[package - head-i386-default][biology/cufflinks] Failed for cufflinks-2.2.1.89_1 in build
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Tue Aug 25 16:26:14 UTC 2020
You are receiving this mail as a port that you maintain
is failing to build on the FreeBSD package build server.
Please investigate the failure and submit a PR to fix
build.
Maintainer: yuri at FreeBSD.org
Last committer: jwb at FreeBSD.org
Ident: $FreeBSD: head/biology/cufflinks/Makefile 544090 2020-08-03 17:40:04Z jwb $
Log URL: http://beefy17.nyi.freebsd.org/data/head-i386-default/p546132_s364744/logs/cufflinks-2.2.1.89_1.log
Build URL: http://beefy17.nyi.freebsd.org/build.html?mastername=head-i386-default&build=p546132_s364744
Log:
=>> Building biology/cufflinks
build started at Tue Aug 25 16:21:50 UTC 2020
port directory: /usr/ports/biology/cufflinks
package name: cufflinks-2.2.1.89_1
building for: FreeBSD head-i386-default-job-05 13.0-CURRENT FreeBSD 13.0-CURRENT 1300111 i386
maintained by: yuri at FreeBSD.org
Makefile ident: $FreeBSD: head/biology/cufflinks/Makefile 544090 2020-08-03 17:40:04Z jwb $
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=======================<phase: check-sanity >============================
===> License BSL accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> cufflinks-2.2.1.89_1 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.14.7.txz
[head-i386-default-job-05] Installing pkg-1.14.7...
[head-i386-default-job-05] Extracting pkg-1.14.7: .......... done
===> cufflinks-2.2.1.89_1 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of cufflinks-2.2.1.89_1
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License BSL accepted by the user
===> Fetching all distfiles required by cufflinks-2.2.1.89_1 for building
===========================================================================
=======================<phase: checksum >============================
===> License BSL accepted by the user
===> Fetching all distfiles required by cufflinks-2.2.1.89_1 for building
=> SHA256 Checksum OK for cole-trapnell-lab-cufflinks-v2.2.1-89-gdc3b0cb_GH0.tar.gz.
=> SHA256 Checksum OK for ea4671149f3054c773d99cea521db75bf7b0658f.patch.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License BSL accepted by the user
===> Fetching all distfiles required by cufflinks-2.2.1.89_1 for building
===> Extracting for cufflinks-2.2.1.89_1
=> SHA256 Checksum OK for cole-trapnell-lab-cufflinks-v2.2.1-89-gdc3b0cb_GH0.tar.gz.
=> SHA256 Checksum OK for ea4671149f3054c773d99cea521db75bf7b0658f.patch.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for cufflinks-2.2.1.89_1
===> Applying distribution patches for cufflinks-2.2.1.89_1
===> Applying FreeBSD patches for cufflinks-2.2.1.89_1 from /usr/ports/biology/cufflinks/files
===========================================================================
=======================<phase: build-depends >============================
===> cufflinks-2.2.1.89_1 depends on file: /usr/local/libdata/pkgconfig/eigen3.pc - not found
===> Installing existing package /packages/All/eigen-3.3.7.txz
[head-i386-default-job-05] Installing eigen-3.3.7...
<snip>
In file included from /usr/local/include/boost/math/special_functions/erf.hpp:15:
In file included from /usr/local/include/boost/math/special_functions/gamma.hpp:24:
In file included from /usr/local/include/boost/math/constants/constants.hpp:13:
In file included from /usr/local/include/boost/math/tools/convert_from_string.hpp:15:
In file included from /usr/local/include/boost/lexical_cast.hpp:30:
In file included from /usr/local/include/boost/range/iterator_range_core.hpp:38:
In file included from /usr/local/include/boost/range/functions.hpp:20:
In file included from /usr/local/include/boost/range/size.hpp:25:
In file included from /usr/local/include/boost/utility.hpp:21:
/usr/local/include/boost/core/checked_delete.hpp:36:5: warning: delete called on non-final 'PoissonDispersionModel' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
delete x;
^
/usr/local/include/boost/smart_ptr/detail/shared_count.hpp:149:20: note: in instantiation of function template specialization 'boost::checked_delete<PoissonDispersionModel>' requested here
boost::checked_delete( p );
^
/usr/local/include/boost/smart_ptr/shared_ptr.hpp:285:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count<PoissonDispersionModel>' requested here
boost::detail::shared_count( p ).swap( pn );
^
/usr/local/include/boost/smart_ptr/shared_ptr.hpp:379:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct<MassDispersionModel, PoissonDispersionModel>' requested here
boost::detail::sp_pointer_construct( this, p, pn );
^
cuffdiff.cpp:1541:60: note: in instantiation of function template specialization 'boost::shared_ptr<MassDispersionModel>::shared_ptr<PoissonDispersionModel>' requested here
boost::shared_ptr<MassDispersionModel> disperser = boost::shared_ptr<MassDispersionModel>(new PoissonDispersionModel(""));
^
In file included from gtf_to_sam.cpp:22:
./hits.h:906:48: warning: field '_expression_file_name' will be initialized after field '_ifs' [-Wreorder-ctor]
HitFactory(insert_table, reference_table), _expression_file_name(expression_file_name), _ifs(expression_file_name.c_str()),
^
gtf_to_sam.cpp:142:86: warning: format specifies type 'int' but the argument has type 'RefID' (aka 'unsigned long long') [-Wformat]
fprintf(stderr, "Warning: Could not find contig name for ID %d, skipping\n", scaff.ref_id());
~~ ^~~~~~~~~~~~~~
%llu
In file included from gtf_to_sam.cpp:23:
In file included from ./bundles.h:16:
In file included from /usr/local/include/boost/random.hpp:36:
In file included from /usr/local/include/boost/random/additive_combine.hpp:27:
/usr/local/include/boost/random/linear_congruential.hpp:140:20: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
if(_x <= 0 && _x != 0) {
~~~~~~~~^~~~~~~~~~
/usr/local/include/boost/random/linear_congruential.hpp:393:11: note: in instantiation of member function 'boost::random::linear_congruential_engine<unsigned long long, 25214903917, 11, 281474976710656>::seed' requested here
{ lcf.seed(cnv(x0)); }
^
3 warnings generated.
mv -f .deps/gtf_to_sam.Tpo .deps/gtf_to_sam.Po
c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++03 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -MT compress_gtf.o -MD -MP -MF .deps/compress_gtf.Tpo -c -o compress_gtf.o compress_gtf.cpp
In file included from compress_gtf.cpp:23:
./hits.h:906:48: warning: field '_expression_file_name' will be initialized after field '_ifs' [-Wreorder-ctor]
HitFactory(insert_table, reference_table), _expression_file_name(expression_file_name), _ifs(expression_file_name.c_str()),
^
In file included from compress_gtf.cpp:24:
In file included from ./bundles.h:16:
In file included from /usr/local/include/boost/random.hpp:36:
In file included from /usr/local/include/boost/random/additive_combine.hpp:27:
/usr/local/include/boost/random/linear_congruential.hpp:140:20: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
if(_x <= 0 && _x != 0) {
~~~~~~~~^~~~~~~~~~
/usr/local/include/boost/random/linear_congruential.hpp:393:11: note: in instantiation of member function 'boost::random::linear_congruential_engine<unsigned long long, 25214903917, 11, 281474976710656>::seed' requested here
{ lcf.seed(cnv(x0)); }
^
In file included from compress_gtf.cpp:29:
./genes.h:210:6: warning: private field '_id' is not used [-Wunused-private-field]
int _id;
^
14 warnings generated.
mv -f .deps/cuffdiff.Tpo .deps/cuffdiff.Po
c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++03 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -MT gffread.o -MD -MP -MF .deps/gffread.Tpo -c -o gffread.o gffread.cpp
mv -f .deps/gffread.Tpo .deps/gffread.Po
c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++03 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -MT cuffquant.o -MD -MP -MF .deps/cuffquant.Tpo -c -o cuffquant.o cuffquant.cpp
3 warnings generated.
mv -f .deps/compress_gtf.Tpo .deps/compress_gtf.Po
c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++03 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -MT cuffnorm.o -MD -MP -MF .deps/cuffnorm.Tpo -c -o cuffnorm.o cuffnorm.cpp
In file included from cuffquant.cpp:19:
./hits.h:906:48: warning: field '_expression_file_name' will be initialized after field '_ifs' [-Wreorder-ctor]
HitFactory(insert_table, reference_table), _expression_file_name(expression_file_name), _ifs(expression_file_name.c_str()),
^
In file included from cuffnorm.cpp:18:
./hits.h:906:48: warning: field '_expression_file_name' will be initialized after field '_ifs' [-Wreorder-ctor]
HitFactory(insert_table, reference_table), _expression_file_name(expression_file_name), _ifs(expression_file_name.c_str()),
^
In file included from cuffquant.cpp:24:
./update_check.h:81:29: warning: 'bzero' call operates on objects of type 'char' while the size is based on a different type 'char *' [-Wsizeof-pointer-memaccess]
bzero(curr_version, sizeof(curr_version));
~~~~~~~~~~~~ ^~~~~~~~~~~~
./update_check.h:81:29: note: did you mean to provide an explicit length?
bzero(curr_version, sizeof(curr_version));
^~~~~~~~~~~~
In file included from cuffnorm.cpp:23:
./update_check.h:81:29: warning: 'bzero' call operates on objects of type 'char' while the size is based on a different type 'char *' [-Wsizeof-pointer-memaccess]
bzero(curr_version, sizeof(curr_version));
~~~~~~~~~~~~ ^~~~~~~~~~~~
./update_check.h:81:29: note: did you mean to provide an explicit length?
bzero(curr_version, sizeof(curr_version));
^~~~~~~~~~~~
In file included from cuffquant.cpp:37:
./replicates.h:224:57: warning: unused variable 's2' [-Wunused-variable]
const vector<boost::shared_ptr<Scaffold> >& s2 = bundles[i-1]->ref_scaffolds();
^
cuffquant.cpp:742:31: warning: unused variable 's2' [-Wunused-variable]
const AbundanceGroup& s2 = prev.transcripts;
^
cuffquant.cpp:760:25: warning: unused variable 'ab_group' [-Wunused-variable]
const AbundanceGroup& ab_group = abundances[i]->transcripts;
^
In file included from cuffnorm.cpp:38:
In file included from ./differential.h:29:
./replicates.h:224:57: warning: unused variable 's2' [-Wunused-variable]
const vector<boost::shared_ptr<Scaffold> >& s2 = bundles[i-1]->ref_scaffolds();
^
cuffquant.cpp:1513:34: warning: format specifies type 'unsigned long' but the argument has type 'size_t' (aka 'unsigned int') [-Wformat]
sprintf(buf, "q%lu", i);
~~~ ^
%u
cuffquant.cpp:1536:2: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation]
srand48(random_seed);
^
cuffquant.cpp:1531:5: note: previous statement is here
if (random_seed == -1)
^
In file included from cuffnorm.cpp:38:
./differential.h:215:5: warning: field 'sample_labels' will be initialized after field 'headers_written' [-Wreorder-ctor]
sample_labels(sls),
^
./differential.h:614:56: warning: more '%' conversions than data arguments [-Wformat]
fprintf(fout, "%s_%d\t%s\t%Lg\t%lg\t%lg\t%lg\n",
~~^
In file included from cuffnorm.cpp:41:
./locfit/local.h:126:9: warning: 'MAX' macro redefined [-Wmacro-redefined]
#define MAX(a,b) (((a)>(b)) ? (a) : (b))
^
/usr/include/sys/param.h:311:9: note: previous definition is here
#define MAX(a,b) (((a)>(b))?(a):(b))
^
In file included from cuffnorm.cpp:41:
./locfit/local.h:127:9: warning: 'MIN' macro redefined [-Wmacro-redefined]
#define MIN(a,b) (((a)<(b)) ? (a) : (b))
^
/usr/include/sys/param.h:310:9: note: previous definition is here
#define MIN(a,b) (((a)<(b))?(a):(b))
^
In file included from cuffquant.cpp:20:
In file included from ./bundles.h:16:
In file included from /usr/local/include/boost/random.hpp:36:
In file included from /usr/local/include/boost/random/additive_combine.hpp:27:
/usr/local/include/boost/random/linear_congruential.hpp:140:20: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
if(_x <= 0 && _x != 0) {
~~~~~~~~^~~~~~~~~~
/usr/local/include/boost/random/linear_congruential.hpp:393:11: note: in instantiation of member function 'boost::random::linear_congruential_engine<unsigned long long, 25214903917, 11, 281474976710656>::seed' requested here
{ lcf.seed(cnv(x0)); }
^
cuffnorm.cpp:1186:38: warning: format specifies type 'unsigned long' but the argument has type 'size_t' (aka 'unsigned int') [-Wformat]
sprintf(buf, "q%lu", i);
~~~ ^
%u
cuffnorm.cpp:1210:2: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation]
srand48(random_seed);
^
cuffnorm.cpp:1205:5: note: previous statement is here
if (random_seed == -1)
^
In file included from cuffnorm.cpp:19:
In file included from ./bundles.h:16:
In file included from /usr/local/include/boost/random.hpp:36:
In file included from /usr/local/include/boost/random/additive_combine.hpp:27:
/usr/local/include/boost/random/linear_congruential.hpp:140:20: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
if(_x <= 0 && _x != 0) {
~~~~~~~~^~~~~~~~~~
/usr/local/include/boost/random/linear_congruential.hpp:393:11: note: in instantiation of member function 'boost::random::linear_congruential_engine<unsigned long long, 25214903917, 11, 281474976710656>::seed' requested here
{ lcf.seed(cnv(x0)); }
^
10 warnings generated.
mv -f .deps/cuffnorm.Tpo .deps/cuffnorm.Po
rm -f libcufflinks.a
ar cru libcufflinks.a clustering.o differential.o common.o assemble.o tokenize.o abundances.o scaffolds.o hits.o genes.o bundles.o filters.o scaffold_graph.o matching_merge.o graph_optimize.o biascorrection.o sampling.o adap.o ar_funs.o arith.o band.o c_args.o c_plot.o cmd.o dens_haz.o dens_int.o dens_odi.o density.o dist.o ev_atree.o ev_interp.o ev_kdtre.o ev_main.o ev_trian.o family.o fitted.o frend.o help.o lf_dercor.o lf_fitfun.o lf_robust.o lf_vari.o lfd.o lfstr.o linalg.o locfit.o m_chol.o m_eigen.o m_jacob.o m_max.o makecmd.o math.o minmax.o nbhd.o pcomp.o pout.o preplot.o random.o readfile.o scb.o scb_cons.o simul.o solve.o startlf.o strings.o vari.o wdiag.o weight.o replicates.o multireads.o jensen_shannon.o tracking.o
ranlib libcufflinks.a
rm -f libgc.a
ar cru libgc.a codons.o GArgs.o GBase.o gdna.o GStr.o GFaSeqGet.o GFastaIndex.o gff.o gff_utils.o gtf_tracking.o
ranlib libgc.a
c++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++03 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -fstack-protector-strong -pthread -L/usr/local/lib -L/usr/local/lib -fstack-protector-strong -o cufflinks cufflinks.o libcufflinks.a libgc.a -lboost_thread -lboost_system -lboost_serialization -lboost_filesystem -lhts -lz
ld: error: duplicate symbol: curwin
>>> defined at startlf.c:236 (locfit/startlf.c:236)
>>> startlf.o:(curwin) in archive libcufflinks.a
>>> defined at c_plot.c:12 (locfit/c_plot.c:12)
>>> c_plot.o:(.bss+0x0) in archive libcufflinks.a
c++: error: linker command failed with exit code 1 (use -v to see invocation)
gmake[3]: *** [Makefile:804: cufflinks] Error 1
gmake[3]: *** Waiting for unfinished jobs....
8 warnings generated.
mv -f .deps/cuffquant.Tpo .deps/cuffquant.Po
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/cufflinks/work/cufflinks-2.2.1-89-gdc3b0cb/src'
gmake[2]: *** [Makefile:402: all-recursive] Error 1
gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/cufflinks/work/cufflinks-2.2.1-89-gdc3b0cb'
gmake[1]: *** [Makefile:343: all] Error 2
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/cufflinks/work/cufflinks-2.2.1-89-gdc3b0cb'
===> Compilation failed unexpectedly.
Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to
the maintainer.
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/cufflinks
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