Hello! I'm trying to install R-3.0.1 on an Ubuntu machine (64 bit, version 13.04). I have uninstalled and installed several times, but to no avail. I keep getting errors about missing ldpaths, and installing packages does not work at all. Here is the information: erin@erin-Lenovo-IdeaPad-Y480:~$ sudo apt-get install r-base Reading package lists... Done Building dependency tree Reading state information... Done The following extra packages will be installed: cdbs dh-translations intltool libblas-dev libblas3 libbz2-dev libjpeg-dev libjpeg-turbo8-dev libjpeg8-dev liblapack-dev liblapack3 libncurses5-dev libpcre3-dev libpcrecpp0 libpng12-dev libreadline-dev libreadline6-dev libtinfo-dev libxml-parser-perl python-scour r-base-core r-base-dev r-base-html r-cran-boot r-cran-class r-cran-cluster r-cran-codetools r-cran-foreign r-cran-kernsmooth r-cran-lattice r-cran-mass r-cran-matrix r-cran-mgcv r-cran-nlme r-cran-nnet r-cran-rpart r-cran-spatial r-cran-survival r-doc-html r-recommended zlib1g-dev Suggested packages: devscripts ncurses-doc python-rsvg ess r-doc-info r-doc-pdf r-mathlib texlive-base texlive-latex-base texlive-generic-recommended texlive-fonts-recommended texlive-fonts-extra texlive-extra-utils texlive-latex-recommended texlive-latex-extra texinfo texi2html The following NEW packages will be installed: cdbs dh-translations intltool libblas-dev libblas3 libbz2-dev libjpeg-dev libjpeg-turbo8-dev libjpeg8-dev liblapack-dev liblapack3 libncurses5-dev libpcre3-dev libpcrecpp0 libpng12-dev libreadline-dev libreadline6-dev libtinfo-dev libxml-parser-perl python-scour r-base r-base-core r-base-dev r-base-html r-cran-boot r-cran-class r-cran-cluster r-cran-codetools r-cran-foreign r-cran-kernsmooth r-cran-lattice r-cran-mass r-cran-matrix r-cran-mgcv r-cran-nlme r-cran-nnet r-cran-rpart r-cran-spatial r-cran-survival r-doc-html r-recommended zlib1g-dev 0 upgraded, 42 newly installed, 0 to remove and 0 not upgraded. Need to get 131 kB/49.4 MB of archives. After this operation, 88.2 MB of additional disk space will be used. Do you want to continue [Y/n]? Y Get:1 http://cran.at.r-project.org/bin/linux/ubuntu/ raring/ r-base 3.0.1-3raring [37.9 kB] Get:2 http://cran.at.r-project.org/bin/linux/ubuntu/ raring/ r-base-html 3.0.1-3raring [92.7 kB] Fetched 131 kB in 1s (73.2 kB/s) Extracting templates from packages: 100% Selecting previously unselected package libpcrecpp0:amd64. (Reading database ... 191688 files and directories currently installed.) Unpacking libpcrecpp0:amd64 (from .../libpcrecpp0_1%3a8.31-2_amd64.deb) ... Selecting previously unselected package libxml-parser-perl. Unpacking libxml-parser-perl (from .../libxml-parser-perl_2.41-1build2_amd64.deb) ... Selecting previously unselected package intltool. Unpacking intltool (from .../intltool_0.50.2-2_all.deb) ... Selecting previously unselected package dh-translations. Unpacking dh-translations (from .../dh-translations_117_all.deb) ... Selecting previously unselected package python-scour. Unpacking python-scour (from .../python-scour_0.26-3_all.deb) ... Selecting previously unselected package cdbs. Unpacking cdbs (from .../cdbs_0.4.120ubuntu1_all.deb) ... Selecting previously unselected package libblas3. Unpacking libblas3 (from .../libblas3_1.2.20110419-5_amd64.deb) ... Selecting previously unselected package libblas-dev. Unpacking libblas-dev (from .../libblas-dev_1.2.20110419-5_amd64.deb) ... Selecting previously unselected package libbz2-dev:amd64. Unpacking libbz2-dev:amd64 (from .../libbz2-dev_1.0.6-4_amd64.deb) ... Selecting previously unselected package libjpeg-turbo8-dev:amd64. Unpacking libjpeg-turbo8-dev:amd64 (from .../libjpeg-turbo8-dev_1.2.1-0ubuntu2_amd64.deb) ... Selecting previously unselected package libjpeg8-dev:amd64. Unpacking libjpeg8-dev:amd64 (from .../libjpeg8-dev_8c-2ubuntu7_amd64.deb) ... Selecting previously unselected package libjpeg-dev. Unpacking libjpeg-dev (from .../libjpeg-dev_8c-2ubuntu7_all.deb) ... Selecting previously unselected package liblapack3. Unpacking liblapack3 (from .../liblapack3_3.4.2-1~exp3_amd64.deb) ... Selecting previously unselected package liblapack-dev. Unpacking liblapack-dev (from .../liblapack-dev_3.4.2-1~exp3_amd64.deb) ... Selecting previously unselected package libtinfo-dev:amd64. Unpacking libtinfo-dev:amd64 (from .../libtinfo-dev_5.9-10ubuntu4_amd64.deb) ... Selecting previously unselected package libncurses5-dev. Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-10ubuntu4_amd64.deb) ... Selecting previously unselected package libpcre3-dev:amd64. Unpacking libpcre3-dev:amd64 (from .../libpcre3-dev_1%3a8.31-2_amd64.deb) ... Selecting previously unselected package zlib1g-dev:amd64. Unpacking zlib1g-dev:amd64 (from .../zlib1g-dev_1%3a1.2.7.dfsg-13ubuntu2_amd64.deb) ... Selecting previously unselected package libpng12-dev. Unpacking libpng12-dev (from .../libpng12-dev_1.2.49-1ubuntu2_amd64.deb) ... Selecting previously unselected package libreadline6-dev:amd64. Unpacking libreadline6-dev:amd64 (from .../libreadline6-dev_6.2-9ubuntu1_amd64.deb) ... Selecting previously unselected package libreadline-dev:amd64. Unpacking libreadline-dev:amd64 (from .../libreadline-dev_6.2-9ubuntu1_amd64.deb) ... Selecting previously unselected package r-base-core. Unpacking r-base-core (from .../r-base-core_3.0.1-3raring_amd64.deb) ... Selecting previously unselected package r-cran-boot. Unpacking r-cran-boot (from .../r-cran-boot_1.3-9-1raring0_all.deb) ... Selecting previously unselected package r-cran-cluster. Unpacking r-cran-cluster (from .../r-cran-cluster_1.14.4-1raring0_amd64.deb) ... Selecting previously unselected package r-cran-foreign. Unpacking r-cran-foreign (from .../r-cran-foreign_0.8.54-1raring0_amd64.deb) ... Selecting previously unselected package r-cran-mass. Unpacking r-cran-mass (from .../r-cran-mass_7.3-27-1raring0_amd64.deb) ... Selecting previously unselected package r-cran-kernsmooth. Unpacking r-cran-kernsmooth (from .../r-cran-kernsmooth_2.23-10-2raring0_amd64.deb) ... Selecting previously unselected package r-cran-lattice. Unpacking r-cran-lattice (from .../r-cran-lattice_0.20-15-1raring0_amd64.deb) ... Selecting previously unselected package r-cran-nlme. Unpacking r-cran-nlme (from .../r-cran-nlme_3.1.110-1raring0_amd64.deb) ... Selecting previously unselected package r-cran-matrix. Unpacking r-cran-matrix (from .../r-cran-matrix_1.0-12-1raring0_amd64.deb) ... Selecting previously unselected package r-cran-mgcv. Unpacking r-cran-mgcv (from .../r-cran-mgcv_1.7-24-1raring0_amd64.deb) ... Selecting previously unselected package r-cran-survival. Unpacking r-cran-survival (from .../r-cran-survival_2.37-4-2raring0_amd64.deb) ... Selecting previously unselected package r-cran-rpart. Unpacking r-cran-rpart (from .../r-cran-rpart_4.1-1-2raring0_amd64.deb) ... Selecting previously unselected package r-cran-class. Unpacking r-cran-class (from .../r-cran-class_7.3-8-1raring0_amd64.deb) ... Selecting previously unselected package r-cran-nnet. Unpacking r-cran-nnet (from .../r-cran-nnet_7.3-7-1raring0_amd64.deb) ... Selecting previously unselected package r-cran-spatial. Unpacking r-cran-spatial (from .../r-cran-spatial_7.3-6-1raring0_amd64.deb) ... Selecting previously unselected package r-cran-codetools. Unpacking r-cran-codetools (from .../r-cran-codetools_0.2-8-2raring0_all.deb) ... Selecting previously unselected package r-recommended. Unpacking r-recommended (from .../r-recommended_3.0.1-3raring_all.deb) ... Selecting previously unselected package r-base. Unpacking r-base (from .../r-base_3.0.1-3raring_all.deb) ... Selecting previously unselected package r-base-dev. Unpacking r-base-dev (from .../r-base-dev_3.0.1-3raring_all.deb) ... Selecting previously unselected package r-doc-html. Unpacking r-doc-html (from .../r-doc-html_3.0.1-3raring_all.deb) ... Selecting previously unselected package r-base-html. Unpacking r-base-html (from .../r-base-html_3.0.1-3raring_all.deb) ... Processing triggers for man-db ... Processing triggers for doc-base ... Processing 8 added doc-base files... Processing triggers for install-info ... Processing triggers for hicolor-icon-theme ... Processing triggers for bamfdaemon ... Rebuilding /usr/share/applications/bamf-2.index... Processing triggers for desktop-file-utils ... Processing triggers for gnome-menus ... Setting up libpcrecpp0:amd64 (1:8.31-2) ... Setting up libxml-parser-perl (2.41-1build2) ... Setting up intltool (0.50.2-2) ... Setting up dh-translations (117) ... Setting up python-scour (0.26-3) ... Setting up cdbs (0.4.120ubuntu1) ... Setting up libblas3 (1.2.20110419-5) ... update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide /usr/lib/libblas.so.3 (libblas.so.3) in auto mode Setting up libblas-dev (1.2.20110419-5) ... update-alternatives: using /usr/lib/libblas/libblas.so to provide /usr/lib/libblas.so (libblas.so) in auto mode Setting up libbz2-dev:amd64 (1.0.6-4) ... Setting up libjpeg-turbo8-dev:amd64 (1.2.1-0ubuntu2) ... Setting up libjpeg8-dev:amd64 (8c-2ubuntu7) ... Setting up libjpeg-dev (8c-2ubuntu7) ... Setting up liblapack3 (3.4.2-1~exp3) ... update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode Setting up liblapack-dev (3.4.2-1~exp3) ... update-alternatives: using /usr/lib/lapack/liblapack.so to provide /usr/lib/liblapack.so (liblapack.so) in auto mode Setting up libtinfo-dev:amd64 (5.9-10ubuntu4) ... Setting up libncurses5-dev (5.9-10ubuntu4) ... Setting up libpcre3-dev:amd64 (1:8.31-2) ... Setting up zlib1g-dev:amd64 (1:1.2.7.dfsg-13ubuntu2) ... Setting up libpng12-dev (1.2.49-1ubuntu2) ... Setting up libreadline6-dev:amd64 (6.2-9ubuntu1) ... Setting up libreadline-dev:amd64 (6.2-9ubuntu1) ... Setting up r-base-core (3.0.1-3raring) ... Creating config file /etc/R/Renviron with new version Setting up r-cran-boot (1.3-9-1raring0) ... Setting up r-cran-cluster (1.14.4-1raring0) ... Setting up r-cran-foreign (0.8.54-1raring0) ... Setting up r-cran-mass (7.3-27-1raring0) ... Setting up r-cran-kernsmooth (2.23-10-2raring0) ... Setting up r-cran-lattice (0.20-15-1raring0) ... Setting up r-cran-nlme (3.1.110-1raring0) ... Setting up r-cran-matrix (1.0-12-1raring0) ... Setting up r-cran-mgcv (1.7-24-1raring0) ... Setting up r-cran-survival (2.37-4-2raring0) ... Setting up r-cran-rpart (4.1-1-2raring0) ... Setting up r-cran-class (7.3-8-1raring0) ... Setting up r-cran-nnet (7.3-7-1raring0) ... Setting up r-cran-spatial (7.3-6-1raring0) ... Setting up r-cran-codetools (0.2-8-2raring0) ... Setting up r-recommended (3.0.1-3raring) ... Setting up r-base (3.0.1-3raring) ... Setting up r-base-dev (3.0.1-3raring) ... Setting up r-doc-html (3.0.1-3raring) ... Setting up r-base-html (3.0.1-3raring) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place erin@erin-Lenovo-IdeaPad-Y480:~$ sudo apt-get install r-base-dev Reading package lists... Done Building dependency tree Reading state information... Done r-base-dev is already the newest version. r-base-dev set to manually installed. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. erin@erin-Lenovo-IdeaPad-Y480:~$ echo $EDITOR emacs erin@erin-Lenovo-IdeaPad-Y480:~$ R /usr/bin/R: line 236: /usr/lib/R/etc/ldpaths: No such file or directory R version 3.0.1 (2013-05-16) -- "Good Sport" Copyright (C) 2013 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R.> install.packages("rlecuyer",depen=TRUE)Installing package into ‘/home/erin/lib/R/library’ (as ‘lib’ is unspecified) --- Please select a CRAN mirror for use in this session --- trying URL 'http://cran.at.r-project.org/src/contrib/rlecuyer_0.3-3.tar.gz' Content type 'application/x-gzip' length 11756 bytes (11 Kb) opened URL =================================================downloaded 11 Kb /usr/lib/R/bin/R: line 140: /usr/lib/R/etc/ldpaths: No such file or directory /usr/lib/R/bin/R: line 236: /usr/lib/R/etc/ldpaths: No such file or directory Error in file(con, "r") : cannot open the connection Calls: <Anonymous> -> sub -> grep -> readLines -> file In addition: Warning message: In file(con, "r") : cannot open file '/usr/lib/R/etc/Makeconf': No such file or directory The downloaded source packages are in ‘/tmp/RtmpV8EZt4/downloaded_packages’ Warning message: In install.packages("rlecuyer", depen = TRUE) : installation of package ‘rlecuyer’ had non-zero exit status>Any help would be much appreciated. I have installed R with Ubuntu on different versions several times successfully. Thanks, Erin [[alternative HTML version deleted]]
Dirk Eddelbuettel
2013-Jul-28 00:38 UTC
[R-sig-Debian] Problem with ldpaths in Ubuntu 13.04
On 28 July 2013 at 00:07, Hodgess, Erin wrote:
| Hello!
|
| I'm trying to install R-3.0.1 on an Ubuntu machine (64 bit, version
13.04). I have uninstalled and installed several times, but to no avail.
|
|
| I keep getting errors about missing ldpaths, and installing packages does not
work at all.
|
| erin at erin-Lenovo-IdeaPad-Y480:~$ R
| /usr/bin/R: line 236: /usr/lib/R/etc/ldpaths: No such file or directory
|
| R version 3.0.1 (2013-05-16) -- "Good Sport"
| Copyright (C) 2013 The R Foundation for Statistical Computing
| Platform: x86_64-pc-linux-gnu (64-bit)
|
| R is free software and comes with ABSOLUTELY NO WARRANTY.
| You are welcome to redistribute it under certain conditions.
| Type 'license()' or 'licence()' for distribution details.
|
| Natural language support but running in an English locale
|
| R is a collaborative project with many contributors.
| Type 'contributors()' for more information and
| 'citation()' on how to cite R or R packages in publications.
|
| Type 'demo()' for some demos, 'help()' for on-line help, or
| 'help.start()' for an HTML browser interface to help.
| Type 'q()' to quit R.
|
Well R is installed as it evidently starts.
It prints one warning about a softlink missing its target:
| /usr/bin/R: line 236: /usr/lib/R/etc/ldpaths: No such file or directory
That is possible -- though it has not happened to me in many dozen installs
over the years.
You can either recreate the softlink by hand (my (verbatim) file is below) or
reinstall __after running 'purge' rather that remove__ ie making sure
you
have nothing left in /etc/R (a convenience location) or /usr/lib/R/
Dirk
edd at max:~$ cat /etc/R/ldpaths
: ${JAVA_HOME=/usr/lib/jvm/java-7-openjdk-amd64/jre}
: ${R_JAVA_LD_LIBRARY_PATH=${JAVA_HOME}/lib/amd64/server}
if test -n ""; then
: ${R_LD_LIBRARY_PATH=${R_HOME}/lib:}
else
: ${R_LD_LIBRARY_PATH=${R_HOME}/lib}
fi
if test -n "${R_JAVA_LD_LIBRARY_PATH}"; then
R_LD_LIBRARY_PATH="${R_LD_LIBRARY_PATH}:${R_JAVA_LD_LIBRARY_PATH}"
fi
## This is DYLD_FALLBACK_LIBRARY_PATH on Darwin (OS X) and LD_LIBRARY_PATH
elsewhere
if test -z "${LD_LIBRARY_PATH}"; then
LD_LIBRARY_PATH="${R_LD_LIBRARY_PATH}"
else
LD_LIBRARY_PATH="${R_LD_LIBRARY_PATH}:${LD_LIBRARY_PATH}"
fi
export LD_LIBRARY_PATH
edd at max:~$
--
Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com