Skip to content

Problems installing packages with R 3.2.0 on Linux Mint 17.1

5 messages · "Dr. Stefan Röttger", Johannes Ranke, Dirk Eddelbuettel

#
Dear R-SIG-Debians,

I have difficulties installing packages from within R through 
install.packages(). R version is 3.2.0 and OS is Linux Mint 17.1.

For most packages, a lot of error messages come up which seem to be 
related to compilation. Installing packages provided by the ubuntu 
distro through apt-get works just fine.

I followed all directions given in CRAN's /bin/linux/ubuntu/readme.html, 
but the problem persists.

Entering install.packages("sem") in R, for example, produces the output 
below.

I would be happy if anyone could give me a hint or recommendation on how 
to get the compilation going.


Best regards,
Stefan



 > install.packages("sem")
Installing package into ?/home/stefan/R/x86_64-pc-linux-gnu-library/3.2?
(as ?lib? is unspecified)
versuche URL 'http://cran.rstudio.com/src/contrib/sem_3.1-5.tar.gz'
Content type 'application/x-gzip' length 146831 bytes (143 KB)
==================================================
downloaded 143 KB

* installing *source* package ?sem? ...
** Paket ?sem? erfolgreich entpackt und MD5 Summen ?berpr?ft
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 
-fstack-protector --param=ssp-buffer-size=4 -Wformat 
-Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c csemnlm.c -o csemnlm.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 
-fstack-protector --param=ssp-buffer-size=4 -Wformat 
-Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c uncmin.c -o uncmin.o
g++ -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector 
--param=ssp-buffer-size=4 -Wformat -Werror=format-security 
-D_FORTIFY_SOURCE=2 -g  -c csem.cpp -o csem.o
In file included from /usr/include/c++/4.8/cctype:42:0,
                  from /usr/include/c++/4.8/bits/localefwd.h:42,
                  from /usr/include/c++/4.8/bits/ios_base.h:40,
                  from /usr/include/c++/4.8/iomanip:40,
                  from csem.h:38,
                  from csem.cpp:38:
/usr/share/R/include/ctype.h:120:55: error: expected ?,? or ?...? before 
?new?
  __extern void chrreplace(char *source, char old, char new);
                                                        ^
In file included from /usr/include/c++/4.8/bits/locale_facets.h:41:0,
                  from /usr/include/c++/4.8/bits/basic_ios.h:37,
                  from /usr/include/c++/4.8/ios:44,
                  from /usr/include/c++/4.8/ostream:38,
                  from /usr/include/c++/4.8/iostream:39,
                  from csem.h:39,
                  from csem.cpp:38:
/usr/include/x86_64-linux-gnu/c++/4.8/bits/ctype_base.h:49:35: error: 
?_ISupper? was not declared in this scope
      static const mask upper     = _ISupper;
                                    ^
/usr/include/x86_64-linux-gnu/c++/4.8/bits/ctype_base.h:50:32: error: 
?_ISlower? was not declared in this scope
      static const mask lower  = _ISlower;
                                 ^
/usr/include/x86_64-linux-gnu/c++/4.8/bits/ctype_base.h:51:32: error: 
?_ISalpha? was not declared in this scope
      static const mask alpha  = _ISalpha;
                                 ^
/usr/include/x86_64-linux-gnu/c++/4.8/bits/ctype_base.h:52:32: error: 
?_ISdigit? was not declared in this scope
      static const mask digit  = _ISdigit;
                                 ^
/usr/include/x86_64-linux-gnu/c++/4.8/bits/ctype_base.h:53:33: error: 
?_ISxdigit? was not declared in this scope
      static const mask xdigit  = _ISxdigit;
                                  ^
/usr/include/x86_64-linux-gnu/c++/4.8/bits/ctype_base.h:54:32: error: 
?_ISspace? was not declared in this scope
      static const mask space  = _ISspace;
                                 ^
/usr/include/x86_64-linux-gnu/c++/4.8/bits/ctype_base.h:55:32: error: 
?_ISprint? was not declared in this scope
      static const mask print  = _ISprint;
                                 ^
/usr/include/x86_64-linux-gnu/c++/4.8/bits/ctype_base.h:56:32: error: 
?_ISalpha? was not declared in this scope
      static const mask graph  = _ISalpha | _ISdigit | _ISpunct;
                                 ^
/usr/include/x86_64-linux-gnu/c++/4.8/bits/ctype_base.h:56:43: error: 
?_ISdigit? was not declared in this scope
      static const mask graph  = _ISalpha | _ISdigit | _ISpunct;
                                            ^
/usr/include/x86_64-linux-gnu/c++/4.8/bits/ctype_base.h:56:54: error: 
?_ISpunct? was not declared in this scope
      static const mask graph  = _ISalpha | _ISdigit | _ISpunct;
                                                       ^
/usr/include/x86_64-linux-gnu/c++/4.8/bits/ctype_base.h:57:32: error: 
?_IScntrl? was not declared in this scope
      static const mask cntrl  = _IScntrl;
                                 ^
/usr/include/x86_64-linux-gnu/c++/4.8/bits/ctype_base.h:58:32: error: 
?_ISpunct? was not declared in this scope
      static const mask punct  = _ISpunct;
                                 ^
/usr/include/x86_64-linux-gnu/c++/4.8/bits/ctype_base.h:59:32: error: 
?_ISalpha? was not declared in this scope
      static const mask alnum  = _ISalpha | _ISdigit;
                                 ^
/usr/include/x86_64-linux-gnu/c++/4.8/bits/ctype_base.h:59:43: error: 
?_ISdigit? was not declared in this scope
      static const mask alnum  = _ISalpha | _ISdigit;
                                            ^
make: *** [csem.o] Fehler 1
ERROR: compilation failed for package ?sem?
* removing ?/home/stefan/R/x86_64-pc-linux-gnu-library/3.2/sem?
Warning in install.packages :
   installation of package ?sem? had non-zero exit status
#
Dear Stefan,

I have no idea where the problem is, but I feel this strong urge to mention 
that install.packages("sem") works fine on Debian squeeze (g++ 4.4.5), wheezy 
(g++ 4.7.2) and jessie (g++ 4.9.2) using the R backport from CRAN...

Kind regards,

Johannes

Am Donnerstag, 7. Mai 2015, 09:39:20 schrieb Dr. Stefan R?ttger:
#
On 7 May 2015 at 13:17, Johannes Ranke wrote:
| I have no idea where the problem is, but I feel this strong urge to mention 
| that install.packages("sem") works fine on Debian squeeze (g++ 4.4.5), wheezy 
| (g++ 4.7.2) and jessie (g++ 4.9.2) using the R backport from CRAN...

+1

As the messages all come from compilation, methinks something is wrong with
the compiler setup.  Maybe icc got added, maybe gcc got broken, maybe
something else you did not tell us.

But the default toolchains on the systems we stand behind all work.

Dirk
#
Dear Dirk, dear Johannes,

thank you very much for your immediate responses.

Could you give me some directions on how to make sure that I have a 
correct compiler setup? I.e., which software / compiler packages are 
assumed by R to be installed?

Maybe I can solve the problem by making a fresh install of all required 
components and deinstalling components that may interfere.

Best regards,
Stefan



Am 07.05.2015 um 13:32 schrieb Dirk Eddelbuettel:
#
Dear Stefan,

you are using Linux Mint 17.1, which is based on Ubuntu 14.04 (using gcc 
4.8.2). I have an Ubuntu 14.04 system with CRAN backports installed and 
install.packages("sem") works there as well.

Again, compiler setup should "just work" on these systems. Still no clue what 
went wrong at your end.

The packages necessary to build R packages from source are pulled by the 
dependencies of r-base-dev, including build-essential, gcc and g++.

g++ gives the error messages in your case.

Kind regards,

Johannes


Am Freitag, 8. Mai 2015, 08:33:22 schrieb Dr. Stefan R?ttger: