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Published 20 hours ago • verified publisher icon sanger-pathogens

Can't locate Bio/Roary/CommandLine/Roary.pm in @INC

Open beudes opened this issue 5 years ago • 15 comments

Dear all

Roary is not working after installing on osx through miniconda3 I have to say that I had also issues while installing Prokka but that has been solved by creating an environment. But now, when I launch Roary from the shell, I receive the following error:

$ roary Can't locate Bio/Roary/CommandLine/Roary.pm in @INC (you may need to install the Bio::Roary::CommandLine::Roary module) (@INC contains: /Users/benoit/lib /miniconda3/lib/perl5/site_perl/5.22.0/darwin-thread-multi-2level /miniconda3/lib/perl5/site_perl/5.22.0 /miniconda3/lib/perl5/5.22.0/darwin-thread-multi-2level /miniconda3/lib/perl5/5.22.0 .) at /miniconda3/bin/roary line 12. BEGIN failed--compilation aborted at /miniconda3/bin/roary line 12.

also below are the packages associated with miniconda3 $ conda list

packages in environment at /miniconda3:

Name Version Build Channel

aragorn 1.2.38 2 bioconda asn1crypto 0.24.0 py37_1003 conda-forge barrnap 0.9 2 bioconda bedtools 2.27.1 h5c9b4e4_3 bioconda blas 1.0 mkl
blast 2.6.0 boost1.64_2 bioconda boost 1.69.0 py37h9888f84_1001 conda-forge boost-cpp 1.69.0 h6f8c590_1000 conda-forge bzip2 1.0.6 h1de35cc_1002 conda-forge ca-certificates 2019.3.9 hecc5488_0 conda-forge cd-hit 4.8.1 hd9629dc_0 bioconda certifi 2019.3.9 py37_0 conda-forge cffi 1.12.2 py37h2d6ddff_1 conda-forge chardet 3.0.4 py37_1003 conda-forge clustalw 2.1 h04f5b5a_3 bioconda conda 4.6.8 py37_0 conda-forge conda-env 2.6.0 1 conda-forge cryptography 2.6.1 py37hc2b1221_0 conda-forge expat 2.2.5 h0a44026_1002 conda-forge fasttree 2.1.10 h470a237_2 bioconda fontconfig 2.13.1 h1e4e890_1000 conda-forge freetype 2.9.1 h597ad8a_1005 conda-forge giflib 5.1.4 h1de35cc_1001 conda-forge gmp 6.1.2 h0a44026_1000 conda-forge graphviz 2.38.0 hc6cc99f_1011 conda-forge hmmer 3.2.1 h0a44026_1 bioconda icu 58.2 h0a44026_1000 conda-forge idna 2.8 py37_1000 conda-forge infernal 1.1.2 h1de35cc_2 bioconda intel-openmp 2019.1 144
jpeg 9c h1de35cc_1001 conda-forge libboost 1.67.0 hebc422b_4
libcxx 7.0.0 h2d50403_1 conda-forge libcxxabi 4.0.1 hebd6815_0 conda-forge libdb 6.1.26 0 bioconda libedit 3.1.20170329 hcfe32e1_1001 conda-forge libffi 3.2.1 1 bioconda libgcc 4.8.5 hdbeacc1_10 conda-forge libgd 2.2.5 h8cbe2a3_1005 conda-forge libgfortran 3.0.1 0 conda-forge libiconv 1.15 h1de35cc_1004 conda-forge libidn11 1.34 h112b980_0 conda-forge libpng 1.6.36 ha441bb4_1000 conda-forge libtiff 4.0.10 h344961e_1002 conda-forge libwebp 1.0.2 h801f6e5_1 conda-forge libxml2 2.9.8 hf14e9c8_1005 conda-forge libxslt 1.1.32 h33a18ac_1002 conda-forge llvm-meta 7.0.0 0 conda-forge mafft 7.407 1 bioconda mcl 14.137 pl526h470a237_4 bioconda minced 0.3.2 0 bioconda mkl 2019.1 144
mkl_fft 1.0.10 py37h1de35cc_1 conda-forge mkl_random 1.0.2 py37h1702cab_2 conda-forge ncurses 6.1 h0a44026_1002 conda-forge nettle 3.4.1 h3efe00b_1002 conda-forge numpy 1.16.2 py37hacdab7b_0
numpy-base 1.16.2 py37h6575580_0
openjdk 11.0.1 h1de35cc_1014 conda-forge openssl 1.1.1b h1de35cc_1 conda-forge paml 4.9 h1de35cc_4 bioconda parallel 20190122 0 conda-forge pcre 8.41 h0a44026_1003 conda-forge perl 5.26.2 h79c3c89_1002 conda-forge perl-aceperl 1.92 pl526_2 bioconda perl-algorithm-diff 1.1903 pl526_2 bioconda perl-algorithm-munkres 0.08 pl526_1 bioconda perl-apache-test 1.40 pl526_1 bioconda perl-app-cpanminus 1.7044 pl526_1 bioconda perl-appconfig 1.71 pl526_1 bioconda perl-archive-tar 2.32 pl526_0 bioconda perl-array-compare 3.0.1 pl526_1 bioconda perl-array-utils 0.5 pl526_2 bioconda perl-autoloader 5.74 pl526_2 bioconda perl-base 2.23 pl526_1 bioconda perl-bio-asn1-entrezgene 1.73 pl526_0 bioconda perl-bio-coordinate 1.007001 pl526_0 bioconda perl-bio-featureio 1.6.905 pl526_1 bioconda perl-bio-phylo 0.58 pl526_1 bioconda perl-bio-samtools 1.43 pl526h1341992_1 bioconda perl-bio-tools-phylo-paml 1.7.3 pl526_0 bioconda perl-bio-tools-run-alignment-clustalw 1.7.4 pl526_0 bioconda perl-bioperl 1.7.2 pl526_9 bioconda perl-bioperl-core 1.7.2 pl526_3 bioconda perl-bioperl-run 1.007002 pl526_3 bioconda perl-business-isbn 3.004 pl526_0 bioconda perl-business-isbn-data 20140910.003 pl526_0 bioconda perl-cache-cache 1.08 pl526_0 bioconda perl-capture-tiny 0.48 pl526_0 bioconda perl-carp 1.38 pl526_2 bioconda perl-cgi 4.40 pl526h470a237_0 bioconda perl-class-data-inheritable 0.08 pl526_1 bioconda perl-class-inspector 1.32 pl526_1 bioconda perl-class-load 0.25 pl526_0 bioconda perl-class-load-xs 0.10 pl526h2d50403_0 bioconda perl-class-method-modifiers 2.12 pl526_0 bioconda perl-clone 0.41 pl526h470a237_0 bioconda perl-common-sense 3.74 pl526_2 bioconda perl-compress-raw-bzip2 2.084 pl526hfc679d8_0 bioconda perl-compress-raw-zlib 2.084 pl526h04f5b5a_1 bioconda perl-constant 1.33 pl526_1 bioconda perl-convert-binary-c 0.78 pl526h2d50403_2 bioconda perl-convert-binhex 1.125 pl526_1 bioconda perl-crypt-rc4 2.02 pl526_1 bioconda perl-data-dumper 2.173 pl526_0 bioconda perl-data-optlist 0.110 pl526_2 bioconda perl-data-stag 0.14 pl526_1 bioconda perl-date-format 2.30 pl526_2 bioconda perl-db-file 1.843 pl526h470a237_0 bioconda perl-dbd-sqlite 1.62 pl526h1de35cc_0 bioconda perl-dbi 1.642 pl526_0 bioconda perl-devel-globaldestruction 0.14 pl526_0 bioconda perl-devel-overloadinfo 0.005 pl526_0 bioconda perl-devel-stacktrace 2.03 pl526_1 bioconda perl-digest-hmac 1.03 pl526_3 bioconda perl-digest-md5 2.55 pl526_0 bioconda perl-digest-md5-file 0.08 pl526_2 bioconda perl-digest-perl-md5 1.9 pl526_1 bioconda perl-digest-sha1 2.13 pl526h2d50403_0 bioconda perl-dist-checkconflicts 0.11 pl526_2 bioconda perl-dynaloader 1.25 pl526_1 bioconda perl-email-date-format 1.005 pl526_2 bioconda perl-encode 2.88 pl526_1 bioconda perl-encode-locale 1.05 pl526_6 bioconda perl-env-path 0.19 pl526_2 bioconda perl-error 0.17027 pl526_1 bioconda perl-eval-closure 0.14 pl526h2d50403_3 bioconda perl-exception-class 1.44 pl526_0 bioconda perl-exporter 5.72 pl526_1 bioconda perl-exporter-tiny 1.002001 pl526_0 bioconda perl-extutils-makemaker 7.34 pl526_3 bioconda perl-file-find-rule 0.34 pl526_5 bioconda perl-file-grep 0.02 pl526_3 bioconda perl-file-listing 6.04 pl526_1 bioconda perl-file-path 2.15 pl526_0 bioconda perl-file-slurp-tiny 0.004 pl526_1 bioconda perl-file-slurper 0.012 pl526_0 bioconda perl-file-sort 1.01 pl526_2 bioconda perl-file-temp 0.2304 pl526_2 bioconda perl-file-which 1.23 pl526_0 bioconda perl-font-afm 1.20 pl526_2 bioconda perl-font-ttf 1.06 pl526_0 bioconda perl-gd 2.70 pl526he941832_0 bioconda perl-getopt-long 2.50 pl526_1 bioconda perl-graph 0.9704 pl526_1 bioconda perl-graph-readwrite 2.09 pl526_2 bioconda perl-graphviz 2.24 pl526h734ff71_0 bioconda perl-html-element-extended 1.18 pl526_1 bioconda perl-html-entities-numbered 0.04 pl526_1 bioconda perl-html-formatter 2.16 pl526_0 bioconda perl-html-parser 3.72 pl526h2d50403_4 bioconda perl-html-tableextract 2.13 pl526_2 bioconda perl-html-tagset 3.20 pl526_3 bioconda perl-html-tidy 1.60 pl526_0 bioconda perl-html-tree 5.07 pl526_1 bioconda perl-html-treebuilder-xpath 0.14 pl526_1 bioconda perl-http-cookies 6.04 pl526_0 bioconda perl-http-daemon 6.01 pl526_1 bioconda perl-http-date 6.02 pl526_3 bioconda perl-http-message 6.18 pl526_0 bioconda perl-http-negotiate 6.01 pl526_3 bioconda perl-image-info 1.38 pl526_1 bioconda perl-image-size 3.300 pl526_2 bioconda perl-importer 0.025 pl526_0 bioconda perl-io-compress 2.084 pl526hfc679d8_0 bioconda perl-io-html 1.001 pl526_2 bioconda perl-io-sessiondata 1.03 pl526_1 bioconda perl-io-socket-ssl 2.060 pl526_0 bioconda perl-io-string 1.08 pl526_3 bioconda perl-io-stringy 2.111 pl526_1 bioconda perl-io-tty 1.12 pl526_1 bioconda perl-io-zlib 1.10 pl526_2 bioconda perl-ipc-run 20180523.0 pl526_0 bioconda perl-ipc-sharelite 0.17 pl526h2d50403_0 bioconda perl-jcode 2.07 pl526_2 bioconda perl-json 4.00 pl526_0 bioconda perl-json-xs 2.34 pl526h2d50403_2 bioconda perl-lib 0.63 pl526_1 bioconda perl-libwww-perl 6.36 pl526_1 bioconda perl-libxml-perl 0.08 pl526_2 bioconda perl-list-moreutils 0.428 pl526_1 bioconda perl-list-moreutils-xs 0.428 pl526_0 bioconda perl-log-log4perl 1.49 pl526_0 bioconda perl-lwp-mediatypes 6.02 pl526_3 bioconda perl-lwp-protocol-https 6.07 pl526_4 bioconda perl-lwp-simple 6.15 pl526h470a237_4 bioconda perl-mailtools 2.20 pl526_0 bioconda perl-math-cdf 0.1 pl526h470a237_4 bioconda perl-math-derivative 1.01 pl526_0 bioconda perl-math-random 0.72 pl526_1 bioconda perl-math-spline 0.02 pl526_2 bioconda perl-mime-base64 3.15 pl526_1 bioconda perl-mime-lite 3.030 pl526_1 bioconda perl-mime-tools 5.508 pl526_1 bioconda perl-mime-types 2.17 pl526_0 bioconda perl-mldbm 2.05 pl526_1 bioconda perl-module-implementation 0.09 pl526_2 bioconda perl-module-pluggable 5.2 pl526_0 bioconda perl-module-runtime 0.016 pl526_0 bioconda perl-module-runtime-conflicts 0.003 pl526_0 bioconda perl-moo 2.003004 pl526_0 bioconda perl-moose 2.2011 pl526h2d50403_0 bioconda perl-mozilla-ca 20180117 pl526_0 bioconda perl-mro-compat 0.13 pl526_0 bioconda perl-net-http 6.18 pl526_0 bioconda perl-net-ssleay 1.74 1 bioconda perl-ntlm 1.09 pl526_4 bioconda perl-number-compare 0.03 pl526_2 bioconda perl-ole-storage_lite 0.19 pl526_3 bioconda perl-package-deprecationmanager 0.17 pl526_0 bioconda perl-package-stash 0.38 pl526h0a44026_1 bioconda perl-package-stash-xs 0.28 pl526hfc679d8_0 bioconda perl-params-util 1.07 pl526h2d50403_3 bioconda perl-parent 0.236 pl526_1 bioconda perl-parse-recdescent 1.967015 pl526_0 bioconda perl-parse-yapp 1.21 pl526_0 bioconda perl-pathtools 3.73 pl526h470a237_2 bioconda perl-pdf-api2 2.033 pl526_0 bioconda perl-perlio-utf8_strict 0.007 pl526h2d50403_0 bioconda perl-pod-escapes 1.07 pl526_1 bioconda perl-pod-usage 1.69 pl526_1 bioconda perl-postscript 0.06 pl526_2 bioconda perl-role-tiny 2.000006 pl526_0 bioconda perl-scalar-list-utils 1.45 pl526h1de35cc_4 bioconda perl-scope-guard 0.21 pl526_2 bioconda perl-set-scalar 1.29 pl526_2 bioconda perl-soap-lite 1.19 pl526_1 bioconda perl-socket 2.027 pl526_1 bioconda perl-sort-naturally 1.03 pl526_2 bioconda perl-spreadsheet-parseexcel 0.65 pl526_2 bioconda perl-spreadsheet-writeexcel 2.40 pl526_2 bioconda perl-statistics-descriptive 3.0702 pl526_0 bioconda perl-storable 3.11 pl526_0 bioconda perl-sub-exporter 0.987 pl526_2 bioconda perl-sub-exporter-progressive 0.001013 pl526_0 bioconda perl-sub-identify 0.12 pl526_1 bioconda perl-sub-info 0.002 pl526_0 bioconda perl-sub-install 0.928 pl526_2 bioconda perl-sub-name 0.21 pl526_1 bioconda perl-sub-quote 2.005001 pl526_0 bioconda perl-sub-uplevel 0.2800 pl526h470a237_0 bioconda perl-svg 2.84 pl526_0 bioconda perl-svg-graph 0.02 pl526_3 bioconda perl-task-weaken 1.06 pl526_0 bioconda perl-template-toolkit 2.26 pl526_1 bioconda perl-term-table 0.013 pl526_0 bioconda perl-test 1.26 pl526_1 bioconda perl-test-builder-tester 1.23_002 pl526_1 bioconda perl-test-deep 1.128 pl526_1 bioconda perl-test-differences 0.64 pl526_2 bioconda perl-test-exception 0.43 pl526_2 bioconda perl-test-files 0.14 pl526_2 bioconda perl-test-harness 3.42 pl526_0 bioconda perl-test-leaktrace 0.16 pl526_1 bioconda perl-test-more 1.001002 pl526_1 bioconda perl-test-most 0.35 pl526_0 bioconda perl-test-output 1.031 pl526_0 bioconda perl-test-requiresinternet 0.05 pl526_0 bioconda perl-test-warn 0.36 pl526_1 bioconda perl-test2-suite 0.000117 pl526_0 bioconda perl-text-csv 1.99 pl526_0 bioconda perl-text-diff 1.45 pl526_0 bioconda perl-text-glob 0.11 pl526_1 bioconda perl-threaded 5.22.0 10 bioconda perl-tie-ixhash 1.23 pl526_2 bioconda perl-time-hires 1.9758 pl526_0 bioconda perl-time-local 1.28 pl526_1 bioconda perl-timedate 2.30 pl526_1 bioconda perl-tree-dag_node 1.31 pl526_0 bioconda perl-try-tiny 0.30 pl526_1 bioconda perl-type-tiny 1.004004 pl526_0 bioconda perl-types-serialiser 1.0 pl526_2 bioconda perl-unicode-map 0.112 pl526h2d50403_2 bioconda perl-uri 1.76 pl526_0 bioconda perl-www-robotrules 6.02 pl526_3 bioconda perl-xml-dom 1.46 pl526_0 bioconda perl-xml-dom-xpath 0.14 pl526_1 bioconda perl-xml-filter-buffertext 1.01 pl526_2 bioconda perl-xml-libxml 2.0132 pl526hbc14f71_0 bioconda perl-xml-libxslt 1.94 pl526_1 bioconda perl-xml-namespacesupport 1.12 pl526_0 bioconda perl-xml-parser 2.44 pl526h3a4f0e9_6 bioconda perl-xml-regexp 0.04 pl526_2 bioconda perl-xml-sax 1.00 pl526_0 bioconda perl-xml-sax-base 1.09 pl526_0 bioconda perl-xml-sax-expat 0.51 pl526_3 bioconda perl-xml-sax-writer 0.57 pl526_0 bioconda perl-xml-simple 2.25 pl526_1 bioconda perl-xml-twig 3.52 pl526_2 bioconda perl-xml-writer 0.625 pl526_2 bioconda perl-xml-xpath 1.44 pl526_0 bioconda perl-xml-xpathengine 0.14 pl526_2 bioconda perl-xsloader 0.24 pl526_0 bioconda perl-yaml 1.27 pl526_0 bioconda pip 19.0.3 py37_0 conda-forge prank v.170427 h04f5b5a_2 bioconda prodigal 2.6.3 1 bioconda prokka 1.11 0 bioconda py-boost 1.67.0 py37h6440ff4_4
pycosat 0.6.3 py37h1de35cc_1001 conda-forge pycparser 2.19 py37_1 conda-forge pyopenssl 19.0.0 py37_0 conda-forge pysocks 1.6.8 py37_1002 conda-forge python 3.7.1 hbdd33cc_1003 conda-forge python.app 1.2 py37h1de35cc_1200 conda-forge readline 7.0 hcfe32e1_1001 conda-forge requests 2.21.0 py37_1000 conda-forge roary 3.12.0 pl526h470a237_1 bioconda ruamel_yaml 0.15.71 py37h1de35cc_1000 conda-forge setuptools 40.8.0 py37_0 conda-forge six 1.12.0 py37_1000 conda-forge sqlite 3.26.0 h1765d9f_1001 conda-forge tbl2asn 25.6 3 bioconda tidyp 1.04 1 bioconda tk 8.6.9 ha441bb4_1000 conda-forge urllib3 1.24.1 py37_1000 conda-forge wheel 0.33.1 py37_0 conda-forge xz 5.2.4 h1de35cc_1001 conda-forge yaml 0.1.7 h1de35cc_1001 conda-forge zlib 1.2.11 h1de35cc_1004 conda-forge zstd 1.3.3 1 conda-forge

Do you have any help? Thanks in advance Benoit.

beudes avatar Mar 14 '19 14:03 beudes

Try: cpanm -f Bio::Roary

dadahan avatar Apr 16 '19 01:04 dadahan

Thanks for your help. I haven't tried the solution since complete uninstallation of miniconda3 and reinstall solved the problem

beudes avatar Apr 16 '19 09:04 beudes

Hi, had the same error as @beudes, was inside a conda environment specifically made for roary, I can confirm that manually reinstalling Bio::Roary using cpanm fixes this.

On my cluster I also had to run module load gcc/7.2.0 and module load libxml2 as some of the required packages depended on XML and a newer gcc. I guess this closes the issue?

philippbayer avatar Jul 08 '19 04:07 philippbayer

@dadahan solution worked for me

wdwvt1 avatar Aug 14 '19 20:08 wdwvt1

@philippbayer I am told by @slugger70 that libxml2 is some conda bug right now!

tseemann avatar Aug 16 '19 03:08 tseemann

This still seems to be an issue, building in a Docker image (ubuntu:xenial).

Installing via: conda install -c bioconda roary

@dadahan 's solution not working in this case.

jambler24 avatar Jun 12 '20 13:06 jambler24

I just had this too (it started after I interrupted roary with Ctrl-C, don't know if that is the cause as it was working prior). The cpanm -f Bio::Roary fix didn't work for me. However @tseemann 's first suggestion for troubleshooting conda problems (https://twitter.com/torstenseemann/status/1173103270899830784?s=20) did:

conda update --all

JamesZlosnik avatar Jul 21 '20 12:07 JamesZlosnik

try: conda activate prokka_roary then: roary -h

TTL928 avatar Jul 23 '21 03:07 TTL928

Try: cpanm -f Bio::Roary

Hello, dadahan! The cpanm -f Bio::Roary fix didn't work for me. It reported the same error. Could you help me?

cylcheyanlin avatar Nov 30 '21 05:11 cylcheyanlin

Hi, I had the same error. It seems like the prokka's issue 519 and the same solution worked for me. prokka Issue 519: Issue after conda install: Can't locate Bio/Root/Version.pm in @INC (you may need to install the Bio::Root::Version module)

conda create --no-channel-priority -c conda-forge -c bioconda -n roary roary

conda activate roary
roary --version
Use of uninitialized value in require at /opt/miniconda3/envs/roary/lib/site_perl/5.26.2/darwin-thread-multi-2level/Encode.pm line 61.
3.13.0

noanoa07 avatar Dec 20 '21 01:12 noanoa07

Apparently, you cannot install prokka and roary in the same environment at the moment. Try installing them in separate environments instead.

sorenwacker avatar Dec 20 '21 21:12 sorenwacker

Try: cpanm -f Bio::Roary

Hi, Ph.D. dadahan. I got the same issue and try to run what you suggested. Sadly, installing DB_File failed and some dependencies. Could you help me? Thank you very much.

cylcheyanlin avatar Apr 01 '22 08:04 cylcheyanlin

Try: cpanm -f Bio::Roary

In my case this didn't work, but as it seemed to be a PERL issue, using: export PERL5LIB=$CONDA_PREFIX/lib/perl5/site_perl/5.22.0/ fixed the problem

DiegoBarMor avatar Apr 05 '22 08:04 DiegoBarMor

Hi there once installed i had this error

Can't locate Bio/Roary/CommandLine/Roary.pm in @INC (you may need to install the Bio::Roary::CommandLine::Roary module) (@INC contains: /home/administrator/lib /home/administrator/miniconda3/lib/perl5/5.32/site_perl /home/administrator/miniconda3/lib/perl5/site_perl /home/administrator/miniconda3/lib/perl5/5.32/vendor_perl /home/administrator/miniconda3/lib/perl5/vendor_perl /home/administrator/miniconda3/lib/perl5/5.32/core_perl /home/administrator/miniconda3/lib/perl5/core_perl .) at /home/administrator/miniconda3/bin/roary line 12. BEGIN failed--compilation aborted at /home/administrator/miniconda3/bin/roary line 12.

I try to follow the discussions and suggestions but still not working

ilarioferrocino avatar Apr 12 '22 14:04 ilarioferrocino

I installed the roary by using below command as suggested by @ DiegoBarqueroMorera

conda install -c bioconda roary
export PERL5LIB=$CONDA_PREFIX/lib/perl5/site_perl/5.22.0/

ZJLEOWANG3 avatar Oct 08 '22 02:10 ZJLEOWANG3