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
Problems installing packages with R 3.2.0 on Linux Mint 17.1
5 messages · "Dr. Stefan Röttger", Johannes Ranke, Dirk Eddelbuettel
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]]
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PD Dr. Johannes Ranke Kronacher Str. 8 79639 Grenzach-Wyhlen
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
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:
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 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:
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:
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
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