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Old 01-22-2014, 06:05 PM   #1
bongbimit
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Location: Ha Noi

Join Date: Dec 2013
Posts: 29
Default help with trinity and jellyfish

Dear all,

When i using Trinity for rna-seq assembly, i setup jellyfish and have an error
Quote:
make all-am
make[1]: Entering directory `/home/huypham/Tools/denovotranscriptome/trinityrnaseq_r20131110/trinity-plugins/jellyfish-1.1.6'
CXX jellyfish/libjellyfish_la-square_binary_matrix.lo
CXX jellyfish/libjellyfish_la-err.lo
In file included from jellyfish/err.cc:17:0:
./jellyfish/err.hpp: In static member function 'static void err::no_t::write(std:stream&, int)':
./jellyfish/err.hpp:42:46: error: ignoring return value of 'char* strerror_r(int, char*, size_t)', declared with attribute warn_unused_result [-Werror=unused-result]
strerror_r(e, err_str, sizeof(err_str));
^
cc1plus: all warnings being treated as errors
make[1]: *** [jellyfish/libjellyfish_la-err.lo] Error 1
make[1]: Leaving directory `/home/huypham/Tools/denovotranscriptome/trinityrnaseq_r20131110/trinity-plugins/jellyfish-1.1.6'
make: *** [all] Error 2
which library i miss in ubuntu ?
thanks in advance
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Old 01-23-2014, 01:16 AM   #2
bongbimit
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Location: Ha Noi

Join Date: Dec 2013
Posts: 29
Default

sr all, i 've just fix this by re-setup of trinity and now i can make jellyfish 1.1.6 tks all for read
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Old 05-13-2015, 02:01 AM   #3
Lovro
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Location: Slovenia

Join Date: Mar 2015
Posts: 19
Default how have you fixed it ?

Hello,

I'm getting the same error when trying to "make" trinity v 2012-06-08 on ubuntu. I was wondering how did you solve the issue...

I'm trying to use this version with virusfinder2.0, since it doesn't seem to work for me with trinity versions 2.0.2 or 2.0.6 ... The latter versions, however, install ok and pass the "runME.sh" test, but don't work with virusfinder2.0.

help please!
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