[package - main-armv7-default][biology/augustus] Failed for augustus-gene-prediction-3.5.0_3 in build
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Date: Wed, 09 Aug 2023 05:51:03 UTC
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@FreeBSD.org
Log URL: https://pkg-status.freebsd.org/ampere2/data/main-armv7-default/pf6493e8ca127_sc2cbd7ffa7/logs/augustus-gene-prediction-3.5.0_3.log
Build URL: https://pkg-status.freebsd.org/ampere2/build.html?mastername=main-armv7-default&build=pf6493e8ca127_sc2cbd7ffa7
Log:
=>> Building biology/augustus
build started at Wed Aug 9 05:40:08 UTC 2023
port directory: /usr/ports/biology/augustus
package name: augustus-gene-prediction-3.5.0_3
building for: FreeBSD main-armv7-default-job-03 14.0-CURRENT FreeBSD 14.0-CURRENT 1400093 arm
maintained by: yuri@FreeBSD.org
Makefile ident:
Poudriere version: 3.2.8-23-ga7f8d188
Host OSVERSION: 1400089
Jail OSVERSION: 1400093
Job Id: 03
!!! Jail is newer than host. (Jail: 1400093, Host: 1400089) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
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=======================<phase: check-sanity >============================
===> License GPLv3 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> augustus-gene-prediction-3.5.0_3 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.20.4.pkg
[main-armv7-default-job-03] Installing pkg-1.20.4...
[main-armv7-default-job-03] Extracting pkg-1.20.4: .......... done
===> augustus-gene-prediction-3.5.0_3 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of augustus-gene-prediction-3.5.0_3
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by augustus-gene-prediction-3.5.0_3 for building
===========================================================================
=======================<phase: checksum >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by augustus-gene-prediction-3.5.0_3 for building
=> SHA256 Checksum OK for Gaius-Augustus-Augustus-v3.5.0_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by augustus-gene-prediction-3.5.0_3 for building
===> Extracting for augustus-gene-prediction-3.5.0_3
=> SHA256 Checksum OK for Gaius-Augustus-Augustus-v3.5.0_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for augustus-gene-prediction-3.5.0_3
===> Applying FreeBSD patches for augustus-gene-prediction-3.5.0_3 from /usr/ports/biology/augustus/files
===========================================================================
=======================<phase: build-depends >============================
===> augustus-gene-prediction-3.5.0_3 depends on package: gmake>=4.3 - not found
===> Installing existing package /packages/All/gmake-4.3_2.pkg
[main-armv7-default-job-03] Installing gmake-4.3_2...
[main-armv7-default-job-03] `-- Installing gettext-runtime-0.22_1...
[main-armv7-default-job-03] | `-- Installing indexinfo-0.3.1...
<snip>
src/Coord_Transform.cpp:89:7: error: use of undeclared identifier 'bind2nd'
bind2nd(finding_intron_lesser_e<Genomic_Data::Intron>(), i));
^
src/Coord_Transform.cpp:93:7: error: use of undeclared identifier 'bind2nd'
bind2nd(finding_intron_lesser_s<Genomic_Data::Intron>(), i));
^
8 errors generated.
make[3]: *** [Makefile:36: build/Coord_Transform.o] Error 1
make[3]: Leaving directory '/wrkdirs/usr/ports/biology/augustus/work/Augustus-3.5.0/auxprogs/utrrnaseq'
gmake[2]: *** [Makefile:10: all] Error 2
gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/augustus/work/Augustus-3.5.0/auxprogs'
gmake[1]: *** [Makefile:16: auxprogs] Error 2
gmake[1]: *** Waiting for unfinished jobs....
c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o evaluation.o evaluation.cc
c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o motif.o motif.cc
c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o geneticcode.o geneticcode.cc
c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o hints.o hints.cc
c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o extrinsicinfo.o extrinsicinfo.cc
extrinsicinfo.cc:918:9: warning: variable 'grpcount' set but not used [-Wunused-but-set-variable]
int grpcount = 0, hintcount=0;
^
extrinsicinfo.cc:918:23: warning: variable 'hintcount' set but not used [-Wunused-but-set-variable]
int grpcount = 0, hintcount=0;
^
extrinsicinfo.cc:1079:9: warning: variable 'numIncompat' set but not used [-Wunused-but-set-variable]
int numIncompat = 0, numWeakerThan = 0, numEqual = 0;
^
extrinsicinfo.cc:1079:26: warning: variable 'numWeakerThan' set but not used [-Wunused-but-set-variable]
int numIncompat = 0, numWeakerThan = 0, numEqual = 0;
^
extrinsicinfo.cc:1079:45: warning: variable 'numEqual' set but not used [-Wunused-but-set-variable]
int numIncompat = 0, numWeakerThan = 0, numEqual = 0;
^
extrinsicinfo.cc:1115:9: warning: variable 'numTrashy' set but not used [-Wunused-but-set-variable]
int numTrashy=0;
^
c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o projectio.o projectio.cc
c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o intronmodel.o intronmodel.cc
6 warnings generated.
c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o exonmodel.o exonmodel.cc
c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o igenicmodel.o igenicmodel.cc
exonmodel.cc:1995:2: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation]
Double seqProb = 1;
^
exonmodel.cc:1986:5: note: previous statement is here
if (!(right-left+1 == Constant::et_coding_len))
^
c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o utrmodel.o utrmodel.cc
1 warning generated.
c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o merkmal.o merkmal.cc
c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o vitmatrix.o vitmatrix.cc
c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o lldouble.o lldouble.cc
c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o mea.o mea.cc
c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o graph.o graph.cc
mea.cc:326:29: warning: variable 'codlength' set but not used [-Wunused-but-set-variable]
int transStart, transEnd, codlength = 0;
^
1 warning generated.
c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o meaPath.o meaPath.cc
c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o exoncand.o exoncand.cc
c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o randseqaccess.o randseqaccess.cc
c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o fasta.o fasta.cc
c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o ncmodel.o ncmodel.cc
c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o parser/parse.o parser/parse.cc
c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o scanner/lex.o scanner/lex.cc
grammar:245:13: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation]
return elementPtr->d_action;
^
grammar:243:9: note: previous statement is here
if (d_debug__)
^
parser/parse.cc:65:16: warning: unused variable 'author' [-Wunused-const-variable]
char const author[] = "Frank B. Brokken (f.b.brokken@rug.nl)";
^
2 warnings generated.
c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o genomicMSA.o genomicMSA.cc
In file included from genomicMSA.cc:10:
In file included from ../include/genomicMSA.hh:11:
../include/alignment.hh:238:89: warning: binding reference member 'a' to stack allocated parameter 'a_' [-Wdangling-field]
IdxSortCriterion(vector<Alignment*> const a_, size_t speciesIdx) : s(speciesIdx), a(a_) {};
^~
../include/alignment.hh:253:31: note: reference member declared here
vector<Alignment*> const &a;
^
c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o geneMSA.o geneMSA.cc
In file included from geneMSA.cc:11:
In file included from ../include/genomicMSA.hh:11:
../include/alignment.hh:238:89: warning: binding reference member 'a' to stack allocated parameter 'a_' [-Wdangling-field]
IdxSortCriterion(vector<Alignment*> const a_, size_t speciesIdx) : s(speciesIdx), a(a_) {};
^~
../include/alignment.hh:253:31: note: reference member declared here
vector<Alignment*> const &a;
^
1 warning generated.
c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o contTimeMC.o contTimeMC.cc
1 warning generated.
c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o codonevo.o codonevo.cc
c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o compgenepred.o compgenepred.cc
In file included from codonevo.cc:10:
In file included from ../include/geneMSA.hh:12:
../include/alignment.hh:238:89: warning: binding reference member 'a' to stack allocated parameter 'a_' [-Wdangling-field]
IdxSortCriterion(vector<Alignment*> const a_, size_t speciesIdx) : s(speciesIdx), a(a_) {};
^~
../include/alignment.hh:253:31: note: reference member declared here
vector<Alignment*> const &a;
^
In file included from compgenepred.cc:8:
In file included from ../include/compgenepred.hh:15:
In file included from ../include/geneMSA.hh:12:
../include/alignment.hh:238:89: warning: binding reference member 'a' to stack allocated parameter 'a_' [-Wdangling-field]
IdxSortCriterion(vector<Alignment*> const a_, size_t speciesIdx) : s(speciesIdx), a(a_) {};
^~
../include/alignment.hh:253:31: note: reference member declared here
vector<Alignment*> const &a;
^
1 warning generated.
c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o phylotree.o phylotree.cc
In file included from phylotree.cc:12:
../include/phylotree.hh:54:10: warning: private field 'label' is not used [-Wunused-private-field]
bool label;
^
1 warning generated.
c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o orthograph.o orthograph.cc
In file included from orthograph.cc:10:
In file included from ../include/orthograph.hh:15:
In file included from ../include/geneMSA.hh:12:
../include/alignment.hh:238:89: warning: binding reference member 'a' to stack allocated parameter 'a_' [-Wdangling-field]
IdxSortCriterion(vector<Alignment*> const a_, size_t speciesIdx) : s(speciesIdx), a(a_) {};
^~
../include/alignment.hh:253:31: note: reference member declared here
vector<Alignment*> const &a;
^
1 warning generated.
c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o orthoexon.o orthoexon.cc
1 warning generated.
c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o alignment.o alignment.cc
c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o speciesgraph.o speciesgraph.cc
In file included from alignment.cc:8:
../include/alignment.hh:238:89: warning: binding reference member 'a' to stack allocated parameter 'a_' [-Wdangling-field]
IdxSortCriterion(vector<Alignment*> const a_, size_t speciesIdx) : s(speciesIdx), a(a_) {};
^~
../include/alignment.hh:253:31: note: reference member declared here
vector<Alignment*> const &a;
^
1 warning generated.
c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o codonMSA.o codonMSA.cc
c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o train_logReg_param.o train_logReg_param.cc
c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o tokenizer.o tokenizer.cc
c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o sqliteDB.o sqliteDB.cc
c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o commontrain.o commontrain.cc
c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o igenictrain.o igenictrain.cc
c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o introntrain.o introntrain.cc
c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o exontrain.o exontrain.cc
c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o utrtrain.o utrtrain.cc
c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o dummy.o dummy.cc
c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -L/usr/local/lib/mysql -fstack-protector-strong -L/usr/local/lib -o prepareAlign pp_prepare_align.cc
c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o pp_fastBlockSearcher.o pp_fastBlockSearcher.cc
cp -f prepareAlign ../bin/
c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -L/usr/local/lib/mysql -fstack-protector-strong -L/usr/local/lib -I../include -I/usr/include/lpsolve -I/usr/include/mysql -o pp_simScore pp_simscore.cc fasta.o types.o properties.o geneticcode.o pp_profile.o lldouble.o -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lboost_serialization -lmysqlclient -lmysqlpp -lsqlite3
c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -L/usr/local/lib/mysql -fstack-protector-strong -L/usr/local/lib -I../include -I/usr/include/lpsolve -I/usr/include/mysql -o load2db load2db.cc fasta.o hints.o types.o properties.o lldouble.o -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lboost_serialization -lmysqlclient -lmysqlpp -lsqlite3
pp_simscore.cc:870:21: warning: unused variable 'count_miss' [-Wunused-variable]
pair <int, int> count_miss;
^
load2db.cc:196:17: warning: result of comparison of constant -1 with expression of type 'FeatureType' is always true [-Wtautological-constant-out-of-range-compare]
if(f.type != -1){
~~~~~~ ^ ~~
1 warning generated.
cp -f load2db ../bin/
c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -L/usr/local/lib/mysql -fstack-protector-strong -L/usr/local/lib -I../include -I/usr/include/lpsolve -I/usr/include/mysql -o getSeq getSeq.cc genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o types.o gene.o evaluation.o motif.o geneticcode.o hints.o extrinsicinfo.o projectio.o intronmodel.o exonmodel.o igenicmodel.o utrmodel.o merkmal.o vitmatrix.o lldouble.o mea.o graph.o meaPath.o exoncand.o randseqaccess.o fasta.o ncmodel.o parser/parse.o scanner/lex.o genomicMSA.o geneMSA.o contTimeMC.o codonevo.o compgenepred.o phylotree.o orthograph.o orthoexon.o alignment.o speciesgraph.o codonMSA.o tr
ain_logReg_param.o tokenizer.o sqliteDB.o dummy.o -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lboost_serialization -lmysqlclient -lmysqlpp -lsqlite3
1 warning generated.
cp -f pp_simScore ../bin/
c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -L/usr/local/lib/mysql -fstack-protector-strong -L/usr/local/lib -I../include -I/usr/include/lpsolve -I/usr/include/mysql -o load2sqlitedb load2sqlitedb.cc fasta.o hints.o types.o properties.o lldouble.o sqliteDB.o -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lboost_serialization -lmysqlclient -lmysqlpp -lsqlite3
cp -f load2sqlitedb ../bin/
echo "-Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE" > cxxflags
c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -L/usr/local/lib/mysql -fstack-protector-strong -L/usr/local/lib -I../include -I/usr/include/lpsolve -I/usr/include/mysql -o augustus augustus.cc genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o types.o gene.o evaluation.o motif.o geneticcode.o hints.o extrinsicinfo.o projectio.o intronmodel.o exonmodel.o igenicmodel.o utrmodel.o merkmal.o vitmatrix.o lldouble.o mea.o graph.o meaPath.o exoncand.o randseqaccess.o fasta.o ncmodel.o parser/parse.o scanner/lex.o genomicMSA.o geneMSA.o contTimeMC.o codonevo.o compgenepred.o phylotree.o orthograph.o orthoexon.o alignment.o speciesgraph.o codonMSA.
o train_logReg_param.o tokenizer.o sqliteDB.o dummy.o -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lboost_serialization -lmysqlclient -lmysqlpp -lsqlite3
cp -f getSeq ../bin/
c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -L/usr/local/lib/mysql -fstack-protector-strong -L/usr/local/lib -I../include -I/usr/include/lpsolve -I/usr/include/mysql -o etraining etraining.cc commontrain.o igenictrain.o introntrain.o exontrain.o utrtrain.o genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o types.o gene.o evaluation.o motif.o geneticcode.o hints.o extrinsicinfo.o projectio.o intronmodel.o exonmodel.o igenicmodel.o utrmodel.o merkmal.o vitmatrix.o lldouble.o mea.o graph.o meaPath.o exoncand.o randseqaccess.o fasta.o ncmodel.o parser/parse.o scanner/lex.o genomicMSA.o geneMSA.o contTimeMC.o codonevo.o compgenepred.o phylot
ree.o orthograph.o orthoexon.o alignment.o speciesgraph.o codonMSA.o train_logReg_param.o tokenizer.o sqliteDB.o -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lboost_serialization -lmysqlclient -lmysqlpp -lsqlite3
In file included from augustus.cc:21:
In file included from ../include/compgenepred.hh:15:
In file included from ../include/geneMSA.hh:12:
../include/alignment.hh:238:89: warning: binding reference member 'a' to stack allocated parameter 'a_' [-Wdangling-field]
IdxSortCriterion(vector<Alignment*> const a_, size_t speciesIdx) : s(speciesIdx), a(a_) {};
^~
../include/alignment.hh:253:31: note: reference member declared here
vector<Alignment*> const &a;
^
cp -f etraining ../bin/
c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -L/usr/local/lib/mysql -fstack-protector-strong -L/usr/local/lib -I../include -I/usr/include/lpsolve -I/usr/include/mysql -o fastBlockSearch fastBlockSearch.cc pp_fastBlockSearcher.o types.o properties.o geneticcode.o pp_profile.o lldouble.o -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lboost_serialization -lmysqlclient -lmysqlpp -lsqlite3
1 warning generated.
cp -f augustus ../bin/
cp -f fastBlockSearch ../bin/
gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/augustus/work/Augustus-3.5.0/src'
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/augustus/work/Augustus-3.5.0'
===> 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/augustus