Compilation on R 4.1.0 fails #14
Comments
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Hello, i just wanted to add that the following attempt to nail the library path did not improve the situation: > Sys.getenv("LD_LIBRARY_PATH")
[1] "/usr/lib64/R/lib:/usr/lib/jvm/jre/lib/amd64/server:/usr/lib/jvm/jre/lib/amd64:/usr/lib/jvm/java/lib/amd64:/usr/java/packages/lib/amd64:/lib:/usr/lib/:/opt/hdf5-1.12.0/lib"
> dyn.load("/opt/gsl-2.7/lib/libgsl.so")
And an additional attempt: > Sys.setenv(LD_LIBRARY_PATH=paste("/opt/gsl-2.7/lib/", Sys.getenv("LD_LIBRARY_PATH"),sep=":"))
> Sys.getenv("LD_LIBRARY_PATH")
[1] "/opt/gsl-2.7/lib/:/opt/hdf5-1.12.0/lib:/usr/lib64/R/lib:/usr/lib/jvm/jre/lib/amd64/server:/usr/lib/jvm/jre/lib/amd64:/usr/lib/jvm/java/lib/amd64:/usr/java/packages/lib/amd64:/lib:/usr/lib/:/opt/hdf5-1.12.0/lib"
>
It looks like the path is known and used at compile time, but missing at launch time? Best |
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Hi there, thanks for this comprehensive post. I have had similar reports from other CentOS users, a system I am not familiar with. Not sure if R-devel or R-help would be appropriate here, it looks (as you say) to be a centos issue. If you resolve the issue, please let me know and I'll add it to the readme. Maybe remove Best wishes, Robin |
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Hello Robin, thank you for your quick response and for your information about what you hear from your CentOS users. So from my perspective, this issue could be closed. Best wishes |
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thanks for letting me know. Would you be able to send me a couple of
sentences describing the problem and solution in a form suitable for adding
to the README?
best wishes
Robin
***@***.***>
…On Fri, Jul 30, 2021 at 12:35 AM kelbstf ***@***.***> wrote:
Hello Robin,
thank you for your quick response and for your information about what you
hear from your CentOS users.
That pointed me to considering dynamic linker run-time bindings,
which non-CentOS systems may not have to, as their os already ships with a
proper release level.
Because i had to compile it from scratch, i had opportunity to miss
updating the dynamic linker run-time bindings afterwards ;-)
After having caught up on that, the compilatin of GSL succeeded.
That also explains why apparently the compilation succeeded, but the run
time access during the test phase failed.
So from my perspective, this issue could be closed.
Best wishes
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Hello Robin, sorry, i just realise i should have been more detailed to make it useful. The core reason in my situation was that the stock CentOS7 GSL is too old (1.15-13.el7) for the gsl-wrapper. ./configure --prefix=/opt/gsl-2.7 Since neither the executable of the OS-level GSL nor the GSL wrapper for R are installed in the default PATH (/lib, /usr/lib, ...), and the custom directory seems to be stored in -rpath-link at compile time and apparently not in -rpath for the run time, shared objects are looked up as a last resort in the directories specified by /etc/ld.so.conf. After having fixed that via vi /etc/ld.so.conf.d/libgsl-x86_64.conf /opt/gsl-2.7/lib/ installation of the gsl wrapper from CRAN in R with no additional specifications worked immediately via: install.packages('gsl')
That's at least my understanding of why this worked. Would that fit your bill? Best wishes |
Hello,
i fail to install "gsl" in R 4.1.0 from CRAN on a CentOS7.8 with gsl 2.7 compiled from sources:
> install.packages('gsl') ... ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Error: package or namespace load failed for ‘gsl’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/opt/R/4.1.0/lib/R/library/00LOCK-gsl/00new/gsl/libs/gsl.so': libgslcblas.so.0: cannot open shared object file: No such file or directory Error: loading failed Execution halted ERROR: loading failedThe strange thing is that the actual compilation seems to work perfectly fine:
configure: creating ./config.status config.status: creating src/Makevars ** libs gcc -std=gnu99 -I"/opt/R/4.1.0/lib/R/include" -DNDEBUG -I/opt/gsl-2.7/include -I. -I/usr/local/include -fpic -g -O2 -c airy.c -o airy.o gcc -std=gnu99 -I"/opt/R/4.1.0/lib/R/include" -DNDEBUG -I/opt/gsl-2.7/include -I. -I/usr/local/include -fpic -g -O2 -c bessel.c -o bessel.o gcc -std=gnu99 -I"/opt/R/4.1.0/lib/R/include" -DNDEBUG -I/opt/gsl-2.7/include -I. -I/usr/local/include -fpic -g -O2 -c clausen.c -o clausen.o gcc -std=gnu99 -I"/opt/R/4.1.0/lib/R/include" -DNDEBUG -I/opt/gsl-2.7/include -I. -I/usr/local/include -fpic -g -O2 -c coulomb.c -o coulomb.o gcc -std=gnu99 -I"/opt/R/4.1.0/lib/R/include" -DNDEBUG -I/opt/gsl-2.7/include -I. -I/usr/local/include -fpic -g -O2 -c coupling.c -o coupling.o gcc -std=gnu99 -I"/opt/R/4.1.0/lib/R/include" -DNDEBUG -I/opt/gsl-2.7/include -I. -I/usr/local/include -fpic -g -O2 -c dawson.c -o dawson.o gcc -std=gnu99 -I"/opt/R/4.1.0/lib/R/include" -DNDEBUG -I/opt/gsl-2.7/include -I. -I/usr/local/include -fpic -g -O2 -c debye.c -o debye.o gcc -std=gnu99 -I"/opt/R/4.1.0/lib/R/include" -DNDEBUG -I/opt/gsl-2.7/include -I. -I/usr/local/include -fpic -g -O2 -c dilog.c -o dilog.o gcc -std=gnu99 -I"/opt/R/4.1.0/lib/R/include" -DNDEBUG -I/opt/gsl-2.7/include -I. -I/usr/local/include -fpic -g -O2 -c ellint.c -o ellint.o gcc -std=gnu99 -I"/opt/R/4.1.0/lib/R/include" -DNDEBUG -I/opt/gsl-2.7/include -I. -I/usr/local/include -fpic -g -O2 -c elljac.c -o elljac.o gcc -std=gnu99 -I"/opt/R/4.1.0/lib/R/include" -DNDEBUG -I/opt/gsl-2.7/include -I. -I/usr/local/include -fpic -g -O2 -c error.c -o error.o gcc -std=gnu99 -I"/opt/R/4.1.0/lib/R/include" -DNDEBUG -I/opt/gsl-2.7/include -I. -I/usr/local/include -fpic -g -O2 -c expint.c -o expint.o gcc -std=gnu99 -I"/opt/R/4.1.0/lib/R/include" -DNDEBUG -I/opt/gsl-2.7/include -I. -I/usr/local/include -fpic -g -O2 -c fermi_dirac.c -o fermi_dirac.o gcc -std=gnu99 -I"/opt/R/4.1.0/lib/R/include" -DNDEBUG -I/opt/gsl-2.7/include -I. -I/usr/local/include -fpic -g -O2 -c gamma.c -o gamma.o gcc -std=gnu99 -I"/opt/R/4.1.0/lib/R/include" -DNDEBUG -I/opt/gsl-2.7/include -I. -I/usr/local/include -fpic -g -O2 -c gegenbauer.c -o gegenbauer.o gcc -std=gnu99 -I"/opt/R/4.1.0/lib/R/include" -DNDEBUG -I/opt/gsl-2.7/include -I. -I/usr/local/include -fpic -g -O2 -c hyperg.c -o hyperg.o gcc -std=gnu99 -I"/opt/R/4.1.0/lib/R/include" -DNDEBUG -I/opt/gsl-2.7/include -I. -I/usr/local/include -fpic -g -O2 -c init.c -o init.o gcc -std=gnu99 -I"/opt/R/4.1.0/lib/R/include" -DNDEBUG -I/opt/gsl-2.7/include -I. -I/usr/local/include -fpic -g -O2 -c laguerre.c -o laguerre.o gcc -std=gnu99 -I"/opt/R/4.1.0/lib/R/include" -DNDEBUG -I/opt/gsl-2.7/include -I. -I/usr/local/include -fpic -g -O2 -c lambert.c -o lambert.o gcc -std=gnu99 -I"/opt/R/4.1.0/lib/R/include" -DNDEBUG -I/opt/gsl-2.7/include -I. -I/usr/local/include -fpic -g -O2 -c legendre.c -o legendre.o gcc -std=gnu99 -I"/opt/R/4.1.0/lib/R/include" -DNDEBUG -I/opt/gsl-2.7/include -I. -I/usr/local/include -fpic -g -O2 -c log.c -o log.o gcc -std=gnu99 -I"/opt/R/4.1.0/lib/R/include" -DNDEBUG -I/opt/gsl-2.7/include -I. -I/usr/local/include -fpic -g -O2 -c poly.c -o poly.o gcc -std=gnu99 -I"/opt/R/4.1.0/lib/R/include" -DNDEBUG -I/opt/gsl-2.7/include -I. -I/usr/local/include -fpic -g -O2 -c pow_int.c -o pow_int.o gcc -std=gnu99 -I"/opt/R/4.1.0/lib/R/include" -DNDEBUG -I/opt/gsl-2.7/include -I. -I/usr/local/include -fpic -g -O2 -c psi.c -o psi.o gcc -std=gnu99 -I"/opt/R/4.1.0/lib/R/include" -DNDEBUG -I/opt/gsl-2.7/include -I. -I/usr/local/include -fpic -g -O2 -c qrng.c -o qrng.o gcc -std=gnu99 -I"/opt/R/4.1.0/lib/R/include" -DNDEBUG -I/opt/gsl-2.7/include -I. -I/usr/local/include -fpic -g -O2 -c rng.c -o rng.o gcc -std=gnu99 -I"/opt/R/4.1.0/lib/R/include" -DNDEBUG -I/opt/gsl-2.7/include -I. -I/usr/local/include -fpic -g -O2 -c synchrotron.c -o synchrotron.o gcc -std=gnu99 -I"/opt/R/4.1.0/lib/R/include" -DNDEBUG -I/opt/gsl-2.7/include -I. -I/usr/local/include -fpic -g -O2 -c transport.c -o transport.o gcc -std=gnu99 -I"/opt/R/4.1.0/lib/R/include" -DNDEBUG -I/opt/gsl-2.7/include -I. -I/usr/local/include -fpic -g -O2 -c trig.c -o trig.o gcc -std=gnu99 -I"/opt/R/4.1.0/lib/R/include" -DNDEBUG -I/opt/gsl-2.7/include -I. -I/usr/local/include -fpic -g -O2 -c vector.c -o vector.o gcc -std=gnu99 -I"/opt/R/4.1.0/lib/R/include" -DNDEBUG -I/opt/gsl-2.7/include -I. -I/usr/local/include -fpic -g -O2 -c zeta.c -o zeta.o gcc -std=gnu99 -shared -L/opt/R/4.1.0/lib/R/lib -L/usr/local/lib -o gsl.so airy.o bessel.o clausen.o coulomb.o coupling.o dawson.o debye.o dilog.o ellint.o elljac.o error.o expint.o fermi_dirac.o gamma.o gegenbauer.o hyperg.o init.o laguerre.o lambert.o legendre.o log.o poly.o pow_int.o psi.o qrng.o rng.o synchrotron.o transport.o trig.o vector.o zeta.o -L/opt/gsl-2.7/lib -lgsl -lgslcblas -lm -L/opt/R/4.1.0/lib/R/lib -lR installing to /opt/R/4.1.0/lib/R/library/00LOCK-gsl/00new/gsl/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package ‘gsl’ finding HTML links ... done Airy html Bessel html Clausen html Coulomb html Coupling html Dawson html Debye html Dilog html Ellint html Elljac html Error html Expint html Fermi-Dirac html Gamma html Gegenbauer html Hyperg html Laguerre html Lambert html Legendre html Log html Misc html Multimin html Poly html Pow_int html Psi html Qrng html Rng html Synchrotron html Transport html Trig html Zeta html gsl-deprecated html gsl-package html ** building package indices ** installing vignettesSession:
Just the access to the result fails.
And i see no reason, because:
> Sys.getenv("PATH") [1] "/opt/R/4.1.0/bin: ... /opt/gsl-2.7/bin:/root/go/bin:/root/bin"The old gsl 1.0 had been removed prior to compiling 2.7, so there is only one instance around...
Does any one have an idea?
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