Dear list members,
I encountered this problem and the solution pointed out in a previous
thread did not work for me.
(e.g. install.packages("RCurl", repos =
"http://www.omegahat.org/R")
I work with Ubuntu Hardy, and installed R 2.6.2 via apt-get.
I really need RCurl in order to use biomaRt ... any help would be
greatly appreciated.
Best wishes,
Emmanuel
================================================> sessionInfo()
R version 2.6.2 (2008-02-08)
x86_64-pc-linux-gnu
locale:
LC_CTYPE=en_CA.UTF-8;LC_NUMERIC=C;LC_TIME=en_CA.UTF-8;LC_COLLATE=en_CA.UTF-8;LC_MONETARY=en_CA.UTF-8;LC_MESSAGES=en_CA.UTF-8;LC_PAPER=en_CA.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_CA.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] rcompgen_0.1-17 tools_2.6.2>
================================================
> install.packages("RCurl", repos =
"http://www.omegahat.org/R")
Warning in install.packages("RCurl", repos =
"http://www.omegahat.org/R") :
argument 'lib' is missing: using
'/usr/local/lib/R/site-library'
trying URL 'http://www.omegahat.org/R/src/contrib/RCurl_0.9-4.tar.gz'
Content type 'application/x-gzip' length 150884 bytes (147 Kb)
opened URL
=================================================downloaded 147 Kb
* Installing *source* package 'RCurl' ...
checking for curl-config... /usr/bin/curl-config
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking how to run the C preprocessor... gcc -E
Version has a libidn field
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include
-DHAVE_LIBIDN_FIELD=1 -fpic -g -O2 -c base64.c -o base64.o
In file included from base64.c:1:
Rcurl.h:52: error: expected specifier-qualifier-list before 'cetype_t'
make: *** [base64.o] Error 1
chmod: cannot access `/usr/local/lib/R/site-library/RCurl/libs/*': No
such file or directory
ERROR: compilation failed for package 'RCurl'
** Removing '/usr/local/lib/R/site-library/RCurl'
The downloaded packages are in
/tmp/RtmpQ8FMBZ/downloaded_packages
Warning message:
In install.packages("RCurl", repos =
"http://www.omegahat.org/R") :
installation of package 'RCurl' had non-zero exit status
===============================================================================
Hi Martin,
are you working on a 64-bit linux distribution and which version of
RCurl are you trying to install? There has been a problem with a
recent version of RCurl and the "R_base64_decode", search the archives
of the Bioconductor mailing list for a thread called
"RCurl loading problem with 64 bit linux distribution".
Please try using the newest versions of R (R-2.7.0 has been released a
few weeks ago) and RCurl, which you can obtain from within R by
typing:
install.packages("RCurl", repos =
"http://www.omegahat.org/R")
The new version of RCurl (>= 0.9.2) worked fine for me, while 0.9.0
and 0.9.1 did not.
Hope this helps.
Joern
martin sikora wrote:
dear list members,
i'm having a problem installing the biomaRt package on my linux
machine, due to the fact of a compilation error with RCurl. i am using
R 2.6.2 on fedora 7, and this is the output i get:
gcc -m32 -std=gnu99 -I/usr/include/R -I/usr/include/R
-DHAVE_LIBIDN_FIELD=1 -I/usr/local/include -fpic -O2 -g -pipe
-Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
-fasynchronous-unwind-tables -c base64.c -o base64.o
In file included from base64.c:1:
Rcurl.h:52: error: expected specifier-qualifier-list before ?cetype_t?
base64.c: In function ?R_base64_decode?:
base64.c:25: warning: pointer targets in assignment differ in signedness
base64.c:39: warning: pointer targets in passing argument 1 of
?Rf_mkString? differ in signedness
base64.c: In function ?R_base64_encode?:
base64.c:60: warning: pointer targets in assignment differ in signedness
make: *** [base64.o] Error 1
as far as i know i have all the necessary libraries installed:
$ yum list installed | grep libxml
libxml2.i386 2.6.31-1.fc7
installed libxml2-devel.i386 2.6.31-1.fc7
installed libxml2-python.i386
2.6.31-1.fc7 installed perl-libxml-perl.noarch
0.08-1.2.1 installed
$ yum list installed | grep curl
curl.i386 7.16.4-1.fc7
installed curl-devel.i386 7.16.4-1.fc7
installed python-pycurl.i386
7.16.0-0.1.20061207.fc installed
as i am not an expert in linux stuff, i was wondering if there
could be any other missing libraries? any other ideas?
cheers
martin
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi Emanuel. The best thing to do is upgrade to R-2.7.2 (or any 2.7.*) and the problem should disappear. It relates to encoding of strings. D. Emmanuel Levy wrote:> Dear list members, > > I encountered this problem and the solution pointed out in a previous > thread did not work for me. > (e.g. install.packages("RCurl", repos = "http://www.omegahat.org/R") > > I work with Ubuntu Hardy, and installed R 2.6.2 via apt-get. > > I really need RCurl in order to use biomaRt ... any help would be > greatly appreciated. > > Best wishes, > > Emmanuel > > ================================================> >> sessionInfo() > R version 2.6.2 (2008-02-08) > x86_64-pc-linux-gnu > > locale: > LC_CTYPE=en_CA.UTF-8;LC_NUMERIC=C;LC_TIME=en_CA.UTF-8;LC_COLLATE=en_CA.UTF-8;LC_MONETARY=en_CA.UTF-8;LC_MESSAGES=en_CA.UTF-8;LC_PAPER=en_CA.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_CA.UTF-8;LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > loaded via a namespace (and not attached): > [1] rcompgen_0.1-17 tools_2.6.2 > > ================================================> > >> install.packages("RCurl", repos = "http://www.omegahat.org/R") > Warning in install.packages("RCurl", repos = "http://www.omegahat.org/R") : > argument 'lib' is missing: using '/usr/local/lib/R/site-library' > trying URL 'http://www.omegahat.org/R/src/contrib/RCurl_0.9-4.tar.gz' > Content type 'application/x-gzip' length 150884 bytes (147 Kb) > opened URL > =================================================> downloaded 147 Kb > > * Installing *source* package 'RCurl' ... > checking for curl-config... /usr/bin/curl-config > checking for gcc... gcc > checking for C compiler default output file name... a.out > checking whether the C compiler works... yes > checking whether we are cross compiling... no > checking for suffix of executables... > checking for suffix of object files... o > checking whether we are using the GNU C compiler... yes > checking whether gcc accepts -g... yes > checking for gcc option to accept ANSI C... none needed > checking how to run the C preprocessor... gcc -E > Version has a libidn field > configure: creating ./config.status > config.status: creating src/Makevars > ** libs > gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include > -DHAVE_LIBIDN_FIELD=1 -fpic -g -O2 -c base64.c -o base64.o > In file included from base64.c:1: > Rcurl.h:52: error: expected specifier-qualifier-list before 'cetype_t' > make: *** [base64.o] Error 1 > chmod: cannot access `/usr/local/lib/R/site-library/RCurl/libs/*': No > such file or directory > ERROR: compilation failed for package 'RCurl' > ** Removing '/usr/local/lib/R/site-library/RCurl' > > The downloaded packages are in > /tmp/RtmpQ8FMBZ/downloaded_packages > Warning message: > In install.packages("RCurl", repos = "http://www.omegahat.org/R") : > installation of package 'RCurl' had non-zero exit status > > ===============================================================================> > Hi Martin, > are you working on a 64-bit linux distribution and which version of > RCurl are you trying to install? There has been a problem with a > recent version of RCurl and the "R_base64_decode", search the archives > of the Bioconductor mailing list for a thread called > "RCurl loading problem with 64 bit linux distribution". > Please try using the newest versions of R (R-2.7.0 has been released a > few weeks ago) and RCurl, which you can obtain from within R by > typing: > install.packages("RCurl", repos = "http://www.omegahat.org/R") > The new version of RCurl (>= 0.9.2) worked fine for me, while 0.9.0 > and 0.9.1 did not. > Hope this helps. > Joern > > > martin sikora wrote: > > dear list members, > > i'm having a problem installing the biomaRt package on my linux > machine, due to the fact of a compilation error with RCurl. i am using > R 2.6.2 on fedora 7, and this is the output i get: > > gcc -m32 -std=gnu99 -I/usr/include/R -I/usr/include/R > -DHAVE_LIBIDN_FIELD=1 -I/usr/local/include -fpic -O2 -g -pipe > -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector > --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic > -fasynchronous-unwind-tables -c base64.c -o base64.o > In file included from base64.c:1: > Rcurl.h:52: error: expected specifier-qualifier-list before ?cetype_t? > base64.c: In function ?R_base64_decode?: > base64.c:25: warning: pointer targets in assignment differ in signedness > base64.c:39: warning: pointer targets in passing argument 1 of > ?Rf_mkString? differ in signedness > base64.c: In function ?R_base64_encode?: > base64.c:60: warning: pointer targets in assignment differ in signedness > make: *** [base64.o] Error 1 > > as far as i know i have all the necessary libraries installed: > > $ yum list installed | grep libxml > libxml2.i386 2.6.31-1.fc7 > installed libxml2-devel.i386 2.6.31-1.fc7 > installed libxml2-python.i386 > 2.6.31-1.fc7 installed perl-libxml-perl.noarch > 0.08-1.2.1 installed > $ yum list installed | grep curl > curl.i386 7.16.4-1.fc7 > installed curl-devel.i386 7.16.4-1.fc7 > installed python-pycurl.i386 > 7.16.0-0.1.20061207.fc installed > > as i am not an expert in linux stuff, i was wondering if there > could be any other missing libraries? any other ideas? > > cheers > martin > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.-----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.9 (Darwin) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iEYEARECAAYFAkjRCr0ACgkQ9p/Jzwa2QP7gywCeLovZ5FGv007HzD8tigg8LJn8 CXYAniuxcC29ygyowNNPgDXZ4ej3pRxk =TMuj -----END PGP SIGNATURE-----
Emmanuel, Please see inline for comments. Le mer. 17 sept. ? 00:59, Emmanuel Levy a ?crit :> Dear list members, > > I encountered this problem and the solution pointed out in a previous > thread did not work for me. > (e.g. install.packages("RCurl", repos = "http://www.omegahat.org/R") > > I work with Ubuntu Hardy, and installed R 2.6.2 via apt-get.Please install the latest version, 2.7.2 from CRAN. See the instructions in the Ubuntu README: http://cran.r-project.org/bin/linux/ubuntu/> I really need RCurl in order to use biomaRt ... any help would be > greatly appreciated.The package compiled just fine here after installing the libcurl4- gnutls-dev (Ubuntu) package. You just have a permission problem; see below.> Best wishes, > > Emmanuel > > ================================================> >> sessionInfo() > R version 2.6.2 (2008-02-08) > x86_64-pc-linux-gnu > > locale: > LC_CTYPE > = > en_CA > .UTF > -8 > ;LC_NUMERIC > = > C > ;LC_TIME > = > en_CA > .UTF > -8 > ;LC_COLLATE > = > en_CA > .UTF > -8 > ;LC_MONETARY > = > en_CA > .UTF > -8 > ;LC_MESSAGES > = > en_CA > .UTF > -8 > ;LC_PAPER > = > en_CA > .UTF > -8 > ;LC_NAME > = > C > ;LC_ADDRESS > =C;LC_TELEPHONE=C;LC_MEASUREMENT=en_CA.UTF-8;LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > loaded via a namespace (and not attached): > [1] rcompgen_0.1-17 tools_2.6.2 >> > > ================================================> > >> install.packages("RCurl", repos = "http://www.omegahat.org/R") > Warning in install.packages("RCurl", repos = "http://www.omegahat.org/R > ") : > argument 'lib' is missing: using '/usr/local/lib/R/site-library'See? R will *try* to install the package in /usr/local/lib/R/site- library, which you do not have access to as a normal user. I do not recommend to install as root instead. The packages you install yourself as a user belong to your home directory. See the "ADMINISTRATION AND MAINTENANCE OF R PACKAGES" section in the Ubuntu README linked above for indications of the "correct" way to do this.> trying URL 'http://www.omegahat.org/R/src/contrib/RCurl_0.9-4.tar.gz' > Content type 'application/x-gzip' length 150884 bytes (147 Kb) > opened URL > =================================================> downloaded 147 Kb > > * Installing *source* package 'RCurl' ... > checking for curl-config... /usr/bin/curl-config > checking for gcc... gcc > checking for C compiler default output file name... a.out > checking whether the C compiler works... yes > checking whether we are cross compiling... no > checking for suffix of executables... > checking for suffix of object files... o > checking whether we are using the GNU C compiler... yes > checking whether gcc accepts -g... yes > checking for gcc option to accept ANSI C... none needed > checking how to run the C preprocessor... gcc -E > Version has a libidn field > configure: creating ./config.status > config.status: creating src/Makevars > ** libs > gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include > -DHAVE_LIBIDN_FIELD=1 -fpic -g -O2 -c base64.c -o base64.o > In file included from base64.c:1: > Rcurl.h:52: error: expected specifier-qualifier-list before 'cetype_t' > make: *** [base64.o] Error 1 > chmod: cannot access `/usr/local/lib/R/site-library/RCurl/libs/*': No > such file or directoryThis should have been the clue. --- Vincent Goulet, Associate Professor ?cole d'actuariat Universit? Laval, Qu?bec Vincent.Goulet at act.ulaval.ca http://vgoulet.act.ulaval.ca> > ERROR: compilation failed for package 'RCurl' > ** Removing '/usr/local/lib/R/site-library/RCurl' > > The downloaded packages are in > /tmp/RtmpQ8FMBZ/downloaded_packages > Warning message: > In install.packages("RCurl", repos = "http://www.omegahat.org/R") : > installation of package 'RCurl' had non-zero exit status > > = > = > = > = > = > = > = > = > = > = > =====================================================================> > Hi Martin, > are you working on a 64-bit linux distribution and which version of > RCurl are you trying to install? There has been a problem with a > recent version of RCurl and the "R_base64_decode", search the archives > of the Bioconductor mailing list for a thread called > "RCurl loading problem with 64 bit linux distribution". > Please try using the newest versions of R (R-2.7.0 has been released a > few weeks ago) and RCurl, which you can obtain from within R by > typing: > install.packages("RCurl", repos = "http://www.omegahat.org/R") > The new version of RCurl (>= 0.9.2) worked fine for me, while 0.9.0 > and 0.9.1 did not. > Hope this helps. > Joern > > > martin sikora wrote: > > dear list members, > > i'm having a problem installing the biomaRt package on my linux > machine, due to the fact of a compilation error with RCurl. i am using > R 2.6.2 on fedora 7, and this is the output i get: > > gcc -m32 -std=gnu99 -I/usr/include/R -I/usr/include/R > -DHAVE_LIBIDN_FIELD=1 -I/usr/local/include -fpic -O2 -g -pipe > -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector > --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic > -fasynchronous-unwind-tables -c base64.c -o base64.o > In file included from base64.c:1: > Rcurl.h:52: error: expected specifier-qualifier-list before ? > cetype_t? > base64.c: In function ?R_base64_decode?: > base64.c:25: warning: pointer targets in assignment differ in > signedness > base64.c:39: warning: pointer targets in passing argument 1 of > ?Rf_mkString? differ in signedness > base64.c: In function ?R_base64_encode?: > base64.c:60: warning: pointer targets in assignment differ in > signedness > make: *** [base64.o] Error 1 > > as far as i know i have all the necessary libraries installed: > > $ yum list installed | grep libxml > libxml2.i386 2.6.31-1.fc7 > installed libxml2-devel.i386 2.6.31-1.fc7 > installed libxml2-python.i386 > 2.6.31-1.fc7 installed perl-libxml-perl.noarch > 0.08-1.2.1 installed > $ yum list installed | grep curl > curl.i386 7.16.4-1.fc7 > installed curl-devel.i386 7.16.4-1.fc7 > installed python-pycurl.i386 > 7.16.0-0.1.20061207.fc installed > > as i am not an expert in linux stuff, i was wondering if there > could be any other missing libraries? any other ideas? > > cheers > martin > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.