[package - head-i386-default][biology/subread] Failed for subread-2.0.1 in build
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Thu Aug 20 08:24:48 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: jwb at FreeBSD.org
Last committer: jwb at FreeBSD.org
Ident: $FreeBSD: head/biology/subread/Makefile 537982 2020-06-05 01:55:49Z jwb $
Log URL: http://beefy17.nyi.freebsd.org/data/head-i386-default/p545479_s364329/logs/subread-2.0.1.log
Build URL: http://beefy17.nyi.freebsd.org/build.html?mastername=head-i386-default&build=p545479_s364329
Log:
=>> Building biology/subread
build started at Thu Aug 20 08:24:36 UTC 2020
port directory: /usr/ports/biology/subread
package name: subread-2.0.1
building for: FreeBSD head-i386-default-job-02 13.0-CURRENT FreeBSD 13.0-CURRENT 1300109 i386
maintained by: jwb at FreeBSD.org
Makefile ident: $FreeBSD: head/biology/subread/Makefile 537982 2020-06-05 01:55:49Z jwb $
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!!! Jail is newer than host. (Jail: 1300109, Host: 1300100) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
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jwb at FreeBSD.org
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=======================<phase: check-sanity >============================
===> License GPLv3 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> subread-2.0.1 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.14.7.txz
[head-i386-default-job-02] Installing pkg-1.14.7...
[head-i386-default-job-02] Extracting pkg-1.14.7: .......... done
===> subread-2.0.1 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of subread-2.0.1
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by subread-2.0.1 for building
===========================================================================
=======================<phase: checksum >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by subread-2.0.1 for building
=> SHA256 Checksum OK for subread-2.0.1-source.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by subread-2.0.1 for building
===> Extracting for subread-2.0.1
=> SHA256 Checksum OK for subread-2.0.1-source.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for subread-2.0.1
===> Applying FreeBSD patches for subread-2.0.1 from /usr/ports/biology/subread/files
===========================================================================
=======================<phase: build-depends >============================
===> subread-2.0.1 depends on package: gmake>=4.3 - not found
===> Installing existing package /packages/All/gmake-4.3_2.txz
[head-i386-default-job-02] Installing gmake-4.3_2...
[head-i386-default-job-02] `-- Installing gettext-runtime-0.21...
[head-i386-default-job-02] | `-- Installing indexinfo-0.3.1...
[head-i386-default-job-02] | `-- Extracting indexinfo-0.3.1: .... done
<snip>
if(0&&memcmp(read + test_len - 1 - 30, TEST_TARGET +strlen(TEST_TARGET) -1 - 30, 30)==0)
~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
gene-value-index.c:457:53: note: use array indexing to silence this warning
if(0&&memcmp(read + test_len - 1 - 30, TEST_TARGET +strlen(TEST_TARGET) -1 - 30, 30)==0)
^
& [ ]
gene-value-index.c:509:53: warning: adding 'unsigned int' to a string does not append to the string [-Wstring-plus-int]
if(0&&memcmp(read + test_len - 1 - 30, TEST_TARGET + strlen(TEST_TARGET) - 31, 30)==0)
~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
gene-value-index.c:509:53: note: use array indexing to silence this warning
if(0&&memcmp(read + test_len - 1 - 30, TEST_TARGET + strlen(TEST_TARGET) - 31, 30)==0)
^
& [ ]
2 warnings generated.
cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o exon-algorithms.o exon-algorithms.c
cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o HelperFunctions.o HelperFunctions.c
HelperFunctions.c:1542:75: warning: implicit conversion from 'unsigned long long' to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-const-int-float-conversion]
SUBREADprintf("\t'%s'\t%016llX\t%llu\t%.9f\n", s, randv, randv, randv*1./0xffffffffffffffffllu);
~^~~~~~~~~~~~~~~~~~~~~
./subread.h:132:44: note: expanded from macro 'SUBREADprintf'
#define SUBREADprintf(...) fprintf(stderr, __VA_ARGS__)
^~~~~~~~~~~
cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o interval_merge.o interval_merge.c
cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o long-hashtable.o long-hashtable.c
1 warning generated.
cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o core-bigtable.o core-bigtable.c
cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o seek-zlib.o seek-zlib.c
cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o input-blc.o input-blc.c
input-blc.c:910:161: warning: format specifies type 'long' but the argument has type 'unsigned int' [-Wformat]
SUBREADprintf("ERROR: the cell barcodes have different lengths (%d!=%ld at %d). The program cannot process the cell barcodes.\n", known_cell_barcode_length, strlen(bcbstr),xx1);
~~~ ^~~~~~~~~~~~~~
%u
./subread.h:132:44: note: expanded from macro 'SUBREADprintf'
#define SUBREADprintf(...) fprintf(stderr, __VA_ARGS__)
^~~~~~~~~~~
1 warning generated.
cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -o genRandomReads gen_rand_reads.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -fstack-protector-strong -L/usr/local/lib -DMAKE_FOR_EXON -DMAKE_STANDALONE -pthread -lsysinfo -lz -lm
cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -o detectionCall detection-calls.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -fstack-protector-strong -L/usr/local/lib -DMAKE_FOR_EXON -DMAKE_STANDALONE -pthread -lsysinfo -lz -lm
gen_rand_reads.c:208:68: warning: implicit conversion from 'unsigned long long' to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-const-int-float-conversion]
double rand_01 = plain_txt_to_long_rand(grc->random_seeds, 16)*1./0xffffffffffffffffllu;
~^~~~~~~~~~~~~~~~~~~~~
gen_rand_reads.c:216:62: warning: implicit conversion from 'unsigned long long' to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-const-int-float-conversion]
rand_01 = plain_txt_to_long_rand(grc->random_seeds, 16)*1./0xffffffffffffffffllu;
~^~~~~~~~~~~~~~~~~~~~~
ld: error: duplicate symbol: replica_index
>>> defined at detection-calls.c
>>> /tmp/detection-calls-ea0a1e.o:(replica_index)
>>> defined at core.c
>>> core.o:(.bss+0x28)
ld: error: duplicate symbol: replica_index
>>> defined at detection-calls.c
>>> /tmp/detection-calls-ea0a1e.o:(replica_index)
>>> defined at core-junction.c
>>> core-junction.o:(.bss+0x0)
ld: error: duplicate symbol: replica_index
>>> defined at detection-calls.c
>>> /tmp/detection-calls-ea0a1e.o:(replica_index)
>>> defined at core-indel.c
>>> core-indel.o:(.bss+0x14)
ld: error: duplicate symbol: replica_index
>>> defined at detection-calls.c
>>> /tmp/detection-calls-ea0a1e.o:(replica_index)
>>> defined at sambam-file.c
>>> sambam-file.o:(.bss+0x8)
ld: error: duplicate symbol: replica_index
>>> defined at detection-calls.c
>>> /tmp/detection-calls-ea0a1e.o:(replica_index)
>>> defined at gene-algorithms.c
>>> gene-algorithms.o:(.bss+0xC)
ld: error: duplicate symbol: replica_index
>>> defined at detection-calls.c
>>> /tmp/detection-calls-ea0a1e.o:(replica_index)
>>> defined at input-files.c
>>> input-files.o:(.bss+0x18)
ld: error: duplicate symbol: replica_index
>>> defined at detection-calls.c
>>> /tmp/detection-calls-ea0a1e.o:(replica_index)
>>> defined at sorted-hashtable.c
>>> sorted-hashtable.o:(.bss+0x0)
ld: error: duplicate symbol: replica_index
>>> defined at detection-calls.c
>>> /tmp/detection-calls-ea0a1e.o:(replica_index)
>>> defined at gene-value-index.c
>>> gene-value-index.o:(.bss+0x0)
ld: error: duplicate symbol: replica_index
>>> defined at detection-calls.c
>>> /tmp/detection-calls-ea0a1e.o:(replica_index)
>>> defined at HelperFunctions.c
>>> HelperFunctions.o:(.bss+0x0)
ld: error: duplicate symbol: replica_index
>>> defined at detection-calls.c
>>> /tmp/detection-calls-ea0a1e.o:(replica_index)
>>> defined at core-bigtable.c
>>> core-bigtable.o:(.bss+0x0)
ld: error: duplicate symbol: replica_index
>>> defined at detection-calls.c
>>> /tmp/detection-calls-ea0a1e.o:(replica_index)
>>> defined at seek-zlib.c
>>> seek-zlib.o:(.bss+0x4)
ld: error: duplicate symbol: replica_index
>>> defined at detection-calls.c
>>> /tmp/detection-calls-ea0a1e.o:(replica_index)
>>> defined at input-blc.c
>>> input-blc.o:(.bss+0x0)
cc: error: linker command failed with exit code 1 (use -v to see invocation)
gmake[1]: *** [/usr/ports/biology/subread/files/Makefile.pkg:44: detectionCall] Error 1
gmake[1]: *** Waiting for unfinished jobs....
2 warnings generated.
ld: error: duplicate symbol: replica_index
>>> defined at gen_rand_reads.c
>>> /tmp/gen_rand_reads-f8f8fb.o:(replica_index)
>>> defined at core.c
>>> core.o:(.bss+0x28)
ld: error: duplicate symbol: replica_index
>>> defined at gen_rand_reads.c
>>> /tmp/gen_rand_reads-f8f8fb.o:(replica_index)
>>> defined at core-junction.c
>>> core-junction.o:(.bss+0x0)
ld: error: duplicate symbol: replica_index
>>> defined at gen_rand_reads.c
>>> /tmp/gen_rand_reads-f8f8fb.o:(replica_index)
>>> defined at core-indel.c
>>> core-indel.o:(.bss+0x14)
ld: error: duplicate symbol: replica_index
>>> defined at gen_rand_reads.c
>>> /tmp/gen_rand_reads-f8f8fb.o:(replica_index)
>>> defined at sambam-file.c
>>> sambam-file.o:(.bss+0x8)
ld: error: duplicate symbol: replica_index
>>> defined at gen_rand_reads.c
>>> /tmp/gen_rand_reads-f8f8fb.o:(replica_index)
>>> defined at gene-algorithms.c
>>> gene-algorithms.o:(.bss+0xC)
ld: error: duplicate symbol: replica_index
>>> defined at gen_rand_reads.c
>>> /tmp/gen_rand_reads-f8f8fb.o:(replica_index)
>>> defined at input-files.c
>>> input-files.o:(.bss+0x18)
ld: error: duplicate symbol: replica_index
>>> defined at gen_rand_reads.c
>>> /tmp/gen_rand_reads-f8f8fb.o:(replica_index)
>>> defined at sorted-hashtable.c
>>> sorted-hashtable.o:(.bss+0x0)
ld: error: duplicate symbol: replica_index
>>> defined at gen_rand_reads.c
>>> /tmp/gen_rand_reads-f8f8fb.o:(replica_index)
>>> defined at gene-value-index.c
>>> gene-value-index.o:(.bss+0x0)
ld: error: duplicate symbol: replica_index
>>> defined at gen_rand_reads.c
>>> /tmp/gen_rand_reads-f8f8fb.o:(replica_index)
>>> defined at HelperFunctions.c
>>> HelperFunctions.o:(.bss+0x0)
ld: error: duplicate symbol: replica_index
>>> defined at gen_rand_reads.c
>>> /tmp/gen_rand_reads-f8f8fb.o:(replica_index)
>>> defined at core-bigtable.c
>>> core-bigtable.o:(.bss+0x0)
ld: error: duplicate symbol: replica_index
>>> defined at gen_rand_reads.c
>>> /tmp/gen_rand_reads-f8f8fb.o:(replica_index)
>>> defined at seek-zlib.c
>>> seek-zlib.o:(.bss+0x4)
ld: error: duplicate symbol: replica_index
>>> defined at gen_rand_reads.c
>>> /tmp/gen_rand_reads-f8f8fb.o:(replica_index)
>>> defined at input-blc.c
>>> input-blc.o:(.bss+0x0)
cc: error: linker command failed with exit code 1 (use -v to see invocation)
gmake[1]: *** [/usr/ports/biology/subread/files/Makefile.pkg:38: genRandomReads] Error 1
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/subread/work/subread-2.0.1-source/src'
===> 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/subread
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