You are receiving this mail as a port that you maintain
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Please investigate the failure and submit a PR to fix
build.

Maintainer:     y...@freebsd.org
Last committer: jbe...@freebsd.org
Ident:          $FreeBSD: branches/2020Q1/biology/cufflinks/Makefile 519824 
2019-12-11 17:53:48Z jbeich $
Log URL:        
http://beefy4.nyi.freebsd.org/data/121i386-quarterly/529160/logs/cufflinks-2.2.1.83_2.log
Build URL:      
http://beefy4.nyi.freebsd.org/build.html?mastername=121i386-quarterly&build=529160
Log:

=>> Building biology/cufflinks
build started at Thu Mar 26 01:36:31 UTC 2020
port directory: /usr/ports/biology/cufflinks
package name: cufflinks-2.2.1.83_2
building for: FreeBSD 121i386-quarterly-job-04 12.1-RELEASE-p3 FreeBSD 
12.1-RELEASE-p3 i386
maintained by: y...@freebsd.org
Makefile ident:      $FreeBSD: branches/2020Q1/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_1.txz
[121i386-quarterly-job-04] Installing pkg-1.12.0_1...
[121i386-quarterly-job-04] Extracting pkg-1.12.0_1: .......... 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  >============================
===========================================================================
=======================<phase: patch          >============================
===>  Patching for cufflinks-2.2.1.83_2
===>  Applying FreeBSD patches for cufflinks-2.2.1.83_2
===========================================================================
=======================<phase: build-depends  >============================
===>   cufflinks-2.2.1.83_2 depends on file: 
/usr/local/libdata/pkgconfig/eigen3.pc - not found
===>   Installing existing package /packages/All/eigen-3.3.7.txz
[121i386-quarterly-job-04] Installing eigen-3.3.7...
[121i386-quarterly-job-04] Extracting eigen-3.3.7: .......... done
===>   cufflinks-2.2.1.83_2 depends on file: 
/usr/local/libdata/pkgconfig/eigen3.pc - found
===>   Returning to build of cufflinks-2.2.1.83_2
===>   cufflinks-2.2.1.83_2 depends on executable: gmake - not found
===>   Installing existing package /packages/All/gmake-4.2.1_3.txz
[121i386-quarterly-job-04] Installing gmake-4.2.1_3...
[121i386-quarterly-job-04] `-- Installing gettext-runtime-0.20.1...
[121i386-quarterly-job-04] |   `-- Installing indexinfo-0.3.1...
[121i386-quarterly-job-04] |   `-- Extracting indexinfo-0.3.1: .... done
[121i386-quarterly-job-04] `-- Extracting gettext-runtime-0.20.1: .......... 
done
[121i386-quarterly-job-04] Extracting gmake-4.2.1_3: .......... done
===>   cufflinks-2.2.1.83_2 depends on executable: gmake - found
<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 cc... (cached) gcc3
checking dependency style of 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:        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 8.0.1 (tags/RELEASE_801/final 
366581) (based on LLVM 8.0.1)
  Host System type:    i386-portbld-freebsd12.1
  Install prefix:      /usr/local
  Install eprefix:     ${prefix}

  See config.h for further configuration information.
  Email <c...@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'
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:397:24: 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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