thr3ads.net - R SIG Debian - [R-sig-Debian] Problems installing packages with R 3.2.0 on Linux Mint 17.1 [May 2015]

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"Dr. Stefan Röttger"

2015-May-07 07:39 UTC

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

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



	[[alternative HTML version deleted]]

Johannes Ranke

2015-May-07 11:17 UTC

head link

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

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
> 
> 
> 
> 	[[alternative HTML version deleted]]
> 
> _______________________________________________
> R-SIG-Debian mailing list
> R-SIG-Debian at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-debian-- 
PD Dr. Johannes Ranke
Kronacher Str. 8
79639 Grenzach-Wyhlen

Dirk Eddelbuettel

2015-May-07 11:32 UTC

head link

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

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

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org

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