pbdSLAP problem installing

[Sylvia Wilkerson]

Hi,

I'm trying to install the pdb R packages in R 3.2.0 on Linux x64, but receive the following error when installing pbdSLAP:

<command-line>: error: macro names must be identifiers
In file included from BI_HypBS.c:1:
Bdef.h:2:15: error: R.h: No such file or directory
Bdef.h:3:24: error: Rinternals.h: No such file or directory
make[1]: *** [BI_HypBS.fo] Error 1
make[1]: Leaving directory `/tmp/RtmpEHdEMn/R.INSTALL55427eabf5c9/pbdSLAP/src/BLACS'
make: *** [libslap.a] Error 2
ERROR: compilation failed for package 'pbdSLAP'
* removing '/usr/local/apps/R/gcc_4.4.7/3.2.0/lib64/R/library/pbdSLAP'

What environment variable needs to be set for the R include folder?

Sylvia
Helix Systems Staff

[Wei-Chen Chen]

Dear Sylvia,

Your R did not give you right ${R_HOME} at installing time.

R CMD INSTALL pbdMPI*.tar.gz --configure-vars="-I/path_to_your_R_include_directory"

Sincerely,
Wei-Chen Chen

[Sylvia Wilkerson]

Thank you Wei-Chen!!

[Erika Dade]

Hello,

I am having a similar problem but with a pbdSLAP  (pbdMPI installed fine on OS X 10.11.1).

$ R CMD INSTALL pbdSLAP --configure-vars="I/Library/Frameworks/R.framework/Versions/3.2/Resources/include/"
WARNING: ignoring environment value of R_HOME
* installing to library ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library’
* installing *source* package ‘pbdSLAP’ ...
** package ‘pbdSLAP’ successfully unpacked and MD5 sums checked
sh: I/Library/Frameworks/R.framework/Versions/3.2/Resources/include/: No such file or directory
ERROR: configuration failed for package ‘pbdSLAP’
* removing ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/pbdSLAP’


BTW, R_HOME is defined as '/Library/Frameworks/R.framework/Versions/3.2/Resources/'
Thank you for any assistance!  I am so stuck.

-Erika

On Wednesday, July 1, 2015 at 8:13:14 PM UTC-4, Wei-Chen Chen wrote:

[Wei-Chen Chen]

What is the "I" for?

sh: I/Library/Frameworks/R.framework/Versions/3.2/Resources/include/: No such file or directory

[Ostrouchov, George]

Erica,

Are you installing from GitHub? The following works for me inside R 3.2 on OS X 10.10 without problems so hopefully it still works on 10.11:

> library(devtools)

> install_github(“RBigData/pbdMPI”)

.

.

.

> install_github(“RBigData/pbdSLAP”)

But also, as Wei-Chen notes, the “I” should be “-I” if you are specifying it.

George

--
Programming with Big Data in R
Simplifying Scalability
http://r-pbd.org/
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[Erika Dade]

Yes, thank you so much for the suggestions and help! 

I had downloaded all the zip files from the pbdR website.  I realize the "-" was missing on the "-I", but still get errors when including it.  I was able to install pbdMPI, but I think because it has no fortran code.

I just tried using github to retrieve and install pbdSLAP.  It still seems to default to gfortran-4.8 and an earlier OS X kernel version. The newest OS X (10.11.2  "El Capitan" version 15) uses gcc5 and gfortran-mp-5.  Here are some of the errors from:
 

> install_github(“RBigData/pbdSLAP”)

...  too much to include, but here is an example of when it hits a fortran source

( cd LAPACK; make double )
gfortran-4.8 -o icopy.fo -c -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/opt/local/include/openmpi-mp  -DMPI2 -DOPENMPI -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -g -O2 -ffloat-store -w -fPIC  -g -O2  -O3 -w icopy.f
gfortran-4.8: warning: couldn’t understand kern.osversion ‘15.2.0
Warning: Nonexistent include directory "/usr/local/include/freetype2"

...  the long list of output finishes with ....

ranlib ../libslap.a
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o pbdSLAP.so slap_blacs.o libslap.a -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran -lquadmath -lm -L/opt/local/lib/openmpi-mp -lmpi -lutil -lpthread -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: directory not found for option '-L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2'
ld: warning: directory not found for option '-L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [pbdSLAP.so] Error 1

ERROR: compilation failed for package ‘pbdSLAP’

* removing ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/pbdSLAP’
Error: Command failed (1)

The latest version of OS X does not allow installs into /usr/local, but uses /opt/local. The equivalent to /usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 is now /opt/local/lib/gcc5/gcc/x86_64-apple-darwin15/5.2.0.

darwin13 was two major OS X releases ago (Mavericks, I think).

I tried installing gfortran-4.8 and creating a symbolic link to it.  That didn't work either.  It still didn't like the new OS kernel version.  I don't know if this is something embedded in the R installation or the pbdSLAP makefiles (I tried editing those too).

I am sure there is a way to do this, but I feel quite lost at the moment!  Any help you can offer will be greatly appreciated.

Thank you so much
Erika

[Erika Dade]

As more footnote, I built ./pbdSLAP/inst/test_intface/intface and its output is simply "Add_".  That is the default for CDEFS, so I assume I don't need to add a different definition for the CDEFS flag.

And here are some definitions on my system:

Erikas-MBP-2:~ erika$ echo $PATH
/opt/local/bin:/opt/local/sbin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin

Erikas-MBP-2:test_intface erika$ gfortran -v
Using built-in specs.
COLLECT_GCC=gfortran
COLLECT_LTO_WRAPPER=/opt/local/libexec/gcc/x86_64-apple-darwin15/5.2.0/lto-wrapper
Target: x86_64-apple-darwin15
Configured with: /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_lang_gcc5/gcc5/work/gcc-5.2.0/configure --prefix=/opt/local --build=x86_64-apple-darwin15 --enable-languages=c,c++,objc,obj-c++,lto,fortran,java --libdir=/opt/local/lib/gcc5 --includedir=/opt/local/include/gcc5 --infodir=/opt/local/share/info --mandir=/opt/local/share/man --datarootdir=/opt/local/share/gcc-5 --with-local-prefix=/opt/local --with-system-zlib --disable-nls --program-suffix=-mp-5 --with-gxx-include-dir=/opt/local/include/gcc5/c++/ --with-gmp=/opt/local --with-mpfr=/opt/local --with-mpc=/opt/local --with-isl=/opt/local --enable-stage1-checking --disable-multilib --enable-lto --enable-libstdcxx-time --with-as=/opt/local/bin/as --with-ld=/opt/local/bin/ld --with-ar=/opt/local/bin/ar --with-bugurl=https://trac.macports.org/newticket --with-pkgversion='MacPorts gcc5 5.2.0_0'
Thread model: posix
gcc version 5.2.0 (MacPorts gcc5 5.2.0_0)

Erikas-MBP-2:~ erika$ /opt/local/bin/gfortran-4.8 -v

gfortran-4.8: warning: couldn’t understand kern.osversion ‘15.2.0

Using built-in specs.
COLLECT_GCC=/opt/local/bin/gfortran-4.8
COLLECT_LTO_WRAPPER=/opt/local/gfortran-4.8/bin/../libexec/gcc/x86_64-apple-darwin13/4.8.2/lto-wrapper
Target: x86_64-apple-darwin13
Configured with: ../gcc-4.8.2/configure --prefix=/usr/local/gfortran --with-gmp=/Users/fx/devel/gcc/deps-static/x86_64 --enable-languages=c,c++,fortran,objc,obj-c++ --build=x86_64-apple-darwin13
Thread model: posix
gcc version 4.8.2 (GCC)