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

Johannes Ranke
Thu, 07 May 2015 11:17:22 -0000

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:
> 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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>
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--
PD Dr. Johannes Ranke
Kronacher Str. 8
79639 Grenzach-Wyhlen