[Transdecoder-users] make fails
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[Transdecoder-users] make fails
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From: Matthew M. <mac...@gm...> - 2014-01-10 18:18:18
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<div style="font-family: Avenir;"><span style="font-family: Avenir;">List,
<br><br>With ~/TransDecoder_r20131117, Ubuntu, gcc 4.7.3<br><br>2
things:<br><br>make test_ffindex fails: (the shared object <span
style="font-weight: bold;">libffindex.so.0.1</span> cannot be found)<br><br>make
test_ffindex<br>cd sample_data &&
./__runMe_use_pfam_MPI_ffindex.sh<br>-parsing cufflinks output:
transcripts.gtf<br>-parsing genome fasta: test.genome.fasta<br>-done
parsing genome.<br>// processing 7000000090838467<br>CMD:
/home/macmanes/TransDecoder_r20131117/util/compute_base_probs.pl
transcripts.fasta 0 > transdecoder.tmp.pfam/base_freqs.dat<br>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<br>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<br>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<br>Partitioning fasta file
transdecoder.tmp.pfam/longest_orfs.pep<br>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<br><span style="text-decoration:
underline; color: rgb(255, 0, 0);">/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</span><br>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.<br>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.<br>make: *** [test_ffindex] Error 2<br><br><br>libffindex.so.0.1
is in ffindex/lib64, but this is not in my path, not will it be in most
users. <br><br><br><span style="font-weight: bold;">make fails on
cd-hit:</span><br>g++ -O2 -DNO_OPENMP cdhit-common.c++ -c<br>cdhit-common.c++:
In constructor ‘TempFile::TempFile(const char*)’:<br>cdhit-common.c++:68:34:
warning: format ‘%x’ expects argument of type ‘unsigned int’, but
argument 3 has type ‘TempFile*’ [-Wformat]<br>cdhit-common.c++: In
member function ‘size_t SequenceDB::MinimalMemory(int, int, int, const
Options&)’:<br>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]<br>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]<br>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]<br>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]<br>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]<br>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]<br>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]<br>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]<br>cdhit-common.c++:
In member function ‘void SequenceDB::DoClustering(int, const
Options&)’:<br>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]<br>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]<br>cdhit-common.c++:
In member function ‘void SequenceDB::DoClustering(const Options&)’:<br>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]<br>In file included
from cdhit-common.c++:28:0:<br>cdhit-common.h: In instantiation of ‘void
Vector<TYPE>::Append(const TYPE&) [with TYPE =
NVector<long int>]’:<br>cdhit-common.c++:704:27: required from
here<br>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]<br>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<br>cdhit-common.h:95:4: note: use
‘this->push_back’ instead<br>cdhit-common.h: In instantiation of
‘void Vector<TYPE>::Append(const TYPE&) [with TYPE =
NVector<int>]’:<br>cdhit-common.c++:705:25: required from here<br>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]<br>cdhit-common.h:95:4: note: declarations in dependent
base ‘std::vector<NVector<int>,
std::allocator<NVector<int> > >’ are not found by
unqualified lookup<br>cdhit-common.h:95:4: note: use
‘this->push_back’ instead<br>cdhit-common.h: In instantiation of
‘void Vector<TYPE>::Append(const TYPE&) [with TYPE =
Sequence*]’:<br>cdhit-common.c++:1247:24: required from here<br>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]<br>cdhit-common.h:95:4: note: declarations in dependent
base ‘std::vector<Sequence*, std::allocator<Sequence*> >’
are not found by unqualified lookup<br>cdhit-common.h:95:4: note: use
‘this->push_back’ instead<br>cdhit-common.h: In instantiation of
‘void Vector<TYPE>::Append(const TYPE&) [with TYPE = int]’:<br>cdhit-common.c++:1895:26:
required from here<br>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]<br>cdhit-common.h:95:4:
note: declarations in dependent base ‘std::vector<int,
std::allocator<int> >’ are not found by unqualified lookup<br>cdhit-common.h:95:4:
note: use ‘this->push_back’ instead<br>make: *** [cdhit-common.o]
Error 1<br><br></span>Thanks, Matt<br><div class="moz-signature"><br><span
style="font-family: Avenir;">_____________________________________<br>
Matthew MacManes, Ph.D. <br>
University of New Hampshire I Assistant Professor<br>
Department of Molecular, Cellular, & Biomedical Sciences<br>
Durham, NH 03824<br>
Phone: 603-862-4052 I Twitter: <a href="https://twitter.com/PeroMHC">@PeroMHC</a><br>
Web: <a href="http://genomebio.org/">genomebio.org</a><br>
Office: 189 Rudman Hall<br>
Laboratory: 145 Rudman Hall<br>
<br>
</span></div></div>
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