Installing from source on OSX 10.10.1 and R 3.2 (devel version)

On Jan 12, 2015, at 2:20 PM, Bryan Hanson <hanson at depauw.edu> wrote:

I?m trying to get R 3.2 working fully so I can test my packages before sending to CRAN.  R 3.2 appears to work OK in general terms.  However, when I try to install some packages I need, I run into errors with the libraries that the install process desires.  I get the same or very similar messages from several packages.  Let?s use amap as an example:

install.packages("amap", type = "source")
[?]
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: *** [amap.so] Error 1
ERROR: compilation failed for package ?amap?
* removing ?/Users/bryanhanson/Library/R/3.2/library/amap?
* restoring previous ?/Users/bryanhanson/Library/R/3.2/library/amap?

The full output is appended after this message.  The problem here is clear in one sense: there no directory on my machine by that name, since on Yosemite it is darwin13.4.0 and gcc is at 4.9.2.  xcode and xquartz have been updated.  I don?t know if this is a problem with a symlink on my system or an issue with the amap package  not yet being fully updated for R 3.2 or a problem with R 3.2 or a mangled gcc install.  All suggestions welcome, there?s a good chance I?m being simple-minded here.

Thank you.  Bryan

=== dir listing

pwd

/usr/local/lib/gcc/x86_64-apple-darwin13.4.0

ls -l

total 16
lrwxr-xr-x   1 bryanhanson  wheel    67 Dec 12 14:29 4.8.2 -> ../../../Cellar/gcc48/4.8.3/lib/gcc/x86_64-apple-darwin13.4.0/4.8.3
lrwxr-xr-x   1 bryanhanson  wheel    67 Dec 12 14:22 4.8.3 -> ../../../Cellar/gcc48/4.8.3/lib/gcc/x86_64-apple-darwin13.4.0/4.8.3
drwxr-xr-x  66 bryanhanson  wheel  2244 Dec 20 10:36 4.9.2

=== SessionInfo()

R Under development (unstable) (2015-01-11 r67421)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.1 (Yosemite)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] sos_1.3-8  brew_1.0-6

loaded via a namespace (and not attached):
[1] tools_3.2.0

=== Full output from install.packages

install.packages("amap", type = "source")
Installing package into ?/Users/bryanhanson/Library/R/3.2/library?
(as ?lib? is unspecified)
trying URL 'http://cran.at.r-project.org/src/contrib/amap_0.8-14.tar.gz'
Content type 'application/x-gzip' length 259358 bytes (253 KB)
opened URL
==================================================
downloaded 253 KB

********
********  Loading Bryan's .Rprofile
********
Loading required package: brew
********
********  Completed Bryan's .Rprofile GET TO WORK!
********
* installing *source* package ?amap? ...
** package ?amap? successfully unpacked and MD5 sums checked
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking for pthread_create in -lpthread... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include/   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c acprob.cpp -o acprob.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include/   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c burt.c -o burt.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include/   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c diss.c -o diss.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include/   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c distance.cpp -o distance.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include/   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c hclust.cpp -o hclust.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include/   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c kmeans.cpp -o kmeans.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include/   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c matrice.cpp -o matrice.o
gfortran-4.8   -fPIC  -g -O2  -c pop.f -o pop.o
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 amap.so acprob.o burt.o diss.o distance.o hclust.o kmeans.o matrice.o pop.o -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: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [amap.so] Error 1
ERROR: compilation failed for package ?amap?
* removing ?/Users/bryanhanson/Library/R/3.2/library/amap?
* restoring previous ?/Users/bryanhanson/Library/R/3.2/library/amap?

gcc --version

On Jan 12, 2015, at 3:29 PM, Simon Urbanek <Simon.Urbanek at r-project.org> wrote:

Bryan,

it means that you have a mismatch between the Fortran compiler used to build R and the one you are using to build packages. Did you remove and/or update Fortran between compiling R and the packages?

Cheers,
Simon

On Jan 12, 2015, at 2:20 PM, Bryan Hanson <hanson at depauw.edu> wrote:

I?m trying to get R 3.2 working fully so I can test my packages before sending to CRAN.  R 3.2 appears to work OK in general terms.  However, when I try to install some packages I need, I run into errors with the libraries that the install process desires.  I get the same or very similar messages from several packages.  Let?s use amap as an example:

install.packages("amap", type = "source")
[?]
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: *** [amap.so] Error 1
ERROR: compilation failed for package ?amap?
* removing ?/Users/bryanhanson/Library/R/3.2/library/amap?
* restoring previous ?/Users/bryanhanson/Library/R/3.2/library/amap?

The full output is appended after this message.  The problem here is clear in one sense: there no directory on my machine by that name, since on Yosemite it is darwin13.4.0 and gcc is at 4.9.2.  xcode and xquartz have been updated.  I don?t know if this is a problem with a symlink on my system or an issue with the amap package  not yet being fully updated for R 3.2 or a problem with R 3.2 or a mangled gcc install.  All suggestions welcome, there?s a good chance I?m being simple-minded here.

Thank you.  Bryan

=== dir listing

pwd

/usr/local/lib/gcc/x86_64-apple-darwin13.4.0

ls -l

total 16
lrwxr-xr-x   1 bryanhanson  wheel    67 Dec 12 14:29 4.8.2 -> ../../../Cellar/gcc48/4.8.3/lib/gcc/x86_64-apple-darwin13.4.0/4.8.3
lrwxr-xr-x   1 bryanhanson  wheel    67 Dec 12 14:22 4.8.3 -> ../../../Cellar/gcc48/4.8.3/lib/gcc/x86_64-apple-darwin13.4.0/4.8.3
drwxr-xr-x  66 bryanhanson  wheel  2244 Dec 20 10:36 4.9.2

=== SessionInfo()

R Under development (unstable) (2015-01-11 r67421)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.1 (Yosemite)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] sos_1.3-8  brew_1.0-6

loaded via a namespace (and not attached):
[1] tools_3.2.0

=== Full output from install.packages

install.packages("amap", type = "source")
Installing package into ?/Users/bryanhanson/Library/R/3.2/library?
(as ?lib? is unspecified)
trying URL 'http://cran.at.r-project.org/src/contrib/amap_0.8-14.tar.gz'
Content type 'application/x-gzip' length 259358 bytes (253 KB)
opened URL
==================================================
downloaded 253 KB

********
********  Loading Bryan's .Rprofile
********
Loading required package: brew
********
********  Completed Bryan's .Rprofile GET TO WORK!
********
* installing *source* package ?amap? ...
** package ?amap? successfully unpacked and MD5 sums checked
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking for pthread_create in -lpthread... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include/   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c acprob.cpp -o acprob.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include/   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c burt.c -o burt.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include/   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c diss.c -o diss.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include/   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c distance.cpp -o distance.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include/   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c hclust.cpp -o hclust.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include/   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c kmeans.cpp -o kmeans.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include/   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c matrice.cpp -o matrice.o
gfortran-4.8   -fPIC  -g -O2  -c pop.f -o pop.o
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 amap.so acprob.o burt.o diss.o distance.o hclust.o kmeans.o matrice.o pop.o -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: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [amap.so] Error 1
ERROR: compilation failed for package ?amap?
* removing ?/Users/bryanhanson/Library/R/3.2/library/amap?
* restoring previous ?/Users/bryanhanson/Library/R/3.2/library/amap?

On Jan 12, 2015, at 3:36 PM, Bryan Hanson <hanson at depauw.edu> wrote:

Hi Simon? I never compiled R myself, I just got R-devel-mavericks.pkg from http://r.research.att.com/ (this morning, though I had the same experience about 3 weeks ago,  and gave up, hoping it was something which would go away?).  I did update gcc back in December, this is what I have installed:

gcc --version

Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/c++/4.2.1
Apple LLVM version 6.0 (clang-600.0.56) (based on LLVM 3.5svn)
Target: x86_64-apple-darwin14.0.0
Thread model: posix

which I notice has an even newer target.

Bryan

On Jan 12, 2015, at 3:29 PM, Simon Urbanek <Simon.Urbanek at r-project.org> wrote:

Bryan,

it means that you have a mismatch between the Fortran compiler used to build R and the one you are using to build packages. Did you remove and/or update Fortran between compiling R and the packages?

Cheers,
Simon

On Jan 12, 2015, at 2:20 PM, Bryan Hanson <hanson at depauw.edu> wrote:

I?m trying to get R 3.2 working fully so I can test my packages before sending to CRAN.  R 3.2 appears to work OK in general terms.  However, when I try to install some packages I need, I run into errors with the libraries that the install process desires.  I get the same or very similar messages from several packages.  Let?s use amap as an example:

install.packages("amap", type = "source")
[?]
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: *** [amap.so] Error 1
ERROR: compilation failed for package ?amap?
* removing ?/Users/bryanhanson/Library/R/3.2/library/amap?
* restoring previous ?/Users/bryanhanson/Library/R/3.2/library/amap?

The full output is appended after this message.  The problem here is clear in one sense: there no directory on my machine by that name, since on Yosemite it is darwin13.4.0 and gcc is at 4.9.2.  xcode and xquartz have been updated.  I don?t know if this is a problem with a symlink on my system or an issue with the amap package  not yet being fully updated for R 3.2 or a problem with R 3.2 or a mangled gcc install.  All suggestions welcome, there?s a good chance I?m being simple-minded here.

Thank you.  Bryan

=== dir listing

pwd

/usr/local/lib/gcc/x86_64-apple-darwin13.4.0

ls -l

total 16
lrwxr-xr-x   1 bryanhanson  wheel    67 Dec 12 14:29 4.8.2 -> ../../../Cellar/gcc48/4.8.3/lib/gcc/x86_64-apple-darwin13.4.0/4.8.3
lrwxr-xr-x   1 bryanhanson  wheel    67 Dec 12 14:22 4.8.3 -> ../../../Cellar/gcc48/4.8.3/lib/gcc/x86_64-apple-darwin13.4.0/4.8.3
drwxr-xr-x  66 bryanhanson  wheel  2244 Dec 20 10:36 4.9.2

=== SessionInfo()

R Under development (unstable) (2015-01-11 r67421)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.1 (Yosemite)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] sos_1.3-8  brew_1.0-6

loaded via a namespace (and not attached):
[1] tools_3.2.0

=== Full output from install.packages

install.packages("amap", type = "source")
Installing package into ?/Users/bryanhanson/Library/R/3.2/library?
(as ?lib? is unspecified)
trying URL 'http://cran.at.r-project.org/src/contrib/amap_0.8-14.tar.gz'
Content type 'application/x-gzip' length 259358 bytes (253 KB)
opened URL
==================================================
downloaded 253 KB

********
********  Loading Bryan's .Rprofile
********
Loading required package: brew
********
********  Completed Bryan's .Rprofile GET TO WORK!
********
* installing *source* package ?amap? ...
** package ?amap? successfully unpacked and MD5 sums checked
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking for pthread_create in -lpthread... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include/   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c acprob.cpp -o acprob.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include/   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c burt.c -o burt.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include/   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c diss.c -o diss.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include/   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c distance.cpp -o distance.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include/   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c hclust.cpp -o hclust.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include/   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c kmeans.cpp -o kmeans.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include/   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c matrice.cpp -o matrice.o
gfortran-4.8   -fPIC  -g -O2  -c pop.f -o pop.o
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 amap.so acprob.o burt.o diss.o distance.o hclust.o kmeans.o matrice.o pop.o -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: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [amap.so] Error 1
ERROR: compilation failed for package ?amap?
* removing ?/Users/bryanhanson/Library/R/3.2/library/amap?
* restoring previous ?/Users/bryanhanson/Library/R/3.2/library/amap?