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Re: [Transdecoder-users] make fails
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From: Matthew M. <mac...@gm...> - 2014-01-11 12:54:27
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Alexie, There is indeed a documented issue with ‘new’ versions of gcc: https://code.google.com/p/cdhit/issues/detail?id=12 A newer version will work: curl -L https://cdhit.googlecode.com/files/cd-hit-v4.6.1-2012-08-27.tgz > cd-hit-v4.6.1-2012-08-27.tgz Same make instructions. I’m happy to update the Transdecoder makefile if you give me write access. 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 Web: genomebio.org Office: 189 Rudman Hall Laboratory: 145 Rudman Hall On Jan 11, 2014, at 12:25 AM, Ale...@cs... wrote: > 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 > Web: genomebio.org > Office: 189 Rudman Hall > Laboratory: 145 Rudman Hall > |
