[R-sig-Debian] Problems installing packages with R 3.2.0 on Linux Mint 17.1

"Dr. Stefan Röttger"
Thu, 07 May 2015 07:39:20 -0000

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



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