Question: Repeatmasker, Can't locate Text/Soundex.pm
1
gravatar for qwzhang0601
2.2 years ago by
qwzhang060160
United States
qwzhang060160 wrote:

Hello:

I have RepeatMasker seems correctly, because it shows "Congratulations! RepeatMasker is now ready to use." (as shown below). But when I run it it reports "Can't locate Text/Soundex.pm...". Then I instill the module by "cpan Text::Soundex", and by the end it tells me "Text::Soundex is up to date (3.05)." It seems the module is already installed, but RepeatMasker still has the same problem, and I can not find where the "Text/Soundex.pm" was installed.

Do you have any suggestions! Many thanks

Congratulations!  RepeatMasker is now ready to use.
The program is installed with a the following repeat libraries:
  Dfam database version Dfam_2.0
  RepeatMasker Combined Database: Dfam_Consensus-20170127
Further documentation on the program may be found here:
  /Users/qwzhang/Documents/tools/RepeatMasker4.0.7/repeatmasker.help

[]$ ./RepeatMasker
Can't locate Text/Soundex.pm in @INC (you may need to install the Text::Soundex module) (@INC contains: /Users/qwzhang/Documents/tools/RepeatMasker4.0.7 /sw/lib/perl5 /sw/lib/perl5/darwin /Users/qwzhang/Documents/tools/vcftools_0.1.13/perl /Users/qwzhang/localperl/lib/site_perl/5.26.0/darwin-thread-multi-2level /Users/qwzhang/localperl/lib/site_perl/5.26.0 /Users/qwzhang/localperl/lib/5.26.0/darwin-thread-multi-2level /Users/qwzhang/localperl/lib/5.26.0 /Users/qwzhang/localperl/lib/site_perl/5.24.0 /Users/qwzhang/localperl/lib/site_perl) at /Users/qwzhang/Documents/tools/RepeatMasker4.0.7/Taxonomy.pm line 83.
BEGIN failed--compilation aborted at /Users/qwzhang/Documents/tools/RepeatMasker4.0.7/Taxonomy.pm line 83.
Compilation failed in require at ./RepeatMasker line 313.
BEGIN failed--compilation aborted at ./RepeatMasker line 313.
zdz-mbp-2012:RepeatMasker4.0.7 qwzhang$ ./RepeatMasker -v
Can't locate Text/Soundex.pm in @INC (you may need to install the Text::Soundex module) (@INC contains: /Users/qwzhang/Documents/tools/RepeatMasker4.0.7 /sw/lib/perl5 /sw/lib/perl5/darwin /Users/qwzhang/Documents/tools/vcftools_0.1.13/perl /Users/qwzhang/localperl/lib/site_perl/5.26.0/darwin-thread-multi-2level /Users/qwzhang/localperl/lib/site_perl/5.26.0 /Users/qwzhang/localperl/lib/5.26.0/darwin-thread-multi-2level /Users/qwzhang/localperl/lib/5.26.0 /Users/qwzhang/localperl/lib/site_perl/5.24.0 /Users/qwzhang/localperl/lib/site_perl) at /Users/qwzhang/Documents/tools/RepeatMasker4.0.7/Taxonomy.pm line 83.
BEGIN failed--compilation aborted at /Users/qwzhang/Documents/tools/RepeatMasker4.0.7/Taxonomy.pm line 83.
Compilation failed in require at ./RepeatMasker line 313.
BEGIN failed--compilation aborted at ./RepeatMasker line 313.

install Text::Soundex
[]$ cpan Text::Soundex
Loading internal null logger. Install Log::Log4perl for logging messages
CPAN: Storable loaded ok (v2.51)
Reading '/Users/qwzhang/.cpan/Metadata'
  Database was generated on Mon, 31 Jul 2017 07:17:02 GMT
CPAN: LWP::UserAgent loaded ok (v6.16)
CPAN: Time::HiRes loaded ok (v1.9719)
Fetching with LWP:
ftp://mirror.jre655.com/CPAN/authors/01mailrc.txt.gz
CPAN: YAML loaded ok (v1.21)
Reading '/Users/qwzhang/.cpan/sources/authors/01mailrc.txt.gz'
CPAN: Compress::Zlib loaded ok (v2.07)
....DONE
Fetching with LWP:
ftp://mirror.jre655.com/CPAN/modules/02packages.details.txt.gz
Reading '/Users/qwzhang/.cpan/sources/modules/02packages.details.txt.gz'
  Database was generated on Wed, 16 Aug 2017 08:41:02 GMT
  New CPAN.pm version (v2.16) available.
  [Currently running version is v2.14]
  You might want to try
    install CPAN
    reload cpan
  to both upgrade CPAN.pm and run the new version without leaving
  the current session.


...DONE
Fetching with LWP:
ftp://mirror.jre655.com/CPAN/modules/03modlist.data.gz
Reading '/Users/qwzhang/.cpan/sources/modules/03modlist.data.gz'
DONE
Writing /Users/qwzhang/.cpan/Metadata
CPAN: Module::CoreList loaded ok (v2.50)
Text::Soundex is up to date (3.05).
repeatmasker • 3.9k views
ADD COMMENTlink modified 8 months ago by virginia.s.markham50 • written 2.2 years ago by qwzhang060160

Have you tried installing repeatmasker using a simple package manager such as homebrew? brew install homebrew/science/repeatmasker works quite well on OSX for me

ADD REPLYlink written 2.2 years ago by cmdcolin1.2k

No. But I just tried it and it reports errors. Thanks

[] $ brew install homebrew/science/repeatmasker ==> Installing repeatmasker from homebrew/science Error: Formulae found in multiple taps: * homebrew/science/hmmer * nextgenusfs/science/hmmer

ADD REPLYlink written 2.2 years ago by qwzhang060160
3
gravatar for miya
2.1 years ago by
miya30
miya30 wrote:

Hello! I have same problem and decide these next decisions:

sudo cpan Text::Soundex

enjoy!

ADD COMMENTlink written 2.1 years ago by miya30
2
gravatar for virginia.s.markham
8 months ago by
virginia.s.markham50 wrote:

I know this is an old thread, but I'll post my answer here in case it helps others. I was having the same problem. I think perl is failing to find the module. First, if you have multiple perl installations, make sure you know which version you're using with which perl. Use perl -E 'say for @INC' to identify where perl is looking for the Text::Soundex module. Installing the module in that location should fix the problem. Alternatively, since I work on a big server and I don't have root privileges, I just installed the module in my home directory (~/perl5/lib/perl5/x86_64-linux-thread-multi/Text/Soundex.pm). Then I did: PERL5LIB=~/perl5/lib/perl5/x86_64-linux-thread-multi/:$PERL5LIB to add my own installation to the top of my perl lib path.

ADD COMMENTlink written 8 months ago by virginia.s.markham50

It depends on your version of Perl I guess, but perl -E 'say for @INC' didn't work for me. I used perl -e "print for @INC" instead.

ADD REPLYlink written 10 weeks ago by jerflynn0
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