[package - 122powerpc64-quarterly][biology/cufflinks] Failed for cufflinks-2.2.1.89_2 in build

From: <pkg-fallout_at_FreeBSD.org>
Date: Tue, 29 Jun 2021 03:51:47 GMT
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
Log URL:        http://foul1.nyi.freebsd.org/data/122powerpc64-quarterly/ae162bd98935/logs/cufflinks-2.2.1.89_2.log
Build URL:      http://foul1.nyi.freebsd.org/build.html?mastername=122powerpc64-quarterly&build=ae162bd98935
Log:

=>> Building biology/cufflinks
build started at Tue Jun 29 03:49:01 UTC 2021
port directory: /usr/ports/biology/cufflinks
package name: cufflinks-2.2.1.89_2
building for: FreeBSD 122powerpc64-quarterly-job-12 12.2-RELEASE FreeBSD 12.2-RELEASE powerpc
maintained by: yuri_at_FreeBSD.org
Makefile ident: 
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CC_OUTPUT_921dbbb2_65ad290d=cc1plus: error: unrecognized command line option "-std=c++14"
CC_OUTPUT_921dbbb2_f2776b26=cc1plus: error: unrecognized command line option "-std=c++17"
CC_OUTPUT_921dbbb2_b2657cc3=yes
CC_OUTPUT_921dbbb2_380987f7=cc1plus: error: unrecognized command line option "-std=gnu++11"
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CC_OUTPUT_921dbbb2_fb62803b=cc1plus: error: unrecognized command line option "-std=gnu++17"
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=======================<phase: check-sanity   >============================
===>  License BSL accepted by the user
===========================================================================
=======================<phase: pkg-depends    >============================
===>   cufflinks-2.2.1.89_2 depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-1.16.3.txz
[122powerpc64-quarterly-job-12] Installing pkg-1.16.3...
[122powerpc64-quarterly-job-12] Extracting pkg-1.16.3: .......... done
===>   cufflinks-2.2.1.89_2 depends on file: /usr/local/sbin/pkg - found
===>   Returning to build of cufflinks-2.2.1.89_2
===========================================================================
=======================<phase: fetch-depends  >============================
===========================================================================
=======================<phase: fetch          >============================
===>  License BSL accepted by the user
===> Fetching all distfiles required by cufflinks-2.2.1.89_2 for building
===========================================================================
=======================<phase: checksum       >============================
===>  License BSL accepted by the user
===> Fetching all distfiles required by cufflinks-2.2.1.89_2 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_2 for building
===>  Extracting for cufflinks-2.2.1.89_2
=> 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_2
===>  Applying distribution patches for cufflinks-2.2.1.89_2
===>  Applying FreeBSD patches for cufflinks-2.2.1.89_2 from /usr/ports/biology/cufflinks/files
===========================================================================
=======================<phase: build-depends  >============================
===>   cufflinks-2.2.1.89_2 depends on file: /usr/local/libdata/pkgconfig/eigen3.pc - not found
===>   Installing existing package /packages/All/eigen-3.3.9.txz
[122powerpc64-quarterly-job-12] Installing eigen-3.3.9...
[122powerpc64-quarterly-job-12] `-- Installing adol-c-2.7.2...
[122powerpc64-quarterly-job-12] |   `-- Installing boost-libs-1.72.0_4...
[122powerpc64-quarterly-job-12] |   | `-- Installing gcc10-10.2.0_1...
[122powerpc64-quarterly-job-12] |   |   `-- Installing binutils-2.33.1_4,1...
[122powerpc64-quarterly-job-12] |   |   | `-- Installing gettext-runtime-0.21...
[122powerpc64-quarterly-job-12] |   |   |   `-- Installing indexinfo-0.3.1...
[122powerpc64-quarterly-job-12] |   |   |   `-- Extracting indexinfo-0.3.1: .... done
[122powerpc64-quarterly-job-12] |   |   | `-- Extracting gettext-runtime-0.21: .......... done
[122powerpc64-quarterly-job-12] |   |   `-- Extracting binutils-2.33.1_4,1: .......... done
[122powerpc64-quarterly-job-12] |   |   `-- Installing gcc9-9.3.0_3...
[122powerpc64-quarterly-job-12] |   |   | `-- Installing gmp-6.2.1...
[122powerpc64-quarterly-job-12] |   |   | `-- Extracting gmp-6.2.1: .......... done
[122powerpc64-quarterly-job-12] |   |   | `-- Installing mpc-1.2.0...
[122powerpc64-quarterly-job-12] |   |   |   `-- Installing mpfr-4.1.0...
<snip>
      |  ^~~~
cufflinks.cpp: In function 'void quantitate_transcript_cluster(AbundanceGroup&, double, std::vector<Gene>&, bool)':
cufflinks.cpp:980:30: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  980 |         for (size_t j = 0; j < N; ++j)
      |                            ~~^~~
cufflinks.cpp:988:30: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  988 |         for (size_t j = 0; j < N; ++j)
      |                            ~~^~~
cufflinks.cpp: In function 'void assemble_bundle(const RefSequenceTable&, HitBundle*, boost::shared_ptr<ReadGroupProperties>, boost::shared_ptr<BiasLearner>, FILE*, FILE*, FILE*, FILE*)':
cufflinks.cpp:1264:55: warning: comparison of integer expressions of different signedness: 'std::vector<MateHit>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
 1264 |     bool bundle_too_large = bundle_ptr->hits().size() >= max_frags_per_bundle;
      |                             ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
cufflinks.cpp:1275:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 1275 |     if (allow_junk_filtering)
      |     ^~
cufflinks.cpp:1279:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 1279 |  if (!final_est_run && bundle_mode==REF_DRIVEN) // Bias needs to be learned
      |  ^~
cufflinks.cpp:1176:17: warning: unused variable 'map_mass' [-Wunused-variable]
 1176 |     long double map_mass = rg_props->normalized_map_mass();
      |                 ^~~~~~~~
cufflinks.cpp: In function 'bool assemble_hits(BundleFactory&, boost::shared_ptr<BiasLearner>)':
cufflinks.cpp:1491:38: warning: comparison of integer expressions of different signedness: 'int' and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare]
 1491 |   if (bundle.right() - bundle.left() > max_gene_length)
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
In file included from GList.hh:8,
                 from GFaSeqGet.h:3,
                 from gff.h:9,
                 from gtf_tracking.h:12,
                 from bundles.h:24,
                 from abundances.h:25,
                 from clustering.h:38,
                 from cufflinks.cpp:20:
GVec.hh: In instantiation of 'void GVec<OBJ>::Grow(int, OBJ&) [with OBJ = GISeg]':
GVec.hh:436:9:   required from 'void GVec<OBJ>::Insert(int, OBJ*) [with OBJ = GISeg]'
GVec.hh:83:48:   required from 'void GVec<OBJ>::idxInsert(int, OBJ&) [with OBJ = GISeg]'
gtf_tracking.h:210:29:   required from here
GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GISeg'; use assignment or value-initialization instead [-Wclass-memaccess]
  364 |         memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ));
      |         ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from bundles.h:24,
                 from abundances.h:25,
                 from clustering.h:38,
                 from cufflinks.cpp:20:
gtf_tracking.h:188:7: note: 'class GISeg' declared here
  188 | class GISeg: public GSeg {
      |       ^~~~~
In file included from abundances.h:23,
                 from clustering.h:38,
                 from clustering.cpp:10:
hits.h: In constructor 'PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)':
hits.h:1002:12: warning: 'PrecomputedExpressionHitFactory::_expression_file_name' will be initialized after [-Wreorder]
 1002 |     string _expression_file_name;
      |            ^~~~~~~~~~~~~~~~~~~~~
hits.h:1001:19: warning:   'std::ifstream PrecomputedExpressionHitFactory::_ifs' [-Wreorder]
 1001 |     std::ifstream _ifs;
      |                   ^~~~
In file included from abundances.h:23,
                 from clustering.h:38,
                 from clustering.cpp:10:
hits.h:903:5: warning:   when initialized here [-Wreorder]
  903 |     PrecomputedExpressionHitFactory(const string& expression_file_name,
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from GList.hh:8,
                 from GFaSeqGet.h:3,
                 from gff.h:9,
                 from gtf_tracking.h:12,
                 from bundles.h:24,
                 from abundances.h:25,
                 from clustering.h:38,
                 from cufflinks.cpp:20:
GVec.hh: In instantiation of 'void GVec<OBJ>::Grow(int, OBJ&) [with OBJ = GXSeg]':
GVec.hh:436:9:   required from 'void GVec<OBJ>::Insert(int, OBJ*) [with OBJ = GXSeg]'
GVec.hh:81:44:   required from 'void GVec<OBJ>::Insert(int, OBJ) [with OBJ = GXSeg]'
GList.hh:231:21:   required from 'int GArray<OBJ>::Add(OBJ*) [with OBJ = GXSeg]'
GList.hh:51:36:   required from 'int GArray<OBJ>::Add(OBJ&) [with OBJ = GXSeg]'
gtf_tracking.h:419:20:   required from here
GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GXSeg'; use assignment or value-initialization instead [-Wclass-memaccess]
  364 |         memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ));
      |         ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from bundles.h:24,
                 from abundances.h:25,
                 from clustering.h:38,
                 from cufflinks.cpp:20:
gtf_tracking.h:359:7: note: 'class GXSeg' declared here
  359 | class GXSeg : public GSeg {
      |       ^~~~~
In file included from GList.hh:8,
                 from GFaSeqGet.h:3,
                 from gff.h:9,
                 from gtf_tracking.h:12,
                 from bundles.h:24,
                 from abundances.h:25,
                 from clustering.h:38,
                 from cufflinks.cpp:20:
GVec.hh: In instantiation of 'void GVec<OBJ>::Grow(int, OBJ&) [with OBJ = GSeg]':
GVec.hh:436:9:   required from 'void GVec<OBJ>::Insert(int, OBJ*) [with OBJ = GSeg]'
GVec.hh:81:44:   required from 'void GVec<OBJ>::Insert(int, OBJ) [with OBJ = GSeg]'
GList.hh:231:21:   required from 'int GArray<OBJ>::Add(OBJ*) [with OBJ = GSeg]'
GList.hh:51:36:   required from 'int GArray<OBJ>::Add(OBJ&) [with OBJ = GSeg]'
gtf_tracking.h:420:19:   required from here
GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GSeg'; use assignment or value-initialization instead [-Wclass-memaccess]
  364 |         memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ));
      |         ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from gff.h:6,
                 from gtf_tracking.h:12,
                 from bundles.h:24,
                 from abundances.h:25,
                 from clustering.h:38,
                 from cufflinks.cpp:20:
GBase.h:286:7: note: 'class GSeg' declared here
  286 | class GSeg {
      |       ^~~~
In file included from GList.hh:8,
                 from GFaSeqGet.h:3,
                 from gff.h:9,
                 from gtf_tracking.h:12,
                 from bundles.h:24,
                 from abundances.h:25,
                 from clustering.h:38,
                 from clustering.cpp:10:
GVec.hh: In instantiation of 'void GVec<OBJ>::Grow(int, OBJ&) [with OBJ = GISeg]':
GVec.hh:436:9:   required from 'void GVec<OBJ>::Insert(int, OBJ*) [with OBJ = GISeg]'
GVec.hh:83:48:   required from 'void GVec<OBJ>::idxInsert(int, OBJ&) [with OBJ = GISeg]'
gtf_tracking.h:210:29:   required from here
GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GISeg'; use assignment or value-initialization instead [-Wclass-memaccess]
  364 |         memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ));
      |         ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from bundles.h:24,
                 from abundances.h:25,
                 from clustering.h:38,
                 from clustering.cpp:10:
gtf_tracking.h:188:7: note: 'class GISeg' declared here
  188 | class GISeg: public GSeg {
      |       ^~~~~
In file included from GList.hh:8,
                 from GFaSeqGet.h:3,
                 from gff.h:9,
                 from gtf_tracking.h:12,
                 from bundles.h:24,
                 from abundances.h:25,
                 from clustering.h:38,
                 from clustering.cpp:10:
GVec.hh: In instantiation of 'void GVec<OBJ>::Grow(int, OBJ&) [with OBJ = GXSeg]':
GVec.hh:436:9:   required from 'void GVec<OBJ>::Insert(int, OBJ*) [with OBJ = GXSeg]'
GVec.hh:81:44:   required from 'void GVec<OBJ>::Insert(int, OBJ) [with OBJ = GXSeg]'
GList.hh:231:21:   required from 'int GArray<OBJ>::Add(OBJ*) [with OBJ = GXSeg]'
GList.hh:51:36:   required from 'int GArray<OBJ>::Add(OBJ&) [with OBJ = GXSeg]'
gtf_tracking.h:419:20:   required from here
GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GXSeg'; use assignment or value-initialization instead [-Wclass-memaccess]
  364 |         memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ));
      |         ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from bundles.h:24,
                 from abundances.h:25,
                 from clustering.h:38,
                 from clustering.cpp:10:
gtf_tracking.h:359:7: note: 'class GXSeg' declared here
  359 | class GXSeg : public GSeg {
      |       ^~~~~
In file included from GList.hh:8,
                 from GFaSeqGet.h:3,
                 from gff.h:9,
                 from gtf_tracking.h:12,
                 from bundles.h:24,
                 from abundances.h:25,
                 from clustering.h:38,
                 from clustering.cpp:10:
GVec.hh: In instantiation of 'void GVec<OBJ>::Grow(int, OBJ&) [with OBJ = GSeg]':
GVec.hh:436:9:   required from 'void GVec<OBJ>::Insert(int, OBJ*) [with OBJ = GSeg]'
GVec.hh:81:44:   required from 'void GVec<OBJ>::Insert(int, OBJ) [with OBJ = GSeg]'
GList.hh:231:21:   required from 'int GArray<OBJ>::Add(OBJ*) [with OBJ = GSeg]'
GList.hh:51:36:   required from 'int GArray<OBJ>::Add(OBJ&) [with OBJ = GSeg]'
gtf_tracking.h:420:19:   required from here
GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GSeg'; use assignment or value-initialization instead [-Wclass-memaccess]
  364 |         memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ));
      |         ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from gff.h:6,
                 from gtf_tracking.h:12,
                 from bundles.h:24,
                 from abundances.h:25,
                 from clustering.h:38,
                 from clustering.cpp:10:
GBase.h:286:7: note: 'class GSeg' declared here
  286 | class GSeg {
      |       ^~~~
gmake[3]: *** [Makefile:1674: cufflinks.o] Error 1
gmake[3]: *** Waiting for unfinished jobs....
gmake[3]: *** [Makefile:1674: clustering.o] Error 1
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/cufflinks/work/cufflinks-2.2.1-89-gdc3b0cb/src'
gmake[2]: *** [Makefile:404: all-recursive] Error 1
gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/cufflinks/work/cufflinks-2.2.1-89-gdc3b0cb'
gmake[1]: *** [Makefile:345: 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
Received on Tue Jun 29 2021 - 03:51:47 UTC

Original text of this message