs/home/me/perl5/lib/perl5/Test/Harness/Results.pm
Installing /beegfs/home/me/perl5/lib/perl5/Test/Harness/Point.pm
Installing /beegfs/home/me/perl5/lib/perl5/Test/Harness/Iterator.pm
Installing /beegfs/home/me/perl5/man/man3/Test::Harness::Point.3
Installing /beegfs/home/me/perl5/man/man3/Test::Harness::Assert.3
Installing /beegfs/home/me/perl5/man/man3/Test::Harness::Results.3
Installing /beegfs/home/me/perl5/man/man3/Test::Harness::Iterator.3
Installing /beegfs/home/me/perl5/man/man3/Test::Harness::Straps.3
MSCHWERN/Test-Harness-Straps-0.30.tar.gz
./Build install -- OK
(/beegfs/data/me/myconda) me@pbil-deb:/beegfs/data/me/TOOLS/Bio-MUST-Apps-HmmCleaner-0.180750/bin$ cpan Bio::MUST::Apps::HmmCleaner
Loading internal null logger. Install Log::Log4perl for logging messages
Reading '/beegfs/home/me/.cpan/Metadata'
Database was generated on Fri, 14 Feb 2020 09:41:03 GMT
Running install for module 'Bio::MUST::Apps::HmmCleaner'
Checksum for /beegfs/home/me/.cpan/sources/authors/id/A/AR/ARNODF/Bio-MUST-Apps-HmmCleaner-0.180750.tar.gz ok
Configuring A/AR/ARNODF/Bio-MUST-Apps-HmmCleaner-0.180750.tar.gz with Makefile.PL
Checking if your kit is complete...
Looks good
Warning: prerequisite Bio::FastParsers::Hmmer 0 not found.
Warning: prerequisite Bio::MUST::Core 0.180230 not found.
Warning: prerequisite Bio::MUST::Core::Ali 0 not found.
Warning: prerequisite Bio::MUST::Core::Constants 0 not found.
Warning: prerequisite Bio::MUST::Core::GeneticCode::Factory 0 not found.
Warning: prerequisite Bio::MUST::Core::IdList 0 not found.
Warning: prerequisite Bio::MUST::Core::Seq 0 not found.
Warning: prerequisite Bio::MUST::Core::SeqMask 0 not found.
Warning: prerequisite Bio::MUST::Core::Utils 0 not found.
Warning: prerequisite Bio::MUST::Drivers 0.180270 not found.
Warning: prerequisite Bio::MUST::Drivers::Hmmer::Model::Temporary 0 not found.
Warning: prerequisite IPC::System::Simple 0 not found.
Warning: prerequisite Smart::Comments 0 not found.
Warning: prerequisite aliased 0 not found.
Generating a Unix-style Makefile
Writing Makefile for Bio::MUST::Apps::HmmCleaner
Writing MYMETA.yml and MYMETA.json
ARNODF/Bio-MUST-Apps-HmmCleaner-0.180750.tar.gz
/beegfs/data/me/myconda/bin/perl Makefile.PL INSTALLDIRS=site -- OK
Running make for A/AR/ARNODF/Bio-MUST-Apps-HmmCleaner-0.180750.tar.gz
---- Unsatisfied dependencies detected during ----
---- ARNODF/Bio-MUST-Apps-HmmCleaner-0.180750.tar.gz ----
Bio::FastParsers::Hmmer [requires]
Bio::MUST::Core [requires]
Bio::MUST::Core::Ali [requires]
Bio::MUST::Core::Constants [requires]
Bio::MUST::Core::GeneticCode::Factory [requires]
Bio::MUST::Core::IdList [requires]
Bio::MUST::Core::Seq [requires]
Bio::MUST::Core::SeqMask [requires]
Bio::MUST::Core::Utils [requires]
Bio::MUST::Drivers [requires]
Bio::MUST::Drivers::Hmmer::Model::Temporary [requires]
IPC::System::Simple [requires]
Smart::Comments [requires]
aliased [requires]
Running install for module 'Bio::FastParsers::Hmmer'
Checksum for /beegfs/home/me/.cpan/sources/authors/id/D/DB/DBAURAIN/Bio-FastParsers-0.180470.tar.gz ok
Configuring D/DB/DBAURAIN/Bio-FastParsers-0.180470.tar.gz with Makefile.PL
Checking if your kit is complete...
Looks good
Warning: prerequisite Const::Fast 0 not found.
Warning: prerequisite Exporter::Easy 0 not found.
Warning: prerequisite Smart::Comments 0 not found.
Warning: prerequisite XML::Bare 0.53 not found.
Warning: prerequisite aliased 0 not found.
Generating a Unix-style Makefile
Writing Makefile for Bio::FastParsers
Writing MYMETA.yml and MYMETA.json
DBAURAIN/Bio-FastParsers-0.180470.tar.gz
/beegfs/data/me/myconda/bin/perl Makefile.PL INSTALLDIRS=site -- OK
Running make for D/DB/DBAURAIN/Bio-FastParsers-0.180470.tar.gz
---- Unsatisfied dependencies detected during ----
---- DBAURAIN/Bio-FastParsers-0.180470.tar.gz ----
Const::Fast [requires]
Exporter::Easy [requires]
Smart::Comments [requires]
XML::Bare [requires]
aliased [requires]
Running install for module 'Const::Fast'
Итак, я подумал, была ли возможность directclty позволить cpan установить все необходимые зависимости?
Я спрашиваю, потому что я получаю следующее сообщение об ошибке при попытке выполнить скрипт, используя Bio :: MUST :: Apps :: HMMCleaner.
Can't locate Smart/Comments.pm in @INC (you may need to install the Smart::Comments module) (@INC contains:
/beegfs/home/me/perl5/lib/perl5/x86_64-linux-thread-multi
/beegfs/home/me/perl5/lib/perl5
/beegfs/data/me/myconda/lib/site_perl/5.26.2/x86_64-linux-thread-multi
/beegfs/data/me/myconda/lib/site_perl/5.26.2
/beegfs/data/me/myconda/lib/5.26.2/x86_64-linux-thread-multi
/beegfs/data/me/myconda/lib/5.26.2
.
) at HmmCleaner.pl line 16. BEGIN failed--compilation aborted at HmmCleaner.pl line 16.
(Разрывы строк добавлены для удобства чтения).
Некоторая отладочная информация:
$ set | grep ^PERL
PERL5LIB=/beegfs/home/me/perl5/lib/perl5
PERL_LOCAL_LIB_ROOT=/beegfs/home/me/perl5
PERL_MB_OPT='--install_base "/beegfs/home/me/perl5"'
PERL_MM_OPT=INSTALL_BASE=/beegfs/home/me/perl5
$ echo 'o conf' | cpan | grep -P '^\s*(make|mbuild)'
Loading internal null logger. Install Log::Log4perl for logging messages
make [/usr/bin/X11/make]
make_arg []
make_install_arg []
make_install_make_command [/usr/bin/X11/make]
makepl_arg [INSTALLDIRS=site]
mbuild_arg []
mbuild_install_arg []
mbuild_install_build_command [./Build]
mbuildpl_arg [--installdirs site]
$ which cpan
/beegfs/data/me/myconda/bin/cpan
$ head -n 1 "$( which cpan )"
#!/beegfs/data/me/myconda/bin/perl
$ which perl
/beegfs/data/me/myconda/bin/perl
$ cpan Smart::Comments
Loading internal null logger. Install Log::Log4perl for logging messages
Reading '/beegfs/home/me/.cpan/Metadata'
Database was generated on Fri, 14 Feb 2020 09:41:03 GMT
Running install for module 'Smart::Comments'
Checksum for /beegfs/home/me/.cpan/sources/authors/id/N/NE/NEILB/Smart-Comments-1.06.tar.gz ok
Configuring N/NE/NEILB/Smart-Comments-1.06.tar.gz with Makefile.PL
Checking if your kit is complete...
Looks good
Generating a Unix-style Makefile
Writing Makefile for Smart::Comments
Writing MYMETA.yml and MYMETA.json
NEILB/Smart-Comments-1.06.tar.gz
/beegfs/data/me/myconda/bin/perl Makefile.PL INSTALLDIRS=site -- OK
Running make for N/NE/NEILB/Smart-Comments-1.06.tar.gz
cp lib/Smart/Comments.pm blib/lib/Smart/Comments.pm
Manifying 1 pod document
NEILB/Smart-Comments-1.06.tar.gz
/usr/bin/X11/make -- OK
Running make test
PERL_DL_NONLAZY=1 "/beegfs/data/me/myconda/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/00.load.t ................. 1/1 # Testing Smart::Comments 1.06
t/00.load.t ................. ok
t/assert.t .................. ok
t/brackets.t ................ ok
t/c_like_for_loop.t ......... ok
t/check.t ................... ok
t/confirm.t ................. ok
t/ensure.t .................. ok
t/ENV_0.t ................... ok
t/ENV_1.t ................... ok
t/ENV_str.t ................. ok
t/insist.t .................. ok
t/labelled_perlish_loop.t ... ok
t/message.t ................. ok
t/perlish_for.t ............. ok
t/perlish_for_percentage.t .. ok
t/pod-coverage.t ............ skipped: Test::Pod::Coverage 1.04 required for testing POD coverage
t/pod.t ..................... skipped: Test::Pod 1.14 required for testing POD
t/require.t ................. ok
t/selective.t ............... ok
t/simple_perlish_for.t ...... ok
t/var.t ..................... ok
t/verify.t .................. ok
t/while.t ................... ok
t/while_num.t ............... ok
All tests successful.
Files=24, Tests=119, 19 wallclock secs ( 0.13 usr 0.08 sys + 2.93 cusr 1.45 csys = 4.59 CPU)
Result: PASS
NEILB/Smart-Comments-1.06.tar.gz
/usr/bin/X11/make test -- OK
Running make install
Manifying 1 pod document
Installing /beegfs/home/me/perl5/lib/perl5/Smart/Comments.pm
Installing /beegfs/home/me/perl5/man/man3/Smart::Comments.3
Appending installation info to /beegfs/home/me/perl5/lib/perl5/x86_64-linux-thread-multi/perllocal.pod
NEILB/Smart-Comments-1.06.tar.gz
/usr/bin/X11/make install -- OK
$ perl -e'use Smart::Comments; print "ok\n"'
ok
Спасибо за вашу помощь.