lpsymphony compilation trouble
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mark.russo ▴ 30
@markrusso-15040
Last seen 3.2 years ago

Hello.

I am having trouble installing lpsymphony 1.7.1 on Ubuntu 14.04 with R 3.4.3. I've tried several things, but always end up with the following error. The CoinPragma.hpp file is definitely in the tar.gz, but the following compile statement is not finding it.

Any suggestions would be welcome.

/bin/bash ../../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I`echo .`  -I/tmp/RtmpieV581/Rbuilda0d5d37ceda/lpsymphony/src/SYMPHONY/include/coin     -w -g -O2   -DOSI_BUILD -c -o OsiAuxInfo.lo OsiAuxInfo.cpp
 g++ -DHAVE_CONFIG_H -I. -I. -I/tmp/RtmpieV581/Rbuilda0d5d37ceda/lpsymphony/src/SYMPHONY/include/coin -w -g -O2 -DOSI_BUILD -c OsiAuxInfo.cpp  -fPIC -DPIC -o OsiAuxInfo.o
OsiAuxInfo.cpp:10:26: fatal error: CoinPragma.hpp: No such file or directory
 #include "CoinPragma.hpp"
                          ^

Mark

-----

(Edit)

I have more information about this problem that may help identify a solution. After repeatedly attempting to install lpsymphony and watching the install log, I have noticed that a different /tmp/Rtmp... path is used for every installation attempt. But, the line above during installation ALWAYS uses /tmp/RtmpieV581. I also watched the content of /tmp during the install and noticed that all necessary include files are created under the dynamically created /tmp/Rtmp... path, and /tmp/RtmpieV581 NEVER exists.

What could explain this behavior?

Note that I am running R in a Docker container on AWS. Could this have an impact?

lpsymphony • 941 views
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Problem persists in Bioconductor 3.10 / R 3.6.1 on Linux 64-bit.

Cloning the repo and manually installing worked fine, however.

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mark.russo ▴ 30
@markrusso-15040
Last seen 3.2 years ago

Thanks Vlad.

Last night I figured out something that allows me to install the package. I extracted all files and grepped for all Rtmp.* files. Following is the result. I was actually a little surprised to see the exact same Rtmp directory that keeps showing up when the build fails. So I deleted all files in the 'pkgconig' directory, recompressed into a tar.gz, and installed again. This time it works.

Am I asking for trouble by removing those files?

Mark

$ grep -rnw '/mnt/lpsymphony/' -e 'Rtmp.*'
/mnt/lpsymphony/src/SYMPHONY/lib/pkgconfig/clp.pc:1:prefix=/tmp/RtmpieV581/Rbuilda0d5d37ceda/lpsymphony/src/SYMPHONY
/mnt/lpsymphony/src/SYMPHONY/lib/pkgconfig/osi.pc:1:prefix=/tmp/RtmpieV581/Rbuilda0d5d37ceda/lpsymphony/src/SYMPHONY
/mnt/lpsymphony/src/SYMPHONY/lib/pkgconfig/coindatasample.pc:1:prefix=/tmp/RtmpQWymdU/Rbuild27854c06e94a/lpsymphony/src/SYMPHONY
/mnt/lpsymphony/src/SYMPHONY/lib/pkgconfig/cgl.pc:1:prefix=/tmp/RtmpieV581/Rbuilda0d5d37ceda/lpsymphony/src/SYMPHONY
/mnt/lpsymphony/src/SYMPHONY/lib/pkgconfig/coinutils.pc:1:prefix=/tmp/RtmpieV581/Rbuilda0d5d37ceda/lpsymphony/src/SYMPHONY
/mnt/lpsymphony/src/SYMPHONY/lib/pkgconfig/osi-unittests.pc:1:prefix=/tmp/RtmpieV581/Rbuilda0d5d37ceda/lpsymphony/src/SYMPHONY
/mnt/lpsymphony/src/SYMPHONY/lib/pkgconfig/symphony.pc:1:prefix=/tmp/RtmpieV581/Rbuilda0d5d37ceda/lpsymphony/src/SYMPHONY
/mnt/lpsymphony/src/SYMPHONY/lib/pkgconfig/symphony-app.pc:1:prefix=/tmp/RtmpieV581/Rbuilda0d5d37ceda/lpsymphony/src/SYMPHONY
/mnt/lpsymphony/src/SYMPHONY/lib/pkgconfig/osi-sym.pc:1:prefix=/tmp/RtmpieV581/Rbuilda0d5d37ceda/lpsymphony/src/SYMPHONY
/mnt/lpsymphony/src/SYMPHONY/lib/pkgconfig/osi-clp.pc:1:prefix=/tmp/RtmpieV581/Rbuilda0d5d37ceda/lpsymphony/src/SYMPHONY
/mnt/lpsymphony/src/SYMPHONY/share/coin/doc/CoinUtils/coinutils_addlibs.txt:1:-L/tmp/RtmpieV581/Rbuilda0d5d37ceda/lpsymphony/src/SYMPHONY/lib -lCoinUtils -llapack -lblas -lm
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Hey Mark, I am happy to hear that you managed to install the package. No those files are not necessary for package install.

Vlad

 

 

 

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This problem still exists in 2021 and deleting pkgconfig folder is still the workaround. May it be fixed once and for all in the package itself?

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@vladislavkim-8059
Last seen 3.0 years ago
Germany

Hi Mark,

I built a minimalistic Docker image with Ubuntu Trusty Tahr and I can't reproduce your error. I deposited my Dockerfile on Github. Check out the branch 'lpsym' (not master) To try it out quickly, maybe you can pull the Docker image from the docker hub (https://hub.docker.com/r/vladkim/lpsym/).

I am not sure how running a Docker container on AWS would make it different. Perhaps, you could also share the essential parts of your Dockerfile here as a comment?

Best regards,

Vlad

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yadongxue • 0
@yadongxue-15480
Last seen 2.6 years ago

lpsymphony_1.8.0.tar.gz

confirm the solution from Mark, which means the problem still exists. so, please make a clean packages or update the "clean" script to do the full cleaning.

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Solution from Mark worked for me as well with lpsymphony_1.11.0.tar.gz

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