Thread: [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>
</body>
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From: <Ale...@cs...> - 2014-01-11 05:25:48
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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
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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 > |
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From: <Ale...@cs...> - 2014-01-11 13:00:08
|
thank you. svn committed a ________________________________ From: Matthew MacManes [mac...@gm...] Sent: Saturday, 11 January 2014 11:54 PM To: Papanicolaou, Alexie (CES, Black Mountain) Cc: tra...@li... Subject: Re: [Transdecoder-users] make fails 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<https://twitter.com/PeroMHC> Web: genomebio.org<http://genomebio.org/> Office: 189 Rudman Hall Laboratory: 145 Rudman Hall On Jan 11, 2014, at 12:25 AM, Ale...@cs...<mailto: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...<mailto:mac...@gm...>] Sent: Saturday, 11 January 2014 5:18 AM To: tra...@li...<mailto: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 |
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From: <Ale...@cs...> - 2014-01-13 01:27:20
|
I assume this is working ok now. I'm making a new release now. p.s the ffindex issues were documented on the website but I guess most people don't read the manual :-) I'll remove the relevant help text as it is now statically linked -- Dr. Alexie Papanicolaou Phone: +61(0) 2 6246 4511| Mobile: +61 (0) 46 85 81 247 CSIRO Ecosystem Sciences, GPO Box 1700, Canberra 2601, ACT, Australia -- CSIRO profile<http://www.csiro.au/Organisation-Structure/Divisions/Ecosystem-Sciences/AlexiePapanicolaou.aspx> -- ResearcherID<http://www.researcherid.com/rid/A-1618-2011> -- Bioinformatics is also an experimental science ________________________________ From: Matthew MacManes [mac...@gm...] Sent: Saturday, 11 January 2014 11:54 PM To: Papanicolaou, Alexie (CES, Black Mountain) Cc: tra...@li... Subject: Re: [Transdecoder-users] make fails 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<https://twitter.com/PeroMHC> Web: genomebio.org<http://genomebio.org/> Office: 189 Rudman Hall Laboratory: 145 Rudman Hall On Jan 11, 2014, at 12:25 AM, Ale...@cs...<mailto: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...<mailto:mac...@gm...>] Sent: Saturday, 11 January 2014 5:18 AM To: tra...@li...<mailto: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 |
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From: <Ale...@cs...> - 2014-01-16 10:15:14
|
Hello I've reverted the change of FFINDEX being statically linked. It is now dynamic again. If not configured correctly and user wants to user MPI, the software complains and asks you to read the manual. new release uploaded thanks a ________________________________ From: Papanicolaou, Alexie (CES, Black Mountain) Sent: Monday, 13 January 2014 12:26 PM To: Matthew MacManes Cc: tra...@li... Subject: RE: [Transdecoder-users] make fails I assume this is working ok now. I'm making a new release now. p.s the ffindex issues were documented on the website but I guess most people don't read the manual :-) I'll remove the relevant help text as it is now statically linked -- Dr. Alexie Papanicolaou Phone: +61(0) 2 6246 4511| Mobile: +61 (0) 46 85 81 247 CSIRO Ecosystem Sciences, GPO Box 1700, Canberra 2601, ACT, Australia -- CSIRO profile<http://www.csiro.au/Organisation-Structure/Divisions/Ecosystem-Sciences/AlexiePapanicolaou.aspx> -- ResearcherID<http://www.researcherid.com/rid/A-1618-2011> -- Bioinformatics is also an experimental science ________________________________ From: Matthew MacManes [mac...@gm...] Sent: Saturday, 11 January 2014 11:54 PM To: Papanicolaou, Alexie (CES, Black Mountain) Cc: tra...@li... Subject: Re: [Transdecoder-users] make fails 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<https://twitter.com/PeroMHC> Web: genomebio.org<http://genomebio.org/> Office: 189 Rudman Hall Laboratory: 145 Rudman Hall On Jan 11, 2014, at 12:25 AM, Ale...@cs...<mailto: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...<mailto:mac...@gm...>] Sent: Saturday, 11 January 2014 5:18 AM To: tra...@li...<mailto: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 |
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