Re: [Transdecoder-users] make fails

[<Ale...@cs...>]

Thanks
ffindex is now static, pls do a svn update.

weird on cd-hit. default make should have been with openmp (-fopenmp). can you please try again?

if it is still happening... hmmm I have gcc 4.6.3 or 4.4.3 and it is ok. not sure what is going on, maybe someone with more engineering knowledge can help? ubuntu distributes cd-hit in a repo so i wonder what does apt-get build-dep say? is there a dependency missing from your system (i thought it had no dependencies)

a


________________________________
From: Matthew MacManes [mac...@gm...]
Sent: Saturday, 11 January 2014 5:18 AM
To: tra...@li...
Subject: [Transdecoder-users] make fails

List,

With ~/TransDecoder_r20131117, Ubuntu, gcc 4.7.3

2 things:

make test_ffindex fails: (the shared object libffindex.so.0.1 cannot be found)

make test_ffindex
cd sample_data && ./__runMe_use_pfam_MPI_ffindex.sh
-parsing cufflinks output: transcripts.gtf
-parsing genome fasta: test.genome.fasta
-done parsing genome.
// processing 7000000090838467
CMD: /home/macmanes/TransDecoder_r20131117/util/compute_base_probs.pl transcripts.fasta 0 > transdecoder.tmp.pfam/base_freqs.dat
CMD: /home/macmanes/TransDecoder_r20131117/util/seq_n_baseprobs_to_logliklihood_vals.pl transdecoder.tmp.pfam/longest_orfs.cds.top_500_longest transdecoder.tmp.pfam/base_freqs.dat > transdecoder.tmp.pfam/hexamer.scores
CMD: /home/macmanes/TransDecoder_r20131117/util/score_CDS_liklihood_all_6_frames.pl transdecoder.tmp.pfam/longest_orfs.cds transdecoder.tmp.pfam/hexamer.scores > transdecoder.tmp.pfam/longest_orfs.cds.scores
CMD: /home/macmanes/TransDecoder_r20131117/pfam_runner.pl --pep transdecoder.tmp.pfam/longest_orfs.pep --pfam_db /media/macmanes/hd2/imitator/pfam/Pfam-AB.hmm.bin --CPU 2 -o transcripts.fasta.transdecoder.pfam.dat  --MPI  --workdir transdecoder.tmp.pfam  --debug
Partitioning fasta file transdecoder.tmp.pfam/longest_orfs.pep
CMD: /home/macmanes/TransDecoder_r20131117/util/bin/ffindex_from_fasta -s transdecoder.tmp.pfam/partition.0.fa.db transdecoder.tmp.pfam/partition.0.fa.db.idx transdecoder.tmp.pfam/partition.0.fa
/home/macmanes/TransDecoder_r20131117/util/bin/ffindex_from_fasta: error while loading shared libraries: libffindex.so.0.1: cannot open shared object file: No such file or directory
Error, cmd: /home/macmanes/TransDecoder_r20131117/util/bin/ffindex_from_fasta -s transdecoder.tmp.pfam/partition.0.fa.db transdecoder.tmp.pfam/partition.0.fa.db.idx transdecoder.tmp.pfam/partition.0.fa died with ret 32512 at /home/macmanes/TransDecoder_r20131117/pfam_runner.pl line 192.
Error, cmd: /home/macmanes/TransDecoder_r20131117/pfam_runner.pl --pep transdecoder.tmp.pfam/longest_orfs.pep --pfam_db /media/macmanes/hd2/imitator/pfam/Pfam-AB.hmm.bin --CPU 2 -o transcripts.fasta.transdecoder.pfam.dat  --MPI  --workdir transdecoder.tmp.pfam  --debug  died with ret 512 at ../TransDecoder line 493.
make: *** [test_ffindex] Error 2


libffindex.so.0.1 is in ffindex/lib64, but this is not in my path, not will it be in most users.


make fails on cd-hit:
g++ -O2 -DNO_OPENMP cdhit-common.c++ -c
cdhit-common.c++: In constructor ‘TempFile::TempFile(const char*)’:
cdhit-common.c++:68:34: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 3 has type ‘TempFile*’ [-Wformat]
cdhit-common.c++: In member function ‘size_t SequenceDB::MinimalMemory(int, int, int, const Options&)’:
cdhit-common.c++:2258:47: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘size_t {aka long unsigned int}’ [-Wformat]
cdhit-common.c++:2262:71: warning: format ‘%i’ expects argument of type ‘int’, but argument 4 has type ‘size_t {aka long unsigned int}’ [-Wformat]
cdhit-common.c++:2262:71: warning: format ‘%i’ expects argument of type ‘int’, but argument 5 has type ‘size_t {aka long unsigned int}’ [-Wformat]
cdhit-common.c++:2266:78: warning: format ‘%i’ expects argument of type ‘int’, but argument 4 has type ‘size_t {aka long unsigned int}’ [-Wformat]
cdhit-common.c++:2266:78: warning: format ‘%i’ expects argument of type ‘int’, but argument 5 has type ‘size_t {aka long unsigned int}’ [-Wformat]
cdhit-common.c++:2271:52: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘size_t {aka long unsigned int}’ [-Wformat]
cdhit-common.c++:2274:51: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘size_t {aka long unsigned int}’ [-Wformat]
cdhit-common.c++:2279:30: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘size_t {aka long unsigned int}’ [-Wformat]
cdhit-common.c++: In member function ‘void SequenceDB::DoClustering(int, const Options&)’:
cdhit-common.c++:2476:90: warning: format ‘%i’ expects argument of type ‘int’, but argument 2 has type ‘std::vector<Sequence*, std::allocator<Sequence*> >::size_type {aka long unsigned int}’ [-Wformat]
cdhit-common.c++:2487:65: warning: format ‘%i’ expects argument of type ‘int’, but argument 2 has type ‘size_t {aka long unsigned int}’ [-Wformat]
cdhit-common.c++: In member function ‘void SequenceDB::DoClustering(const Options&)’:
cdhit-common.c++:2994:65: warning: format ‘%i’ expects argument of type ‘int’, but argument 2 has type ‘size_t {aka long unsigned int}’ [-Wformat]
In file included from cdhit-common.c++:28:0:
cdhit-common.h: In instantiation of ‘void Vector<TYPE>::Append(const TYPE&) [with TYPE = NVector<long int>]’:
cdhit-common.c++:704:27:   required from here
cdhit-common.h:95:4: error: ‘push_back’ was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive]
cdhit-common.h:95:4: note: declarations in dependent base ‘std::vector<NVector<long int>, std::allocator<NVector<long int> > >’ are not found by unqualified lookup
cdhit-common.h:95:4: note: use ‘this->push_back’ instead
cdhit-common.h: In instantiation of ‘void Vector<TYPE>::Append(const TYPE&) [with TYPE = NVector<int>]’:
cdhit-common.c++:705:25:   required from here
cdhit-common.h:95:4: error: ‘push_back’ was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive]
cdhit-common.h:95:4: note: declarations in dependent base ‘std::vector<NVector<int>, std::allocator<NVector<int> > >’ are not found by unqualified lookup
cdhit-common.h:95:4: note: use ‘this->push_back’ instead
cdhit-common.h: In instantiation of ‘void Vector<TYPE>::Append(const TYPE&) [with TYPE = Sequence*]’:
cdhit-common.c++:1247:24:   required from here
cdhit-common.h:95:4: error: ‘push_back’ was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive]
cdhit-common.h:95:4: note: declarations in dependent base ‘std::vector<Sequence*, std::allocator<Sequence*> >’ are not found by unqualified lookup
cdhit-common.h:95:4: note: use ‘this->push_back’ instead
cdhit-common.h: In instantiation of ‘void Vector<TYPE>::Append(const TYPE&) [with TYPE = int]’:
cdhit-common.c++:1895:26:   required from here
cdhit-common.h:95:4: error: ‘push_back’ was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive]
cdhit-common.h:95:4: note: declarations in dependent base ‘std::vector<int, std::allocator<int> >’ are not found by unqualified lookup
cdhit-common.h:95:4: note: use ‘this->push_back’ instead
make: *** [cdhit-common.o] Error 1

Thanks, Matt

_____________________________________
Matthew MacManes, Ph.D.
University of New Hampshire  I  Assistant Professor
Department of Molecular, Cellular, & Biomedical Sciences
Durham, NH  03824
Phone: 603-862-4052  I  Twitter: @PeroMHC<https://twitter.com/PeroMHC>
Web: genomebio.org<http://genomebio.org/>
Office: 189 Rudman Hall
Laboratory: 145 Rudman Hall