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  • ensembl-gh-mirror
  • Bio-DB-HTS
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  • #82

Closed
Open
Created Feb 20, 2019 by Marek Szuba@mks

Problems when installing Bio::DB::HTS, possibly due to memory leak

Created by: AndreVidas

Hi Ensembl team.

I'm trying to install Bio::DB::HTS, but I get the following error during the installation:

sudo cpanm Bio::DB::HTS Password: --> Working on Bio::DB::HTS Fetching http://www.cpan.org/authors/id/A/AV/AVULLO/Bio-DB-HTS-2.11.tar.gz ... OK Configuring Bio-DB-HTS-2.11 ... OK

Broadcast Message from _distnote@SUND33194
(no tty) at 15:41 CET...

perl(90621,0x11b35c5c0) malloc: *** error for object 0x7fe849915dd0: pointer be ing realloc'd was not allocated
FAIL ! Installing Bio::DB::HTS failed. See /Users/gdn417/.cpanm/work/1550673676.90567/build.log for details. Retry with --force to force install it.

Broadcast Message from _distnote@SUND33194
(no tty) at 15:41 CET...

perl(90627,0x1103895c0) malloc: *** error for object 0x7fca65d00840: pointer be ing realloc'd was not allocated
SUND33194:bin gdn417$ cpan -D Bio Reading '/Users/gdn417/.cpan/Metadata' Database was generated on Tue, 19 Feb 2019 23:17:03 GMT Can't call method "userid" on an undefined value at /System/Library/Perl/5.18/App/Cpan.pm line 1146. SUND33194:bin gdn417$ cpan -D Bio/DB/HTS Reading '/Users/gdn417/.cpan/Metadata' Database was generated on Tue, 19 Feb 2019 23:17:03 GMT Can't call method "userid" on an undefined value at /System/Library/Perl/5.18/App/Cpan.pm line 1146. SUND33194:bin gdn417$ cpan -D Bio/DB/HTS.pm Reading '/Users/gdn417/.cpan/Metadata' Database was generated on Tue, 19 Feb 2019 23:17:03 GMT Can't call method "userid" on an undefined value at /System/Library/Perl/5.18/App/Cpan.pm line 1146. SUND33194:bin gdn417$ cpan -D HEJ Reading '/Users/gdn417/.cpan/Metadata' Database was generated on Tue, 19 Feb 2019 23:17:03 GMT Can't call method "userid" on an undefined value at /System/Library/Perl/5.18/App/Cpan.pm line 1146.

installedModules.txt

Do you have any idea of why this is happening? From what I could read from other posts on stackoverflow etc. this might have something to do with memory leak in C.

I have attached a list of my installed modules.

Best, André

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