bitseq (homebrew/science/bitseq) on "Red Hat Enterprise Linux Server release 7.2 (Maipo)" - Homebrew build logs

# bitseq - 2016-09-11_13-19-13.txt

Homebrew build logs for homebrew/science/bitseq on "Red Hat Enterprise Linux Server release 7.2 (Maipo)"
Build date: 2016-09-11 13:19:13

00.config.out

HOMEBREW_VERSION: 0.9.9
ORIGIN: https://github.com/Linuxbrew/brew
HEAD: c4af6483033a3c1ff8a4492f881bb8100459dced
Last commit: 11 days ago
Core tap ORIGIN: https://github.com/Linuxbrew/homebrew-core
Core tap HEAD: 4979add803641db3143b1903a7c91b29644b5958
Core tap last commit: 4 days ago
HOMEBREW_PREFIX: /home/linuxbrew/.linuxbrew
HOMEBREW_REPOSITORY: /home/linuxbrew/.linuxbrew
HOMEBREW_CELLAR: /home/linuxbrew/.linuxbrew/Cellar
HOMEBREW_BOTTLE_DOMAIN: https://linuxbrew.bintray.com
CPU: 72-core 64-bit haswell
Homebrew Ruby: 2.3.1 => /home/linuxbrew/.linuxbrew/Cellar/ruby/2.3.1/bin/ruby
Clang: N/A
Git: 2.9.3 => /home/linuxbrew/.linuxbrew/bin/git
Perl: /bin/perl => /usr/bin/perl
Python: /home/linuxbrew/.linuxbrew/bin/python => /home/linuxbrew/.linuxbrew/Cellar/python/2.7.12_1/bin/python2.7
Ruby: /home/linuxbrew/.linuxbrew/bin/ruby => /home/linuxbrew/.linuxbrew/Cellar/ruby/2.3.1/bin/ruby
Java: 1.8.0_102
Kernel: Linux 3.10.0-327.28.3.el7.x86_64 x86_64 GNU/Linux
OS: Red Hat Enterprise Linux Server release 7.2 (Maipo)
Codename: Maipo
OS glibc: 2.17
OS gcc: 4.8.5
Linuxbrew glibc: 2.19
Linuxbrew gcc: 5.3.0
Linuxbrew xorg: 20160314

00.doctor.out

Please note that these warnings are just used to help the Homebrew maintainers
with debugging if you file an issue. If everything you use Homebrew for is
working fine: please don't worry and just ignore them. Thanks!

Warning: "config" scripts exist outside your system or Homebrew directories.
`./configure` scripts often look for *-config scripts to determine if
software packages are installed, and what additional flags to use when
compiling and linking.

Having additional scripts in your path can confuse software installed via
Homebrew if the config script overrides a system or Homebrew provided
script of the same name. We found the following "config" scripts:
    /bin/pkg-config
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    /bin/ncurses5-config
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    /bin/nss-config
    /bin/curl-config
    /bin/ncursesw5-config
    /bin/freetype-config
    /bin/libpng-config
    /bin/libpng15-config
    /bin/gdlib-config
    /bin/nspr-config
    /bin/nss-util-config
    /bin/apr-1-config
    /bin/pcre-config
    /bin/python2-config
    /bin/python-config
    /bin/python2.7-config
    /bin/nss-softokn-config
    /bin/kde4-config
    /bin/apu-1-config
    /bin/gpg-error-config
    /bin/libgcrypt-config
    /bin/xml2-config
    /bin/icu-config
    /bin/krb5-config
    /bin/libgnutls-config
    /bin/sdl-config
    /bin/xslt-config
    /bin/sane-config
    /bin/cups-config
    /bin/net-snmp-config
    /bin/pcap-config

Warning: You have unlinked kegs in your Cellar
Leaving kegs unlinked can lead to build-trouble and cause brews that depend on
those kegs to fail to run properly once built. Run `brew link` on these:
    hdf4
    numpy
    libdivsufsort
    circlator

00.tap.out

Formula: bitseq
Tap: homebrew/science
Path: /home/linuxbrew/.linuxbrew/Library/Taps/homebrew/homebrew-science/bitseq.rb

01.make

2016-09-11 13:19:13 +1000

make
LDFLAGS=-Wl,-dead_strip

g++ -DBS_VERSION=\"0.7.5\" -Wall -mtune=generic -O2 -pipe -ffunction-sections -fdata-sections -c ArgumentParser.cpp
g++ -DBS_VERSION=\"0.7.5\" -Wall -mtune=generic -O2 -pipe -isystem/home/linuxbrew/.linuxbrew/include  -c -o common.o common.cpp
g++ -DBS_VERSION=\"0.7.5\" -Wall -mtune=generic -O2 -pipe -I . -ffunction-sections -fdata-sections -c FileHeader.cpp
g++ -DBS_VERSION=\"0.7.5\" -Wall -mtune=generic -O2 -pipe -ffunction-sections -fdata-sections -c misc.cpp
g++ -DBS_VERSION=\"0.7.5\" -Wall -mtune=generic -O2 -pipe -ffunction-sections -fdata-sections -c MyTimer.cpp
g++ -DBS_VERSION=\"0.7.5\" -Wall -mtune=generic -O2 -pipe -isystem/home/linuxbrew/.linuxbrew/include  -c -o TranscriptInfo.o TranscriptInfo.cpp
g++ -DBS_VERSION=\"0.7.5\" -Wall -mtune=generic -O2 -pipe -ffunction-sections -fdata-sections -c PosteriorSamples.cpp
g++ -DBS_VERSION=\"0.7.5\" -Wall -mtune=generic -O2 -pipe -I . -c CollapsedSampler.cpp
g++ -DBS_VERSION=\"0.7.5\" -Wall -mtune=generic -O2 -pipe -isystem/home/linuxbrew/.linuxbrew/include  -c -o GibbsParameters.o GibbsParameters.cpp
g++ -DBS_VERSION=\"0.7.5\" -Wall -mtune=generic -O2 -pipe -I . -c GibbsSampler.cpp
g++ -DBS_VERSION=\"0.7.5\" -Wall -mtune=generic -O2 -pipe -I . -c Sampler.cpp
g++ -DBS_VERSION=\"0.7.5\" -Wall -mtune=generic -O2 -pipe -isystem/home/linuxbrew/.linuxbrew/include  -c -o TagAlignments.o TagAlignments.cpp
g++ -DBS_VERSION=\"0.7.5\" -Wall -mtune=generic -O2 -pipe -isystem/home/linuxbrew/.linuxbrew/include  -c -o transposeFiles.o transposeFiles.cpp
g++ -DBS_VERSION=\"0.7.5\" -Wall -mtune=generic -O2 -pipe -isystem/home/linuxbrew/.linuxbrew/include  -c -o lowess.o lowess.cpp
g++ -DBS_VERSION=\"0.7.5\" -Wall -mtune=generic -O2 -pipe -isystem/home/linuxbrew/.linuxbrew/include  -c -o TranscriptExpression.o TranscriptExpression.cpp
g++ -DBS_VERSION=\"0.7.5\" -Wall -mtune=generic -O2 -pipe -fopenmp -DSUPPORT_OPENMP -c SimpleSparse.cpp
g++ -DBS_VERSION=\"0.7.5\" -Wall -mtune=generic -O2 -pipe -I . -fopenmp -DSUPPORT_OPENMP -c VariationalBayes.cpp 
g++ -DBS_VERSION=\"0.7.5\" -Wall -mtune=generic -O2 -pipe -fopenmp -DSUPPORT_OPENMP -c ReadDistribution.cpp
make --directory samtools
g++ -DBS_VERSION=\"0.7.5\" -Wall -mtune=generic -O2 -pipe -isystem/home/linuxbrew/.linuxbrew/include  -c -o TranscriptSequence.o TranscriptSequence.cpp
make[1]: Entering directory `/tmp/bitseq-20160911-138390-1x5oyrm/BitSeq-0.7.5/samtools'
make[1]: warning: jobserver unavailable: using -j1.  Add `+' to parent make rule.
gcc -c -O2 -mtune=generic -ffunction-sections -fdata-sections  -I. sam.c -o sam.o
gcc -c -O2 -mtune=generic -ffunction-sections -fdata-sections  -I. bam.c -o bam.o
ReadDistribution.cpp: In member function 'bool ReadDistribution::observed(ns_rD::fragmentP)':
ReadDistribution.cpp:265:30: warning: suggest parentheses around operand of '!' or change '&' to '&&' or '!' to '~' [-Wparentheses]
        (! frag->second->core.flag & BAM_FREVERSE))){
                              ^
ReadDistribution.cpp: In member function 'bool ReadDistribution::getP(ns_rD::fragmentP, double&, double&)':
ReadDistribution.cpp:687:35: warning: suggest parentheses around operand of '!' or change '&' to '&&' or '!' to '~' [-Wparentheses]
             (! frag->second->core.flag & BAM_FREVERSE))){
                                   ^
gcc -c -O2 -mtune=generic -ffunction-sections -fdata-sections  -I. sam_header.c -o sam_header.o
gcc -c -O2 -mtune=generic -ffunction-sections -fdata-sections  -I. kstring.c -o kstring.o
gcc -c -O2 -mtune=generic -ffunction-sections -fdata-sections  -I. faidx.c -o faidx.o
gcc -c -O2 -mtune=generic -ffunction-sections -fdata-sections  -I. razf.c -o razf.o
gcc -c -O2 -mtune=generic -ffunction-sections -fdata-sections  -I. bgzf.c -o bgzf.o
g++ -DBS_VERSION=\"0.7.5\" -Wall -mtune=generic -O2 -pipe -Wl,-dead_strip convertSamples.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o TranscriptInfo.o -o convertSamples
g++ -DBS_VERSION=\"0.7.5\" -Wall -mtune=generic -O2 -pipe -I . -Wl,-dead_strip estimateDE.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o PosteriorSamples.o -o estimateDE
g++ -DBS_VERSION=\"0.7.5\" -Wall -mtune=generic -O2 -pipe -I . -fopenmp -DSUPPORT_OPENMP -Wl,-dead_strip estimateExpression.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o CollapsedSampler.o GibbsParameters.o GibbsSampler.o Sampler.o TagAlignments.o TranscriptInfo.o transposeFiles.o -o estimateExpression
g++ -DBS_VERSION=\"0.7.5\" -Wall -mtune=generic -O2 -pipe -I . -Wl,-dead_strip estimateHyperPar.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o lowess.o PosteriorSamples.o TranscriptExpression.o -o estimateHyperPar
g++ -DBS_VERSION=\"0.7.5\" -Wall -mtune=generic -O2 -pipe -I . -fopenmp -DSUPPORT_OPENMP -Wl,-dead_strip estimateVBExpression.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o SimpleSparse.o TagAlignments.o TranscriptInfo.o transposeFiles.o VariationalBayes.o -o estimateVBExpression
g++ -DBS_VERSION=\"0.7.5\" -Wall -mtune=generic -O2 -pipe -Wl,-dead_strip extractSamples.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o PosteriorSamples.o -o extractSamples
g++ -DBS_VERSION=\"0.7.5\" -Wall -mtune=generic -O2 -pipe -Wl,-dead_strip getFoldChange.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o PosteriorSamples.o -o getFoldChange
g++ -DBS_VERSION=\"0.7.5\" -Wall -mtune=generic -O2 -pipe -Wl,-dead_strip getGeneExpression.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o PosteriorSamples.o TranscriptInfo.o -o getGeneExpression
g++ -DBS_VERSION=\"0.7.5\" -Wall -mtune=generic -O2 -pipe -Wl,-dead_strip getPPLR.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o PosteriorSamples.o -o getPPLR
g++ -DBS_VERSION=\"0.7.5\" -Wall -mtune=generic -O2 -pipe -Wl,-dead_strip getVariance.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o PosteriorSamples.o -o getVariance
g++ -DBS_VERSION=\"0.7.5\" -Wall -mtune=generic -O2 -pipe -Wl,-dead_strip getWithinGeneExpression.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o PosteriorSamples.o TranscriptInfo.o -o getWithinGeneExpression
g++ -DBS_VERSION=\"0.7.5\" -Wall -mtune=generic -O2 -pipe -Wl,-dead_strip transposeLargeFile.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o transposeFiles.o -o transposeLargeFile
gcc -c -O2 -mtune=generic -ffunction-sections -fdata-sections  -I. bam_import.c -o bam_import.o
/home/linuxbrew/.linuxbrew/bin/ld: warning: cannot find entry symbol ad_strip; defaulting to 0000000000402710
misc.o: In function `ns_genes::prepareInput(ArgumentParser const&, TranscriptInfo*, PosteriorSamples*, long*, long*, long*)':
misc.cpp:(.text._ZN8ns_genes12prepareInputERK14ArgumentParserP14TranscriptInfoP16PosteriorSamplesPlS7_S7_+0x5b): undefined reference to `TranscriptInfo::readInfo(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)'
misc.cpp:(.text._ZN8ns_genes12prepareInputERK14ArgumentParserP14TranscriptInfoP16PosteriorSamplesPlS7_S7_+0xa4): undefined reference to `TranscriptInfo::getG() const'
misc.cpp:(.text._ZN8ns_genes12prepareInputERK14ArgumentParserP14TranscriptInfoP16PosteriorSamplesPlS7_S7_+0xe5): undefined reference to `PosteriorSamples::initSet(long*, long*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)'
misc.cpp:(.text._ZN8ns_genes12prepareInputERK14ArgumentParserP14TranscriptInfoP16PosteriorSamplesPlS7_S7_+0x11d): undefined reference to `TranscriptInfo::getM() const'
misc.cpp:(.text._ZN8ns_genes12prepareInputERK14ArgumentParserP14TranscriptInfoP16PosteriorSamplesPlS7_S7_+0x1d3): undefined reference to `TranscriptInfo::getM() const'
misc.o: In function `ns_misc::readConditions(ArgumentParser const&, long*, long*, long*, Conditions*)':
misc.cpp:(.text._ZN7ns_misc14readConditionsERK14ArgumentParserPlS3_S3_P10Conditions+0x11f): undefined reference to `Conditions::init(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >, long*, long*, long*)'
misc.cpp:(.text._ZN7ns_misc14readConditionsERK14ArgumentParserPlS3_S3_P10Conditions+0x29d): undefined reference to `Conditions::setNorm(std::vector<double, std::allocator<double> >)'
misc.o: In function `ns_genes::updateGenes(ArgumentParser const&, TranscriptInfo*, long*)':
misc.cpp:(.text._ZN8ns_genes11updateGenesERK14ArgumentParserP14TranscriptInfoPl+0x775): undefined reference to `TranscriptInfo::updateGeneNames(std::map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::less<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > const&)'
misc.cpp:(.text._ZN8ns_genes11updateGenesERK14ArgumentParserP14TranscriptInfoPl+0xb4f): undefined reference to `TranscriptInfo::getG() const'
misc.cpp:(.text._ZN8ns_genes11updateGenesERK14ArgumentParserP14TranscriptInfoPl+0xb73): undefined reference to `TranscriptInfo::updateGeneNames(std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&)'
collect2: error: ld returned 1 exit status
make: *** [transposeLargeFile] Error 1
make: *** Waiting for unfinished jobs....
gcc -c -O2 -mtune=generic -ffunction-sections -fdata-sections  -I. bam_aux.c -o bam_aux.o
/home/linuxbrew/.linuxbrew/bin/ld: warning: cannot find entry symbol ad_strip; defaulting to 0000000000402a70
misc.o: In function `ns_genes::prepareInput(ArgumentParser const&, TranscriptInfo*, PosteriorSamples*, long*, long*, long*)':
misc.cpp:(.text._ZN8ns_genes12prepareInputERK14ArgumentParserP14TranscriptInfoP16PosteriorSamplesPlS7_S7_+0xe5): undefined reference to `PosteriorSamples::initSet(long*, long*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)'
misc.o: In function `ns_misc::readConditions(ArgumentParser const&, long*, long*, long*, Conditions*)':
misc.cpp:(.text._ZN7ns_misc14readConditionsERK14ArgumentParserPlS3_S3_P10Conditions+0x11f): undefined reference to `Conditions::init(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >, long*, long*, long*)'
misc.cpp:(.text._ZN7ns_misc14readConditionsERK14ArgumentParserPlS3_S3_P10Conditions+0x29d): undefined reference to `Conditions::setNorm(std::vector<double, std::allocator<double> >)'
collect2: error: ld returned 1 exit status
make: *** [convertSamples] Error 1
gcc -c -O2 -mtune=generic -ffunction-sections -fdata-sections  -I. bam_pileup.c -o bam_pileup.o
/home/linuxbrew/.linuxbrew/bin/ld: warning: cannot find entry symbol ad_strip; defaulting to 0000000000402be0
misc.o: In function `ns_genes::prepareInput(ArgumentParser const&, TranscriptInfo*, PosteriorSamples*, long*, long*, long*)':
misc.cpp:(.text._ZN8ns_genes12prepareInputERK14ArgumentParserP14TranscriptInfoP16PosteriorSamplesPlS7_S7_+0x5b): undefined reference to `TranscriptInfo::readInfo(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)'
misc.cpp:(.text._ZN8ns_genes12prepareInputERK14ArgumentParserP14TranscriptInfoP16PosteriorSamplesPlS7_S7_+0xa4): undefined reference to `TranscriptInfo::getG() const'
misc.cpp:(.text._ZN8ns_genes12prepareInputERK14ArgumentParserP14TranscriptInfoP16PosteriorSamplesPlS7_S7_+0x11d): undefined reference to `TranscriptInfo::getM() const'
misc.cpp:(.text._ZN8ns_genes12prepareInputERK14ArgumentParserP14TranscriptInfoP16PosteriorSamplesPlS7_S7_+0x1d3): undefined reference to `TranscriptInfo::getM() const'
misc.o: In function `ns_genes::updateGenes(ArgumentParser const&, TranscriptInfo*, long*)':
misc.cpp:(.text._ZN8ns_genes11updateGenesERK14ArgumentParserP14TranscriptInfoPl+0x775): undefined reference to `TranscriptInfo::updateGeneNames(std::map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::less<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > const&)'
misc.cpp:(.text._ZN8ns_genes11updateGenesERK14ArgumentParserP14TranscriptInfoPl+0xb4f): undefined reference to `TranscriptInfo::getG() const'
misc.cpp:(.text._ZN8ns_genes11updateGenesERK14ArgumentParserP14TranscriptInfoPl+0xb73): undefined reference to `TranscriptInfo::updateGeneNames(std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&)'
collect2: error: ld returned 1 exit status
make: *** [extractSamples] Error 1
/home/linuxbrew/.linuxbrew/bin/ld: warning: cannot find entry symbol ad_strip; defaulting to 00000000004028b0
misc.o: In function `ns_genes::prepareInput(ArgumentParser const&, TranscriptInfo*, PosteriorSamples*, long*, long*, long*)':
misc.cpp:(.text._ZN8ns_genes12prepareInputERK14ArgumentParserP14TranscriptInfoP16PosteriorSamplesPlS7_S7_+0x5b): undefined reference to `TranscriptInfo::readInfo(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)'
misc.cpp:(.text._ZN8ns_genes12prepareInputERK14ArgumentParserP14TranscriptInfoP16PosteriorSamplesPlS7_S7_+0xa4): undefined reference to `TranscriptInfo::getG() const'
misc.cpp:(.text._ZN8ns_genes12prepareInputERK14ArgumentParserP14TranscriptInfoP16PosteriorSamplesPlS7_S7_+0x11d): undefined reference to `TranscriptInfo::getM() const'
misc.cpp:(.text._ZN8ns_genes12prepareInputERK14ArgumentParserP14TranscriptInfoP16PosteriorSamplesPlS7_S7_+0x1d3): undefined reference to `TranscriptInfo::getM() const'
misc.o: In function `ns_genes::updateGenes(ArgumentParser const&, TranscriptInfo*, long*)':
misc.cpp:(.text._ZN8ns_genes11updateGenesERK14ArgumentParserP14TranscriptInfoPl+0x775): undefined reference to `TranscriptInfo::updateGeneNames(std::map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::less<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > const&)'
misc.cpp:(.text._ZN8ns_genes11updateGenesERK14ArgumentParserP14TranscriptInfoPl+0xb4f): undefined reference to `TranscriptInfo::getG() const'
misc.cpp:(.text._ZN8ns_genes11updateGenesERK14ArgumentParserP14TranscriptInfoPl+0xb73): undefined reference to `TranscriptInfo::updateGeneNames(std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&)'
collect2: error: ld returned 1 exit status
make: *** [getVariance] Error 1
/home/linuxbrew/.linuxbrew/bin/ld: warning: cannot find entry symbol ad_strip; defaulting to 0000000000402ba0
misc.o: In function `ns_genes::prepareInput(ArgumentParser const&, TranscriptInfo*, PosteriorSamples*, long*, long*, long*)':
misc.cpp:(.text._ZN8ns_genes12prepareInputERK14ArgumentParserP14TranscriptInfoP16PosteriorSamplesPlS7_S7_+0x5b): undefined reference to `TranscriptInfo::readInfo(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)'
misc.cpp:(.text._ZN8ns_genes12prepareInputERK14ArgumentParserP14TranscriptInfoP16PosteriorSamplesPlS7_S7_+0xa4): undefined reference to `TranscriptInfo::getG() const'
misc.cpp:(.text._ZN8ns_genes12prepareInputERK14ArgumentParserP14TranscriptInfoP16PosteriorSamplesPlS7_S7_+0x11d): undefined reference to `TranscriptInfo::getM() const'
misc.cpp:(.text._ZN8ns_genes12prepareInputERK14ArgumentParserP14TranscriptInfoP16PosteriorSamplesPlS7_S7_+0x1d3): undefined reference to `TranscriptInfo::getM() const'
misc.o: In function `ns_genes::updateGenes(ArgumentParser const&, TranscriptInfo*, long*)':
misc.cpp:(.text._ZN8ns_genes11updateGenesERK14ArgumentParserP14TranscriptInfoPl+0x775): undefined reference to `TranscriptInfo::updateGeneNames(std::map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::less<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > const&)'
misc.cpp:(.text._ZN8ns_genes11updateGenesERK14ArgumentParserP14TranscriptInfoPl+0xb4f): undefined reference to `TranscriptInfo::getG() const'
misc.cpp:(.text._ZN8ns_genes11updateGenesERK14ArgumentParserP14TranscriptInfoPl+0xb73): undefined reference to `TranscriptInfo::updateGeneNames(std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&)'
collect2: error: ld returned 1 exit status
make: *** [getFoldChange] Error 1
make[1]: Leaving directory `/tmp/bitseq-20160911-138390-1x5oyrm/BitSeq-0.7.5/samtools'
/home/linuxbrew/.linuxbrew/bin/ld: warning: cannot find entry symbol ad_strip; defaulting to 0000000000402c20
misc.o: In function `ns_genes::prepareInput(ArgumentParser const&, TranscriptInfo*, PosteriorSamples*, long*, long*, long*)':
misc.cpp:(.text._ZN8ns_genes12prepareInputERK14ArgumentParserP14TranscriptInfoP16PosteriorSamplesPlS7_S7_+0x5b): undefined reference to `TranscriptInfo::readInfo(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)'
misc.cpp:(.text._ZN8ns_genes12prepareInputERK14ArgumentParserP14TranscriptInfoP16PosteriorSamplesPlS7_S7_+0xa4): undefined reference to `TranscriptInfo::getG() const'
misc.cpp:(.text._ZN8ns_genes12prepareInputERK14ArgumentParserP14TranscriptInfoP16PosteriorSamplesPlS7_S7_+0x11d): undefined reference to `TranscriptInfo::getM() const'
misc.cpp:(.text._ZN8ns_genes12prepareInputERK14ArgumentParserP14TranscriptInfoP16PosteriorSamplesPlS7_S7_+0x1d3): undefined reference to `TranscriptInfo::getM() const'
misc.o: In function `ns_genes::updateGenes(ArgumentParser const&, TranscriptInfo*, long*)':
misc.cpp:(.text._ZN8ns_genes11updateGenesERK14ArgumentParserP14TranscriptInfoPl+0x775): undefined reference to `TranscriptInfo::updateGeneNames(std::map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::less<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > const&)'
misc.cpp:(.text._ZN8ns_genes11updateGenesERK14ArgumentParserP14TranscriptInfoPl+0xb4f): undefined reference to `TranscriptInfo::getG() const'
misc.cpp:(.text._ZN8ns_genes11updateGenesERK14ArgumentParserP14TranscriptInfoPl+0xb73): undefined reference to `TranscriptInfo::updateGeneNames(std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&)'
collect2: error: ld returned 1 exit status
make: *** [getPPLR] Error 1
/home/linuxbrew/.linuxbrew/bin/ld: warning: cannot find entry symbol ad_strip; defaulting to 0000000000402c60
/home/linuxbrew/.linuxbrew/bin/ld: warning: cannot find entry symbol ad_strip; defaulting to 0000000000402ba0
/home/linuxbrew/.linuxbrew/bin/ld: warning: cannot find entry symbol ad_strip; defaulting to 0000000000402ff0
misc.o: In function `ns_genes::prepareInput(ArgumentParser const&, TranscriptInfo*, PosteriorSamples*, long*, long*, long*)':
misc.cpp:(.text._ZN8ns_genes12prepareInputERK14ArgumentParserP14TranscriptInfoP16PosteriorSamplesPlS7_S7_+0xe5): undefined reference to `PosteriorSamples::initSet(long*, long*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)'
misc.o: In function `ns_misc::readConditions(ArgumentParser const&, long*, long*, long*, Conditions*)':
misc.cpp:(.text._ZN7ns_misc14readConditionsERK14ArgumentParserPlS3_S3_P10Conditions+0x11f): undefined reference to `Conditions::init(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >, long*, long*, long*)'
misc.cpp:(.text._ZN7ns_misc14readConditionsERK14ArgumentParserPlS3_S3_P10Conditions+0x29d): undefined reference to `Conditions::setNorm(std::vector<double, std::allocator<double> >)'
collect2: error: ld returned 1 exit status
make: *** [estimateVBExpression] Error 1
/home/linuxbrew/.linuxbrew/bin/ld: warning: cannot find entry symbol ad_strip; defaulting to 0000000000402d00
misc.o: In function `ns_genes::prepareInput(ArgumentParser const&, TranscriptInfo*, PosteriorSamples*, long*, long*, long*)':
misc.cpp:(.text._ZN8ns_genes12prepareInputERK14ArgumentParserP14TranscriptInfoP16PosteriorSamplesPlS7_S7_+0x5b): undefined reference to `TranscriptInfo::readInfo(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)'
misc.cpp:(.text._ZN8ns_genes12prepareInputERK14ArgumentParserP14TranscriptInfoP16PosteriorSamplesPlS7_S7_+0xa4): undefined reference to `TranscriptInfo::getG() const'
misc.cpp:(.text._ZN8ns_genes12prepareInputERK14ArgumentParserP14TranscriptInfoP16PosteriorSamplesPlS7_S7_+0x11d): undefined reference to `TranscriptInfo::getM() const'
misc.cpp:(.text._ZN8ns_genes12prepareInputERK14ArgumentParserP14TranscriptInfoP16PosteriorSamplesPlS7_S7_+0x1d3): undefined reference to `TranscriptInfo::getM() const'
misc.o: In function `ns_genes::updateGenes(ArgumentParser const&, TranscriptInfo*, long*)':
misc.cpp:(.text._ZN8ns_genes11updateGenesERK14ArgumentParserP14TranscriptInfoPl+0x775): undefined reference to `TranscriptInfo::updateGeneNames(std::map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::less<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > const&)'
misc.cpp:(.text._ZN8ns_genes11updateGenesERK14ArgumentParserP14TranscriptInfoPl+0xb4f): undefined reference to `TranscriptInfo::getG() const'
misc.cpp:(.text._ZN8ns_genes11updateGenesERK14ArgumentParserP14TranscriptInfoPl+0xb73): undefined reference to `TranscriptInfo::updateGeneNames(std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&)'
collect2: error: ld returned 1 exit status
make: *** [estimateDE] Error 1
/home/linuxbrew/.linuxbrew/bin/ld: warning: cannot find entry symbol ad_strip; defaulting to 0000000000402db0
misc.o: In function `ns_genes::prepareInput(ArgumentParser const&, TranscriptInfo*, PosteriorSamples*, long*, long*, long*)':
misc.cpp:(.text._ZN8ns_genes12prepareInputERK14ArgumentParserP14TranscriptInfoP16PosteriorSamplesPlS7_S7_+0x5b): undefined reference to `TranscriptInfo::readInfo(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)'
misc.cpp:(.text._ZN8ns_genes12prepareInputERK14ArgumentParserP14TranscriptInfoP16PosteriorSamplesPlS7_S7_+0xa4): undefined reference to `TranscriptInfo::getG() const'
misc.cpp:(.text._ZN8ns_genes12prepareInputERK14ArgumentParserP14TranscriptInfoP16PosteriorSamplesPlS7_S7_+0x11d): undefined reference to `TranscriptInfo::getM() const'
misc.cpp:(.text._ZN8ns_genes12prepareInputERK14ArgumentParserP14TranscriptInfoP16PosteriorSamplesPlS7_S7_+0x1d3): undefined reference to `TranscriptInfo::getM() const'
misc.o: In function `ns_genes::updateGenes(ArgumentParser const&, TranscriptInfo*, long*)':
misc.cpp:(.text._ZN8ns_genes11updateGenesERK14ArgumentParserP14TranscriptInfoPl+0x775): undefined reference to `TranscriptInfo::updateGeneNames(std::map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::less<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > const&)'
misc.cpp:(.text._ZN8ns_genes11updateGenesERK14ArgumentParserP14TranscriptInfoPl+0xb4f): undefined reference to `TranscriptInfo::getG() const'
misc.cpp:(.text._ZN8ns_genes11updateGenesERK14ArgumentParserP14TranscriptInfoPl+0xb73): undefined reference to `TranscriptInfo::updateGeneNames(std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&)'
collect2: error: ld returned 1 exit status
make: *** [estimateHyperPar] Error 1
/home/linuxbrew/.linuxbrew/bin/ld: warning: cannot find entry symbol ad_strip; defaulting to 0000000000402f70
misc.o: In function `ns_genes::prepareInput(ArgumentParser const&, TranscriptInfo*, PosteriorSamples*, long*, long*, long*)':
misc.cpp:(.text._ZN8ns_genes12prepareInputERK14ArgumentParserP14TranscriptInfoP16PosteriorSamplesPlS7_S7_+0xe5): undefined reference to `PosteriorSamples::initSet(long*, long*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)'
misc.o: In function `ns_misc::readConditions(ArgumentParser const&, long*, long*, long*, Conditions*)':
misc.cpp:(.text._ZN7ns_misc14readConditionsERK14ArgumentParserPlS3_S3_P10Conditions+0x11f): undefined reference to `Conditions::init(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >, long*, long*, long*)'
misc.cpp:(.text._ZN7ns_misc14readConditionsERK14ArgumentParserPlS3_S3_P10Conditions+0x29d): undefined reference to `Conditions::setNorm(std::vector<double, std::allocator<double> >)'
collect2: error: ld returned 1 exit status
make: *** [estimateExpression] Error 1

HOMEBREW_VERSION: 0.9.9
ORIGIN: https://github.com/Linuxbrew/brew
HEAD: c4af6483033a3c1ff8a4492f881bb8100459dced
Last commit: 11 days ago
Core tap ORIGIN: https://github.com/Linuxbrew/homebrew-core
Core tap HEAD: 4979add803641db3143b1903a7c91b29644b5958
Core tap last commit: 4 days ago
HOMEBREW_PREFIX: /home/linuxbrew/.linuxbrew
HOMEBREW_REPOSITORY: /home/linuxbrew/.linuxbrew
HOMEBREW_CELLAR: /home/linuxbrew/.linuxbrew/Cellar
HOMEBREW_BOTTLE_DOMAIN: https://linuxbrew.bintray.com
CPU: 72-core 64-bit haswell
Homebrew Ruby: 2.3.1 => /home/linuxbrew/.linuxbrew/Cellar/ruby/2.3.1/bin/ruby
Clang: N/A
Git: 2.9.3 => /home/linuxbrew/.linuxbrew/bin/git
Perl: /bin/perl => /usr/bin/perl
Python: /home/linuxbrew/.linuxbrew/bin/python => /home/linuxbrew/.linuxbrew/Cellar/python/2.7.12_1/bin/python2.7
Ruby: /home/linuxbrew/.linuxbrew/bin/ruby => /home/linuxbrew/.linuxbrew/Cellar/ruby/2.3.1/bin/ruby
Java: 1.8.0_102
Kernel: Linux 3.10.0-327.28.3.el7.x86_64 x86_64 GNU/Linux
OS: Red Hat Enterprise Linux Server release 7.2 (Maipo)
Codename: Maipo
OS glibc: 2.17
OS gcc: 4.8.5
Linuxbrew glibc: 2.19
Linuxbrew gcc: 5.3.0
Linuxbrew xorg: 20160314

CC: /home/linuxbrew/.linuxbrew/bin/gcc-5 => /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/bin/gcc-5
CXX: /home/linuxbrew/.linuxbrew/bin/g++-5 -std=c++11
OBJC: /home/linuxbrew/.linuxbrew/bin/gcc-5
OBJCXX: /home/linuxbrew/.linuxbrew/bin/g++-5
CFLAGS: -Os -w -pipe -march=native
CXXFLAGS: -Os -w -pipe -march=native
CPPFLAGS: -isystem/home/linuxbrew/.linuxbrew/include
LDFLAGS: -L/home/linuxbrew/.linuxbrew/lib -Wl,--dynamic-linker=/home/linuxbrew/.linuxbrew/lib/ld.so -Wl,-rpath,/home/linuxbrew/.linuxbrew/lib
MAKEFLAGS: -j72
CMAKE_PREFIX_PATH: /home/linuxbrew/.linuxbrew
PKG_CONFIG_LIBDIR: /home/linuxbrew/.linuxbrew/lib/pkgconfig:/home/linuxbrew/.linuxbrew/share/pkgconfig
PATH: /home/linuxbrew/.linuxbrew/bin:/home/linuxbrew/.linuxbrew/sbin:/home/linuxbrew/perl5/bin:/bio/perl5/bin:/home/linuxbrew/.linuxbrew/bin:/home/linuxbrew/.linuxbrew/sbin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/bio/sw/hierBAPS:/bio/sw/brat:/bio/sw/mauve:/bio/sw/splitstree4:/bio/sw/vbc/fqa-tools:/bio/sw/vbc/misc:/bio/sw/tablet:/home/tseemann/git/wombac/bin:/home/tseemann/git/snippy/bin:/home/tseemann/git/barrnap/bin:/home/tseemann/git/nullarbor/bin:/home/tseemann/git/prokka/bin:/home/tseemann/git/mlst/bin:/home/tseemann/git/abricate/bin:/home/tseemann/git/mdu-tools/bin:/home/linuxbrew/.linuxbrew/Library/Homebrew/cask/cmd:/home/linuxbrew/.linuxbrew/Library/Homebrew/shims/scm
CPATH: /home/linuxbrew/.linuxbrew/include
LD_LIBRARY_PATH: /home/linuxbrew/.linuxbrew/Cellar/bitseq/0.7.5/lib:/home/linuxbrew/.linuxbrew/Cellar/bitseq/0.7.5
LD_RUN_PATH: /home/linuxbrew/.linuxbrew/lib
LIBRARY_PATH: /home/linuxbrew/.linuxbrew/lib