[package - head-armv7-default][biology/cufflinks] Failed for cufflinks-2.2.1.83_2 in build
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Wed Jan 29 11:27:29 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: jbeich at FreeBSD.org
Ident: $FreeBSD: head/biology/cufflinks/Makefile 519824 2019-12-11 17:53:48Z jbeich $
Log URL: http://beefy12.nyi.freebsd.org/data/head-armv7-default/p524456_s357186/logs/cufflinks-2.2.1.83_2.log
Build URL: http://beefy12.nyi.freebsd.org/build.html?mastername=head-armv7-default&build=p524456_s357186
Log:
=>> Building biology/cufflinks
build started at Wed Jan 29 11:25:32 UTC 2020
port directory: /usr/ports/biology/cufflinks
package name: cufflinks-2.2.1.83_2
building for: FreeBSD head-armv7-default-job-13 13.0-CURRENT FreeBSD 13.0-CURRENT 1300076 arm
maintained by: yuri at FreeBSD.org
Makefile ident: $FreeBSD: head/biology/cufflinks/Makefile 519824 2019-12-11 17:53:48Z jbeich $
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=======================<phase: check-sanity >============================
===> License BSL accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> cufflinks-2.2.1.83_2 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.12.0.txz
[head-armv7-default-job-13] Installing pkg-1.12.0...
[head-armv7-default-job-13] Extracting pkg-1.12.0: .......... done
===> cufflinks-2.2.1.83_2 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of cufflinks-2.2.1.83_2
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License BSL accepted by the user
===> Fetching all distfiles required by cufflinks-2.2.1.83_2 for building
===========================================================================
=======================<phase: checksum >============================
===> License BSL accepted by the user
===> Fetching all distfiles required by cufflinks-2.2.1.83_2 for building
=> SHA256 Checksum OK for cole-trapnell-lab-cufflinks-v2.2.1-83-gb4fa050_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License BSL accepted by the user
===> Fetching all distfiles required by cufflinks-2.2.1.83_2 for building
===> Extracting for cufflinks-2.2.1.83_2
=> SHA256 Checksum OK for cole-trapnell-lab-cufflinks-v2.2.1-83-gb4fa050_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
<snip>
checking whether CTL_HW is declared... no
checking whether HW_PHYSMEM is declared... no
checking how to create a pax tar archive... gnutar
checking dependency style of /nxb-bin/usr/bin/cc... (cached) gcc3
checking dependency style of /nxb-bin/usr/bin/c++... (cached) gcc3
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating config.h
config.status: executing depfiles commands
-- cufflinks 2.2.2 Configuration Results --
C++ compiler: /nxb-bin/usr/bin/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 -pthread -I/usr/local/include -I/usr/local/include -fstack-protector-strong -L/usr/lib
GCC version: FreeBSD clang version 9.0.1 (git at github.com:llvm/llvm-project.git c1a0a213378a458fbea1a5c77b315c7dce08fd05) (based on LLVM 9.0.1)
Host System type: armv7-portbld-freebsd13.0
Install prefix: /usr/local
Install eprefix: ${prefix}
See config.h for further configuration information.
Email <cole at cs.umd.edu> with questions and bug reports.
===========================================================================
=======================<phase: build >============================
===> Building for cufflinks-2.2.1.83_2
gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/cufflinks/work/cufflinks-2.2.1-83-gb4fa050'
gmake all-recursive
gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/cufflinks/work/cufflinks-2.2.1-83-gb4fa050'
Making all in src
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/cufflinks/work/cufflinks-2.2.1-83-gb4fa050/src'
/nxb-bin/usr/bin/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 -pthread -I/usr/local/include -I/usr/local/include -MT cufflinks.o -MD -MP -MF .deps/cufflinks.Tpo -c -o cufflinks.o cufflinks.cpp
In file included from cufflinks.cpp:15:
./hits.h:906:48: warning: field '_expression_file_name' will be initialized after field '_ifs' [-Wreorder]
HitFactory(insert_table, reference_table), _expression_file_name(expression_file_name), _ifs(expression_file_name.c_str()),
^
In file included from cufflinks.cpp:19:
./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 cufflinks.cpp:20:
In file included from ./clustering.h:38:
In file included from ./abundances.h:25:
In file included from ./bundles.h:24:
In file included from ./gtf_tracking.h:12:
In file included from ./gff.h:11:
./GHash.hh:90:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register int pos=fCurrentEntry;
^~~~~~~~~
./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register int i,n,p,x,h;
^~~~~~~~~
./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register int i,n,p,x,h;
^~~~~~~~~
./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register int i,n,p,x,h;
^~~~~~~~~
./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register int i,n,p,x,h;
^~~~~~~~~
./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register int i,n,p,x,h;
^~~~~~~~~
./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register int p,i,x,h,n;
^~~~~~~~~
./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register int p,i,x,h,n;
^~~~~~~~~
./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register int p,i,x,h,n;
^~~~~~~~~
./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register int p,i,x,h,n;
^~~~~~~~~
./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register int p,i,x,h,n;
^~~~~~~~~
./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register int p,i,x,h,n;
^~~~~~~~~
./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register int p,i,x,h,n;
^~~~~~~~~
./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register int p,i,x,h,n;
^~~~~~~~~
./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register int p,i,x,h,n;
^~~~~~~~~
./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register int p,i,x,h,n;
^~~~~~~~~
./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register int p,i,x,h,n;
^~~~~~~~~
./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register int p,i,x,h,n;
^~~~~~~~~
./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register int p,i,x,h,n;
^~~~~~~~~
./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register int p,i,x,h,n;
^~~~~~~~~
./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register int p,i,x,h,n;
^~~~~~~~~
./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register int p,x,h,n;
^~~~~~~~~
./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register int p,x,h,n;
^~~~~~~~~
./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register int p,x,h,n;
^~~~~~~~~
./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register int p,x,h,n;
^~~~~~~~~
./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register int p,x,h,n;
^~~~~~~~~
./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register int p,x,h,n;
^~~~~~~~~
./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register int p,x,h,n;
^~~~~~~~~
./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register int p,x,h,n;
^~~~~~~~~
./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register int p,x,h,n;
^~~~~~~~~
./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register int p,x,h,n;
^~~~~~~~~
./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register int p,x,h,n;
^~~~~~~~~
./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register int p,x,h,n;
^~~~~~~~~
./GHash.hh:416:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register int pos=fCurrentEntry;
^~~~~~~~~
./GHash.hh:429:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register int pos=fCurrentEntry;
^~~~~~~~~
./GHash.hh:443:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register int pos=fCurrentEntry;
^~~~~~~~~
./GHash.hh:461:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register int pos=0;
^~~~~~~~~
./GHash.hh:469:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register int pos=fCapacity-1;
^~~~~~~~~
./GHash.hh:496:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register int i;
^~~~~~~~~
./GHash.hh:553:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register int i;
^~~~~~~~~
In file included from cufflinks.cpp:28:
./replicates.h:224:57: warning: unused variable 's2' [-Wunused-variable]
const vector<boost::shared_ptr<Scaffold> >& s2 = bundles[i-1]->ref_scaffolds();
^
cufflinks.cpp:1176:17: warning: unused variable 'map_mass' [-Wunused-variable]
long double map_mass = rg_props->normalized_map_mass();
^
cufflinks.cpp:1522:3: error: reference to 'thread' is ambiguous
thread asmbl(assemble_bundle,
^
/usr/include/c++/v1/__threading_support:404:24: note: candidate found by name lookup is 'std::__1::thread'
class _LIBCPP_TYPE_VIS thread;
^
/usr/local/include/boost/thread/detail/thread.hpp:163:29: note: candidate found by name lookup is 'boost::thread'
class BOOST_THREAD_DECL thread
^
In file included from cufflinks.cpp:23:
In file included from ./filters.h:18:
./genes.h:210:6: warning: private field '_id' is not used [-Wunused-private-field]
int _id;
^
45 warnings and 1 error generated.
gmake[3]: *** [Makefile:1672: cufflinks.o] Error 1
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/cufflinks/work/cufflinks-2.2.1-83-gb4fa050/src'
gmake[2]: *** [Makefile:400: all-recursive] Error 1
gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/cufflinks/work/cufflinks-2.2.1-83-gb4fa050'
gmake[1]: *** [Makefile:341: all] Error 2
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/cufflinks/work/cufflinks-2.2.1-83-gb4fa050'
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/cufflinks
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