Compile issue 'undefined reference to straw'

[mmterpstra]

Cannot use the current straw.cpp to find the straw function but by including the ../python/old the compilation works:

straw-86c2939e3695e31a5a41f53cc1231f7fcb77fb87/C++$ g++ -lz -std=c++11 -o straw main.cpp straw.cpp
/tmp/cc4rs88z.o:main.cpp:function main: error: undefined reference to 'straw(std::string, std::string, int, std::string, std::string, std::string, std::vector<int, std::allocator<int> >&, std::vector<int, std::allocator<int> >&, std::vector<float, std::allocator<float> >&)'
#working version
straw-86c2939e3695e31a5a41f53cc1231f7fcb77fb87/C++$ g++ -lz -std=c++11 -o straw main.cpp straw.cpp ../python/old/straw.cpp

ps: also try to include a makefile or include it into the README for this project.

[nchernia]

Thanks for the feedback. I'm currently working on straw.cpp right now to add URL support. It's strange that you had to use an old version of the straw.cpp, I was able to compile the current Git version very recently, I will look into it. There is a README. The README directs you to the wiki, where you will find instructions on compiling the C++ version (as well as information for our Python and R users). https://github.com/theaidenlab/straw/wiki/CPP

…

On Thu, Feb 16, 2017 at 3:10 PM, mmterpstra ***@***.***> wrote: Cannot use the current straw.cpp to find the straw function but by including the ../python/old the compilation works: straw-86c2939e3695e31a5a41f53cc1231f7fcb77fb87/C++$ g++ -lz -std=c++11 -o straw main.cpp straw.cpp /tmp/cc4rs88z.o:main.cpp:function main: error: undefined reference to 'straw(std::string, std::string, int, std::string, std::string, std::string, std::vector<int, std::allocator<int> >&, std::vector<int, std::allocator<int> >&, std::vector<float, std::allocator<float> >&)' #working version straw-86c2939e3695e31a5a41f53cc1231f7fcb77fb87/C++$ g++ -lz -std=c++11 -o straw main.cpp straw.cpp ../python/old/straw.cpp ps: also try to include a makefile or include it into the README for this project. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#7>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABWiW5uRMcgIeFam1YWeCtK62qsdOtplks5rdFjJgaJpZM4MDDeG> .

-- Neva Cherniavsky Durand, Ph.D. Staff Scientist, Aiden Lab www.aidenlab.org

[mmterpstra]

I've seen the wiki yes.
PS: I use centos with the lua bases environment module system (lmod) and software build with easybuild. my env is something like:
$ ml -t list
EasyBuild/2.1.1
GCC/4.9.3-binutils-2.25
binutils/2.25-GCC-4.9.3-binutils-2.25
GNU/4.9.3-2.25
numactl/2.0.10-GNU-4.9.3-2.25
hwloc/1.11.0-GNU-4.9.3-2.25
OpenMPI/1.8.8-GNU-4.9.3-2.25
OpenBLAS/0.2.14-GNU-4.9.3-2.25-LAPACK-3.5.0
gompi/2015b
FFTW/3.3.4-gompi-2015b
ScaLAPACK/2.0.2-gompi-2015b-OpenBLAS-0.2.14-LAPACK-3.5.0
foss/2015b
zlib/1.2.8-foss-2015b
libreadline/6.3-foss-2015b
ncurses/5.9-foss-2015b
libpng/1.6.21-foss-2015b
NASM/2.11.08-foss-2015b
libjpeg-turbo/1.4.2-foss-2015b
LibTIFF/4.0.4-foss-2015b
Tcl/8.6.4-foss-2015b
Tk/8.6.4-foss-2015b-no-X11
cURL/7.47.1-foss-2015b
libxml2/2.9.2-foss-2015b
bzip2/1.0.6-foss-2015b
freetype/2.6.1-foss-2015b
pixman/0.32.8-foss-2015b
fontconfig/2.11.94-foss-2015b
expat/2.1.0-foss-2015b
cairo/1.14.6-foss-2015b
Java/1.8.0_45
PCRE/8.37-foss-2015b
R/3.2.1-foss-2015b

[mmterpstra]

this is a suggested makefile:
CC=g++
#for linux
CPPFLAGS=-O2 -lz -std=c++11
#for mac
#CPPFLAGS=-O2 -lz
#for windows
#CPPFLAGS=???

bin/straw: C++/straw.cpp C++/main.cpp C++/straw.h
cd C++ && $(CC) $(CPPFLAGS) main.cpp straw.cpp ../python/old/straw.cpp -o ../$@

[nchernia]

Thanks! The old folder in python should be deleted. I'll be pushing updates soon.

…

On Thu, Feb 16, 2017 at 3:32 PM, mmterpstra ***@***.***> wrote: this is a suggested makefile: CC=g++ #for linux CPPFLAGS=-O2 -lz -std=c++11 #for mac #CPPFLAGS=-O2 -lz #for windows #CPPFLAGS=??? bin/straw: C++/straw.cpp C++/main.cpp C++/straw.h cd C++ && $(CC) $(CPPFLAGS) main.cpp straw.cpp ../python/old/straw.cpp -o ../$@ — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#7 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABWiW6A4mexsEz4MHwI_2XkeoWX4sTOhks5rdF3jgaJpZM4MDDeG> .

-- Neva Cherniavsky Durand, Ph.D. Staff Scientist, Aiden Lab www.aidenlab.org

[nchernia]

I am really puzzled by your issue. The files are exactly the same: diff ../python/old/straw.cpp straw.cpp returns nothing. On Thu, Feb 16, 2017 at 3:33 PM, Neva Durand <neva@broadinstitute.org> wrote:

…

Thanks! The old folder in python should be deleted. I'll be pushing updates soon. On Thu, Feb 16, 2017 at 3:32 PM, mmterpstra ***@***.***> wrote: > this is a suggested makefile: > CC=g++ > #for linux > CPPFLAGS=-O2 -lz -std=c++11 > #for mac > #CPPFLAGS=-O2 -lz > #for windows > #CPPFLAGS=??? > > bin/straw: C++/straw.cpp C++/main.cpp C++/straw.h > cd C++ && $(CC) $(CPPFLAGS) main.cpp straw.cpp ../python/old/straw.cpp -o > ../$@ > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub > <#7 (comment)>, > or mute the thread > <https://github.com/notifications/unsubscribe-auth/ABWiW6A4mexsEz4MHwI_2XkeoWX4sTOhks5rdF3jgaJpZM4MDDeG> > . > -- Neva Cherniavsky Durand, Ph.D. Staff Scientist, Aiden Lab www.aidenlab.org

-- Neva Cherniavsky Durand, Ph.D. Staff Scientist, Aiden Lab www.aidenlab.org

[nchernia]

I just tried the current version on Linux and had no trouble compiling. I don't understand why you'd need two copies of the exact same file? On Thu, Feb 16, 2017 at 3:42 PM, Neva Durand <neva@broadinstitute.org> wrote:

…

I am really puzzled by your issue. The files are exactly the same: diff ../python/old/straw.cpp straw.cpp returns nothing. On Thu, Feb 16, 2017 at 3:33 PM, Neva Durand ***@***.***> wrote: > Thanks! > > The old folder in python should be deleted. I'll be pushing updates soon. > > On Thu, Feb 16, 2017 at 3:32 PM, mmterpstra ***@***.***> > wrote: > >> this is a suggested makefile: >> CC=g++ >> #for linux >> CPPFLAGS=-O2 -lz -std=c++11 >> #for mac >> #CPPFLAGS=-O2 -lz >> #for windows >> #CPPFLAGS=??? >> >> bin/straw: C++/straw.cpp C++/main.cpp C++/straw.h >> cd C++ && $(CC) $(CPPFLAGS) main.cpp straw.cpp ../python/old/straw.cpp >> -o ../$@ >> >> — >> You are receiving this because you commented. >> Reply to this email directly, view it on GitHub >> <#7 (comment)>, >> or mute the thread >> <https://github.com/notifications/unsubscribe-auth/ABWiW6A4mexsEz4MHwI_2XkeoWX4sTOhks5rdF3jgaJpZM4MDDeG> >> . >> > > > > -- > Neva Cherniavsky Durand, Ph.D. > Staff Scientist, Aiden Lab > www.aidenlab.org > -- Neva Cherniavsky Durand, Ph.D. Staff Scientist, Aiden Lab www.aidenlab.org

-- Neva Cherniavsky Durand, Ph.D. Staff Scientist, Aiden Lab www.aidenlab.org

[mmterpstra]

After a new login it works...might be our module system giving quirks. Sorry for the bother.

$ g++ -lz -std=c++11 -o straw main.cpp straw.cpp

/straw-86c2939e3695e31a5a41f53cc1231f7fcb77fb87/C++$ ml -t list
EasyBuild/2.1.1
GCC/4.9.3-binutils-2.25
binutils/2.25-GCC-4.9.3-binutils-2.25
GNU/4.9.3-2.25
numactl/2.0.10-GNU-4.9.3-2.25
hwloc/1.11.0-GNU-4.9.3-2.25
OpenMPI/1.8.8-GNU-4.9.3-2.25
OpenBLAS/0.2.14-GNU-4.9.3-2.25-LAPACK-3.5.0
gompi/2015b
FFTW/3.3.4-gompi-2015b
ScaLAPACK/2.0.2-gompi-2015b-OpenBLAS-0.2.14-LAPACK-3.5.0
foss/2015b
R/3.2.2-foss-2015b-bioconductor
zlib/1.2.8-foss-2015b

[nchernia]

Glad to hear it. Thanks for the Makefile suggestion.

…

On Fri, Feb 17, 2017 at 9:53 AM mmterpstra ***@***.***> wrote: After a new login it works...might be our module system giving quirks. Sorry for the bother. $ g++ -lz -std=c++11 -o straw main.cpp straw.cpp /straw-86c2939e3695e31a5a41f53cc1231f7fcb77fb87/C++$ ml -t list EasyBuild/2.1.1 GCC/4.9.3-binutils-2.25 binutils/2.25-GCC-4.9.3-binutils-2.25 GNU/4.9.3-2.25 numactl/2.0.10-GNU-4.9.3-2.25 hwloc/1.11.0-GNU-4.9.3-2.25 OpenMPI/1.8.8-GNU-4.9.3-2.25 OpenBLAS/0.2.14-GNU-4.9.3-2.25-LAPACK-3.5.0 gompi/2015b FFTW/3.3.4-gompi-2015b ScaLAPACK/2.0.2-gompi-2015b-OpenBLAS-0.2.14-LAPACK-3.5.0 foss/2015b R/3.2.2-foss-2015b-bioconductor zlib/1.2.8-foss-2015b — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#7 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABWiW-DWUfIDRECvVnxXVJxxQeheFbo6ks5rdWAQgaJpZM4MDDeG> .