[package - head-amd64-default][biology/cufflinks] Failed for cufflinks-2.2.1.83_1 in build

pkg-fallout at FreeBSD.org pkg-fallout at FreeBSD.org
Sat Nov 9 23:17:06 UTC 2019


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 509290 2019-08-19 15:35:27Z jbeich $
Log URL:        http://beefy18.nyi.freebsd.org/data/head-amd64-default/p517099_s354566/logs/cufflinks-2.2.1.83_1.log
Build URL:      http://beefy18.nyi.freebsd.org/build.html?mastername=head-amd64-default&build=p517099_s354566
Log:

=>> Building biology/cufflinks
build started at Sat Nov  9 23:15:26 UTC 2019
port directory: /usr/ports/biology/cufflinks
package name: cufflinks-2.2.1.83_1
building for: FreeBSD head-amd64-default-job-18 13.0-CURRENT FreeBSD 13.0-CURRENT 1300056 amd64
maintained by: yuri at FreeBSD.org
Makefile ident:      $FreeBSD: head/biology/cufflinks/Makefile 509290 2019-08-19 15:35:27Z jbeich $
Poudriere version: 3.2.8-5-gc81843e5
Host OSVERSION: 1300047
Jail OSVERSION: 1300056
Job Id: 18




!!! Jail is newer than host. (Jail: 1300056, Host: 1300047) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!



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=======================<phase: check-sanity   >============================
===>  License BSL accepted by the user
===========================================================================
=======================<phase: pkg-depends    >============================
===>   cufflinks-2.2.1.83_1 depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-1.12.0.txz
[head-amd64-default-job-18] Installing pkg-1.12.0...
[head-amd64-default-job-18] Extracting pkg-1.12.0: .......... done
===>   cufflinks-2.2.1.83_1 depends on file: /usr/local/sbin/pkg - found
===>   Returning to build of cufflinks-2.2.1.83_1
===========================================================================
=======================<phase: fetch-depends  >============================
===========================================================================
=======================<phase: fetch          >============================
===>  License BSL accepted by the user
===> Fetching all distfiles required by cufflinks-2.2.1.83_1 for building
===========================================================================
=======================<phase: checksum       >============================
===>  License BSL accepted by the user
===> Fetching all distfiles required by cufflinks-2.2.1.83_1 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_1 for building
===>  Extracting for cufflinks-2.2.1.83_1
=> 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_1
===>  Applying FreeBSD patches for cufflinks-2.2.1.83_1
===========================================================================
=======================<phase: build-depends  >============================
===>   cufflinks-2.2.1.83_1 depends on file: /usr/local/libdata/pkgconfig/eigen3.pc - not found
===>   Installing existing package /packages/All/eigen-3.3.7.txz
[head-amd64-default-job-18] Installing eigen-3.3.7...
[head-amd64-default-job-18] Extracting eigen-3.3.7: .......... done
===>   cufflinks-2.2.1.83_1 depends on file: /usr/local/libdata/pkgconfig/eigen3.pc - found
===>   Returning to build of cufflinks-2.2.1.83_1
===>   cufflinks-2.2.1.83_1 depends on executable: gmake - not found
===>   Installing existing package /packages/All/gmake-4.2.1_3.txz
[head-amd64-default-job-18] Installing gmake-4.2.1_3...
[head-amd64-default-job-18] `-- Installing gettext-runtime-0.20.1...
<snip>
./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 clustering.cpp:10:
In file included from ./clustering.h:38:
In file included from ./abundances.h:23:
./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 clustering.cpp:10:
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]: *** Waiting for unfinished jobs....
41 warnings generated.
mv -f .deps/clustering.Tpo .deps/clustering.Po
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'
===> 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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