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Viral Annotation DefineR: classification and annotation of viral sequences based on RefSeq annotation
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Error in install from Inline module #43

Closed minhtrung1997 closed 4 months ago

minhtrung1997 commented 3 years ago

I've tried download and install for the first time. I got this message when running ./vadr-install.sh linux (also attach a 1install.log : 1install.log

Warning: prerequisite Inline 0.51 not found. Warning: prerequisite Inline::MakeMaker 0.45 not found. Generating a Unix-style Makefile Writing Makefile for Bio::Easel Writing MYMETA.yml and MYMETA.json cp lib/Bio/Easel/Random.pm blib/lib/Bio/Easel/Random.pm cp lib/Bio/Easel/SqFile.c blib/lib/Bio/Easel/SqFile.c cp lib/Bio/Easel/SqFile.typemap blib/lib/Bio/Easel/SqFile.typemap cp lib/Bio/Easel/Random.c blib/lib/Bio/Easel/Random.c cp lib/Bio/Easel/SqFile.pm blib/lib/Bio/Easel/SqFile.pm cp lib/Bio/Easel/Random.typemap blib/lib/Bio/Easel/Random.typemap cp lib/Bio/Easel.pm blib/lib/Bio/Easel.pm cp lib/Bio/Easel/MSA.c blib/lib/Bio/Easel/MSA.c cp lib/Bio/Easel/MSA.typemap blib/lib/Bio/Easel/MSA.typemap cp lib/Bio/Easel/MSA.pm blib/lib/Bio/Easel/MSA.pm cp scripts/esl-alidepair.pl blib/script/esl-alidepair.pl "/home/kt/anaconda3/envs/kt/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/esl-alidepair.pl cp scripts/esl-ssplit.pl blib/script/esl-ssplit.pl "/home/kt/anaconda3/envs/kt/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/esl-ssplit.pl "/home/kt/anaconda3/envs/kt/bin/perl" -Mblib -MInline=NOISY,INSTALL -MBio::Easel::MSA -e1 0.01 blib/arch Can't locate Inline.pm in @INC (you may need to install the Inline module) (@INC contains: /media/kt/data/TRUNG/2.Tool/vadr/Bio-Easel/blib/arch /media/kt/data/TRUNG/2.Tool/vadr/Bio-Easel/blib/lib /home/kt/anaconda3/envs/kt/lib/site_perl/5.26.2/x86_64-linux-thread-multi /home/kt/anaconda3/envs/kt/lib/site_perl/5.26.2 /home/kt/anaconda3/envs/kt/lib/5.26.2/x86_64-linux-thread-multi /home/kt/anaconda3/envs/kt/lib/5.26.2 .). BEGIN failed--compilation aborted. make: *** [Makefile:963: MSA.inl] Error 2 Then when I install Inline conda install -c bioconda perl-inline run vadr-install.sh build to patch, another error I send in file install-build.log !

vadr-install-build.log Please give it a fix soon. Thank you

nawrockie commented 3 years ago

@minhtrung1997 it looks like you don't have the Inline perl module installed, see here:

https://github.com/ncbi/vadr/blob/master/documentation/install.md#-if-installation-or-do-install-tests-localsh-fails-because-the-inline-or-lwp-perl-modules-are-not-installed

minhtrung1997 commented 2 years ago

Yeah after following your instruction, I'm able to install 2nd_install.log But when I run the test, it encounters another error

$./do-install-tests-local.sh

./do-install-tests-local.sh: line 6: /v-test.pl: No such file or directory ./do-install-tests-local.sh: line 12: /v-test.pl: No such file or directory FAIL: at least one test failed [do-install-tests-local.sh]

I run perl v-test.pl

Can't locate Bio/Easel/MSA.pm in @INC (you may need to install the Bio::Easel::MSA module) (@INC contains: /home/kt/anaconda3/envs/kt/lib/site_perl/5.26.2/x86_64-linux-thread-multi /home/kt/anaconda3/envs/kt/lib/site_perl/5.26.2 /home/kt/anaconda3/envs/kt/lib/5.26.2/x86_64-linux-thread-multi /home/kt/anaconda3/envs/kt/lib/5.26.2 .) at v-test.pl line 7. BEGIN failed--compilation aborted at v-test.pl line 7.

When I try install Bio::Easel::MSA through Cpan:

Reading '/home/kt/.cpan/Metadata' Database was generated on Wed, 24 Nov 2021 00:17:02 GMT Warning: Cannot install Bio::Easel::MSA, don't know what it is. Try the command

i /Bio::Easel::MSA/

to find objects with matching identifiers.

Please give me a recommendation

nawrockie commented 2 years ago

@minhtrung1997 : It looks like you need to set up environment variables as explained here:

https://github.com/ncbi/vadr/blob/master/documentation/install.md#instructions-for-setting-environment-variables-output-by-vadr-installsh

minhtrung1997 commented 2 years ago

Thank you very much the issues resolved but there still a bug in v-build image

Although I've already run cpan install Inline::C

cpan install LWP::Simple

cpan install LWP::Protocol::https

Also my virus namely ASFV need to build another protein set. Please help

minhtrung1997 commented 2 years ago

when i check the module, it's still there image

minhtrung1997 commented 2 years ago

But when not use sudo, it's not image

nawrockie commented 2 years ago

It looks like your $PERL5LIB environment variable doesn't include the necessary paths. It should include: $VADRBIOEASELDIR/blib/lib and $VADRBIOEASELDIR/blib/arch for Bio/Easel/MSA.pm

and it looks like it should also include: /usr/local/share/perl/5.26.1/LWP/Protocol/https.pm

For https.pm.

If you do echo $PERL5LIB it will show you the paths included.

rpetit3 commented 2 years ago

@minhtrung1997

Have you tried just using the version of VADR on bioconda?

conda create -n vadr -c conda-forge -c bioconda vadr
minhtrung1997 commented 2 years ago

It work for now. Many thanks

xiaoli-dong commented 3 months ago

I got the same error message while I am running vadr as singularity image:

Singularity> fasta-trim-terminal-ambigs.pl Use of uninitialized value in subroutine entry at /usr/local/lib/perl5/5.32/site_perl/Bio/Easel/MSA.pm line 60. Use of uninitialized value in subroutine entry at /usr/local/lib/perl5/5.32/site_perl/Bio/Easel/SqFile.pm line 59. Can't locate sqp_seq.pm in @INC (you may need to install the sqp_seq module) (@INC contains: /usr/local/lib/perl5/5.32/site_perl /usr/local/lib/perl5/site_perl /usr/local/lib/perl5/5.32/vendor_perl /usr/local/lib/perl5/vendor_perl /usr/local/lib/perl5/5.32/core_perl /usr/local/lib/perl5/core_perl .) at /usr/local/bin/fasta-trim-terminal-ambigs.pl line 17.