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Sequence alignment on Hadoop
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Perl syntax check fails for almost every file in the lib package #71

Open magicDGS opened 6 years ago

magicDGS commented 6 years ago

Running perl -c in each of the lib packages, only ReadToolsUtils and Utility passes the checks:

Can't locate Utility.pm in @INC (you may need to install the Utility module) (@INC contains: /Users/daniel/workspaces/distmap_robmaz/lib/perl5/site_perl/../lib/perl5/site_perl /usr/local/Cellar/perl/5.26.1/lib/perl5/site_perl/5.26.1/darwin-thread-multi-2level /usr/local/Cellar/perl/5.26.1/lib/perl5/site_perl/5.26.1 /usr/local/Cellar/perl/5.26.1/lib/perl5/5.26.1/darwin-thread-multi-2level /usr/local/Cellar/perl/5.26.1/lib/perl5/5.26.1 /usr/local/lib/perl5/site_perl/5.26.1/darwin-thread-multi-2level /usr/local/lib/perl5/site_perl/5.26.1) at lib/perl5/site_perl/DataCleanup.pm line 7.
BEGIN failed--compilation aborted at lib/perl5/site_perl/DataCleanup.pm line 7.
Can't locate Utility.pm in @INC (you may need to install the Utility module) (@INC contains: /Users/daniel/workspaces/distmap_robmaz/lib/perl5/site_perl/../lib/perl5/site_perl /usr/local/Cellar/perl/5.26.1/lib/perl5/site_perl/5.26.1/darwin-thread-multi-2level /usr/local/Cellar/perl/5.26.1/lib/perl5/site_perl/5.26.1 /usr/local/Cellar/perl/5.26.1/lib/perl5/5.26.1/darwin-thread-multi-2level /usr/local/Cellar/perl/5.26.1/lib/perl5/5.26.1 /usr/local/lib/perl5/site_perl/5.26.1/darwin-thread-multi-2level /usr/local/lib/perl5/site_perl/5.26.1) at lib/perl5/site_perl/DataDownload.pm line 7.
BEGIN failed--compilation aborted at lib/perl5/site_perl/DataDownload.pm line 7.
Can't locate Utility.pm in @INC (you may need to install the Utility module) (@INC contains: /Users/daniel/workspaces/distmap_robmaz/lib/perl5/site_perl/../lib/perl5/site_perl /usr/local/Cellar/perl/5.26.1/lib/perl5/site_perl/5.26.1/darwin-thread-multi-2level /usr/local/Cellar/perl/5.26.1/lib/perl5/site_perl/5.26.1 /usr/local/Cellar/perl/5.26.1/lib/perl5/5.26.1/darwin-thread-multi-2level /usr/local/Cellar/perl/5.26.1/lib/perl5/5.26.1 /usr/local/lib/perl5/site_perl/5.26.1/darwin-thread-multi-2level /usr/local/lib/perl5/site_perl/5.26.1) at lib/perl5/site_perl/DataDownloadAndMerge.pm line 8.
BEGIN failed--compilation aborted at lib/perl5/site_perl/DataDownloadAndMerge.pm line 8.
Can't locate Utility.pm in @INC (you may need to install the Utility module) (@INC contains: /Users/daniel/workspaces/distmap_robmaz/lib/perl5/site_perl/../lib/perl5/site_perl /usr/local/Cellar/perl/5.26.1/lib/perl5/site_perl/5.26.1/darwin-thread-multi-2level /usr/local/Cellar/perl/5.26.1/lib/perl5/site_perl/5.26.1 /usr/local/Cellar/perl/5.26.1/lib/perl5/5.26.1/darwin-thread-multi-2level /usr/local/Cellar/perl/5.26.1/lib/perl5/5.26.1 /usr/local/lib/perl5/site_perl/5.26.1/darwin-thread-multi-2level /usr/local/lib/perl5/site_perl/5.26.1) at lib/perl5/site_perl/DataMerge.pm line 7.
BEGIN failed--compilation aborted at lib/perl5/site_perl/DataMerge.pm line 7.
Can't locate Utility.pm in @INC (you may need to install the Utility module) (@INC contains: /Users/daniel/workspaces/distmap_robmaz/lib/perl5/site_perl/../lib/perl5/site_perl /usr/local/Cellar/perl/5.26.1/lib/perl5/site_perl/5.26.1/darwin-thread-multi-2level /usr/local/Cellar/perl/5.26.1/lib/perl5/site_perl/5.26.1 /usr/local/Cellar/perl/5.26.1/lib/perl5/5.26.1/darwin-thread-multi-2level /usr/local/Cellar/perl/5.26.1/lib/perl5/5.26.1 /usr/local/lib/perl5/site_perl/5.26.1/darwin-thread-multi-2level /usr/local/lib/perl5/site_perl/5.26.1) at lib/perl5/site_perl/DataProcess.pm line 14.
BEGIN failed--compilation aborted at lib/perl5/site_perl/DataProcess.pm line 14.
Can't locate Utility.pm in @INC (you may need to install the Utility module) (@INC contains: /Users/daniel/workspaces/distmap_robmaz/lib/perl5/site_perl/../lib/perl5/site_perl /usr/local/Cellar/perl/5.26.1/lib/perl5/site_perl/5.26.1/darwin-thread-multi-2level /usr/local/Cellar/perl/5.26.1/lib/perl5/site_perl/5.26.1 /usr/local/Cellar/perl/5.26.1/lib/perl5/5.26.1/darwin-thread-multi-2level /usr/local/Cellar/perl/5.26.1/lib/perl5/5.26.1 /usr/local/lib/perl5/site_perl/5.26.1/darwin-thread-multi-2level /usr/local/lib/perl5/site_perl/5.26.1) at lib/perl5/site_perl/DataUpload.pm line 7.
BEGIN failed--compilation aborted at lib/perl5/site_perl/DataUpload.pm line 7.
Can't locate Utility.pm in @INC (you may need to install the Utility module) (@INC contains: /Users/daniel/workspaces/distmap_robmaz/lib/perl5/site_perl/../lib/perl5/site_perl /usr/local/Cellar/perl/5.26.1/lib/perl5/site_perl/5.26.1/darwin-thread-multi-2level /usr/local/Cellar/perl/5.26.1/lib/perl5/site_perl/5.26.1 /usr/local/Cellar/perl/5.26.1/lib/perl5/5.26.1/darwin-thread-multi-2level /usr/local/Cellar/perl/5.26.1/lib/perl5/5.26.1 /usr/local/lib/perl5/site_perl/5.26.1/darwin-thread-multi-2level /usr/local/lib/perl5/site_perl/5.26.1) at lib/perl5/site_perl/DownloadTrimmedRead.pm line 12.
BEGIN failed--compilation aborted at lib/perl5/site_perl/DownloadTrimmedRead.pm line 12.
Can't locate Utility.pm in @INC (you may need to install the Utility module) (@INC contains: /Users/daniel/workspaces/distmap_robmaz/lib/perl5/site_perl/../lib/perl5/site_perl /usr/local/Cellar/perl/5.26.1/lib/perl5/site_perl/5.26.1/darwin-thread-multi-2level /usr/local/Cellar/perl/5.26.1/lib/perl5/site_perl/5.26.1 /usr/local/Cellar/perl/5.26.1/lib/perl5/5.26.1/darwin-thread-multi-2level /usr/local/Cellar/perl/5.26.1/lib/perl5/5.26.1 /usr/local/lib/perl5/site_perl/5.26.1/darwin-thread-multi-2level /usr/local/lib/perl5/site_perl/5.26.1) at lib/perl5/site_perl/GenomeIndex.pm line 11.
BEGIN failed--compilation aborted at lib/perl5/site_perl/GenomeIndex.pm line 11.
Can't locate Utility.pm in @INC (you may need to install the Utility module) (@INC contains: /Users/daniel/workspaces/distmap_robmaz/lib/perl5/site_perl/../lib/perl5/site_perl /usr/local/Cellar/perl/5.26.1/lib/perl5/site_perl/5.26.1/darwin-thread-multi-2level /usr/local/Cellar/perl/5.26.1/lib/perl5/site_perl/5.26.1 /usr/local/Cellar/perl/5.26.1/lib/perl5/5.26.1/darwin-thread-multi-2level /usr/local/Cellar/perl/5.26.1/lib/perl5/5.26.1 /usr/local/lib/perl5/site_perl/5.26.1/darwin-thread-multi-2level /usr/local/lib/perl5/site_perl/5.26.1) at lib/perl5/site_perl/HadoopMapping.pm line 10.
BEGIN failed--compilation aborted at lib/perl5/site_perl/HadoopMapping.pm line 10.
Can't locate Utility.pm in @INC (you may need to install the Utility module) (@INC contains: /Users/daniel/workspaces/distmap_robmaz/lib/perl5/site_perl/../lib/perl5/site_perl /usr/local/Cellar/perl/5.26.1/lib/perl5/site_perl/5.26.1/darwin-thread-multi-2level /usr/local/Cellar/perl/5.26.1/lib/perl5/site_perl/5.26.1 /usr/local/Cellar/perl/5.26.1/lib/perl5/5.26.1/darwin-thread-multi-2level /usr/local/Cellar/perl/5.26.1/lib/perl5/5.26.1 /usr/local/lib/perl5/site_perl/5.26.1/darwin-thread-multi-2level /usr/local/lib/perl5/site_perl/5.26.1) at lib/perl5/site_perl/HadoopTrimming.pm line 10.
BEGIN failed--compilation aborted at lib/perl5/site_perl/HadoopTrimming.pm line 10.
lib/perl5/site_perl/ReadToolsUtils.pm syntax OK
Can't locate Utility.pm in @INC (you may need to install the Utility module) (@INC contains: /Users/daniel/workspaces/distmap_robmaz/lib/perl5/site_perl/../lib/perl5/site_perl /usr/local/Cellar/perl/5.26.1/lib/perl5/site_perl/5.26.1/darwin-thread-multi-2level /usr/local/Cellar/perl/5.26.1/lib/perl5/site_perl/5.26.1 /usr/local/Cellar/perl/5.26.1/lib/perl5/5.26.1/darwin-thread-multi-2level /usr/local/Cellar/perl/5.26.1/lib/perl5/5.26.1 /usr/local/lib/perl5/site_perl/5.26.1/darwin-thread-multi-2level /usr/local/lib/perl5/site_perl/5.26.1) at lib/perl5/site_perl/TrimDataMerge.pm line 7.
BEGIN failed--compilation aborted at lib/perl5/site_perl/TrimDataMerge.pm line 7.
lib/perl5/site_perl/Utility.pm syntax OK