I need your help solving this particular problem.
I am trying to install the Rgdal package, but I can't seem to be able to get past the installation. The output seems fairly normal at first (as far as I can tell).
* installing *source* package 'rgdal' ...
** package 'rgdal' successfully unpacked and MD5 sums checked
configure: CC: gcc -std=gnu99
configure: CXX: g++
configure: rgdal: 1.1-10
checking for /usr/bin/svnversion... no
configure: svn revision: 622
checking for gdal-config... /afs/ics.muni.cz/software/R-3.0.3/bin/gdal- config
checking gdal-config usability... yes
configure: GDAL: 1.10.1
checking GDAL version >= 1.6.3... yes
checking for gcc... gcc -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking gdal.h usability... yes
checking gdal.h presence... yes
checking for gdal.h... yes
checking gdal: linking with --libs only... no
checking gdal: linking with --libs and --dep-libs... no
And then it gives me a warning message:
/usr/bin/ld: warning: libhdf5.so.6, needed by /software/R-3.0.3 lib/libgdal.so, not found (try using -rpath or -rpath-link)
Then it continues with a long list of undefined references:
/software/R-3.0.3/lib/libgdal.so: undefined reference to `H5Dread'
/software/R-3.0.3/lib/libgdal.so: undefined reference to `H5Dget_create_plist'
/software/R-3.0.3/lib/libgdal.so: undefined reference to `H5Pclose'
/software/R-3.0.3/lib/libgdal.so: undefined reference to `H5Sget_simple_extent_ndims'
I would be eternally grateful for any help or suggestions as I don't really understand what went wrong. Looking this problem up did not yield any useful results.
Related
I have some trouble installing Rcplex on linux.
I tried:
R CMD INSTALL --configure-args="
--with-cplex-dir='/opt/ibm/ILOG/CPLEX_Studio129/cplex'" Rcplex_0.3-3.tar.gz
then I get this error:
* installing *source* package ‘Rcplex’ ...
** package ‘Rcplex’ successfully unpacked and MD5 sums checked
checking for gawk... gawk
checking for gcc... gcc -std=gnu99
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 -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ANSI C... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for egrep... grep -E
checking for ANSI C header files... no
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking ilcplex/cplex.h usability... yes
checking ilcplex/cplex.h presence... yes
checking for ilcplex/cplex.h... yes
checking for library containing CPXversion... no
configure: error: Could not link CPLEX library using -L/opt/ibm/ILOG/CPLEX_Studio129/cplex/lib/x86-64_linux/static_pic -l$(CPLEXLIB) -lm -lpthread -ldl
ERROR: configuration failed for package ‘Rcplex’
I also tried this:
R CMD INSTALL --configure-args="--with-cplex-include=/opt/ibm/ILOG/CPLEX_Studio129/cplex/include \
--with-cplex-cflags=-fPIC \
--with-cplex-lib=/opt/ibm/ILOG/CPLEX_Studio129/cplex/lib/x86-64_linux/static_pic' \
-lcplex -lm -lpthread'" Rcplex_0.3-3.tar.gz
and get this error:
* installing *source* package ‘Rcplex’ ...
** package ‘Rcplex’ successfully unpacked and MD5 sums checked
checking for gcc... gcc -std=gnu99
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 -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ANSI C... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for egrep... grep -E
checking for ANSI C header files... no
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking ilcplex/cplex.h usability... yes
checking ilcplex/cplex.h presence... yes
checking for ilcplex/cplex.h... yes
checking for library containing CPXversion... no
configure: error: Could not link CPLEX library using /opt/ibm/ILOG/CPLEX_Studio129/cplex/lib/x86-64_linux/static_pic -lcplex -lm -lpthread
ERROR: configuration failed for package ‘Rcplex’
I think your best course of action is to look into what exactly the configure script tries to run. Maybe it expects another version of CPLEX?
I experienced the same problem installing the Rcplex 0.3-3 package for R3.6.1 on Ubuntu 18.04 with CPLEX 12.9.
Turns out that the Rcplex package was developed and tested with CPLEX 12.6.3. When I installed this older version of CPLEX on Ubuntu, I was able to install Rcplex 0.3-3 by following the instructions in the INSTALL file.
On my system, this command did the trick:
sudo R CMD INSTALL --configure-args="PKG_CFLAGS=-fPIC PKG_CPPFLAGS=-I/opt/ibm/ILOG/CPLEX_Studio1263/cplex/include PKG_LIBS='-L/opt/ibm/ILOG/CPLEX_Studio1263/cplex/lib/x86-64_linux/static_pic -lcplex -lm -lpthread'" Rcplex_0.3-3.tar.gz
This appears to be an issue with the Linux version of Rcplex only. I was able to install Rcplex with the latest version of CPLEX on my Mac.
I have udunits2 R package installed but units R package still fails even if I use configure.arg containing correct headers and libs:
$ ls /path/apps/udunits/2.2.26/x86_64-linux-2.6-rhel6/include/
converter.h udunits2.h udunits.h
$ ls /path/apps/udunits/2.2.26/x86_64-linux-2.6-rhel6/lib/
libudunits2.a libudunits2.so libudunits2.so.0.1.0
libudunits2.la libudunits2.so.0
Log from package installation:
> library(udunits2)
udunits system database read
configure.args = c(
'--with-udunits2-lib=/path/apps/udunits/2.2.26/x86_64-linux-2.6-rhel6/lib/',
'--with-udunits2-include=/path/apps/udunits/2.2.26/x86_64-linux-2.6-rhel6/include/'
)
> install_packages("units", reps, configure.args = configure.args)
* installing *source* package ‘units’ ...
** package ‘units’ successfully unpacked and MD5 sums checked
configure: units: 0.6-0
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking how to run the C++ preprocessor... g++ -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdbool.h that conforms to C99... no
checking for _Bool... no
checking for error_at_line... yes
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for XML_ParserCreate in -lexpat... yes
checking udunits2.h usability... no
checking udunits2.h presence... no
checking for udunits2.h... no
checking udunits2/udunits2.h usability... no
checking udunits2/udunits2.h presence... no
checking for udunits2/udunits2.h... no
checking for ut_read_xml in -ludunits2... yes
configure: error: in `/tmp/RtmpPvLQ81/R.INSTALL1c932925e979/units':
configure: error:
--------------------------------------------------------------------------------
udunits2.h not found!
If the udunits2 library is installed in a non-standard location, use:
--configure-args='--with-udunits2-lib=/usr/local/lib'
for example, if the library was not found, and/or
--configure-args='--with-udunits2-include=/usr/include/udunits2'
if the header was not found, replacing paths with appropriate values for your
installation. You can alternatively use the UDUNITS2_INCLUDE and UDUNITS2_LIBS
environment variables.
If udunits2 is not installed, please install it.
It is required for this package.
------------------------------------------
File udunits2.h exists in path:
$ls /path/apps/udunits/2.2.26/x86_64-linux-2.6-rhel6/include/:
converter.h udunits2.h udunits.h
Setting environment variable doesn't help too:
export UDUNITS2_INCLUDE="/path/apps/udunits/2.2.26/x86_64-linux-2.6-rhel6/include"
export UDUNITS2_LIB="/apps/udunits/2.2.26/x86_64-linux-2.6-rhel6/lib"
Any ideas why units fails to install?
I have R (ver. 3.1.2) installed and I tried to install rgdal package. First I downloaded the package source (tar.gz) from here. Finally I installed the sp package on which rgdal depends. Then I run R and typed install.packages("/home/umberto/Scaricati/rgdal_1.1-3.tar.gz").
It seems it cannot find lgdal, below is the error I received:
Installing package into ‘/home/umberto/R/x86_64-pc-linux-gnu-library/3.1’
(as ‘lib’ is unspecified)
inferring 'repos = NULL' from 'pkgs'
* installing *source* package ‘rgdal’ ...
** package ‘rgdal’ successfully unpacked and MD5 sums checked
configure: CC: gcc -std=gnu99
configure: CXX: g++
configure: rgdal: 1.1-3
checking for /usr/bin/svnversion... yes
configure: svn revision: 594
checking for gdal-config... /usr/local/bin/gdal-config
checking gdal-config usability... yes
configure: GDAL: 1.11.0
checking GDAL version >= 1.6.3... yes
checking for gcc... gcc -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking gdal.h usability... yes
checking gdal.h presence... yes
checking for gdal.h... yes
checking gdal: linking with --libs only... no
checking gdal: linking with --libs and --dep-libs... no
/usr/bin/ld: cannot find -lgdal
collect2: error: ld returned 1 exit status
/usr/bin/ld: cannot find -lgdal
collect2: error: ld returned 1 exit status
configure: Install failure: compilation and/or linkage problems.
configure: error: GDALAllRegister not found in libgdal.
ERROR: configuration failed for package ‘rgdal’
* removing ‘/home/umberto/R/x86_64-pc-linux-gnu-library/3.1/rgdal’
Warning message:
In install.packages("/home/umberto/Scaricati/rgdal_1.1-3.tar.gz") :
installation of package ‘/home/umberto/Scaricati/rgdal_1.1-3.tar.gz’ had non-zero exit status
I have environment below,
CentOS release 6.4, R version 3.2.2.
I wanted to install the "rgl" package for R.
At the beginning, I used install.packages("rgl"), it throws error below:
Installing package into ‘/usr/lib64/R/library’
(as ‘lib’ is unspecified)
trying URL 'http://mirror.bjtu.edu.cn/cran/src/contrib/rgl_0.95.1367.tar.gz'
Content type 'application/octet-stream' length 2033202 bytes (1.9 MB)
==================================================
downloaded 1.9 MB
* installing *source* package ‘rgl’ ...
** package ‘rgl’ successfully unpacked and MD5 sums checked
checking for gcc... gcc -m64 -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -m64 -std=gnu99 accepts -g... yes
checking for gcc -m64 -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -m64 -std=gnu99 -E
checking for gcc... (cached) gcc -m64 -std=gnu99
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc -m64 -std=gnu99 accepts -g... (cached) yes
checking for gcc -m64 -std=gnu99 option to accept ISO C89... (cached) none needed
checking whether __attribute__((visibility())) is supported... yes
checking whether gcc -m64 -std=gnu99 accepts -fvisibility... yes
checking whether accepts -fvisibility... no
checking for libpng-config... no
checking libpng... checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking png.h usability... no
checking png.h presence... no
checking for png.h... no
checking for png_read_update_info in -lpng... no
configure: libpng header and lib found
configure: using libpng dynamic linkage
checking for X... no
configure: error: X11 not found but required, configure aborted.
ERROR: configuration failed for package ‘rgl’
* removing ‘/usr/lib64/R/library/rgl’
The downloaded source packages are in
‘/tmp/Rtmp6mou8m/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("rgl") :
installation of package ‘rgl’ had non-zero exit status
Then I tried to install the "rgl" package using R CMD．I downloaded the "rgl_0.95.1367.tar.gz" from http://cran.at.r-project.org/web/packages/rgl/index.html. I installed it by R CMD INSTALL command:
[root#srv005 RFile]# R CMD INSTALL -l rgl_0.95.1367.tar.gz
Error: ERROR: no packages specified
[root#srv005 RFile]# R CMD INSTALL rgl_0.95.1367.tar.gz
* installing to library ?.usr/lib64/R/library?
* installing *source* package ?.gl?....
** package ?.gl?.successfully unpacked and MD5 sums checked
checking for gcc... gcc -m64 -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -m64 -std=gnu99 accepts -g... yes
checking for gcc -m64 -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -m64 -std=gnu99 -E
checking for gcc... (cached) gcc -m64 -std=gnu99
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc -m64 -std=gnu99 accepts -g... (cached) yes
checking for gcc -m64 -std=gnu99 option to accept ISO C89... (cached) none needed
checking whether __attribute__((visibility())) is supported... yes
checking whether gcc -m64 -std=gnu99 accepts -fvisibility... yes
checking whether accepts -fvisibility... no
checking for libpng-config... no
checking libpng... checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking png.h usability... no
checking png.h presence... no
checking for png.h... no
checking for png_read_update_info in -lpng... no
configure: libpng header and lib found
configure: using libpng dynamic linkage
checking for X... no
configure: error: X11 not found but required, configure aborted.
ERROR: configuration failed for package ?.gl?
* removing ?.usr/lib64/R/library/rgl?
It doesn't work neither.
Is there anyone knows how to install this "rgl" package in CentOS? Or the package can't be installed in the CentOS at all? Thanks.
On RHEL you have to install libX11-devel, AFAIR
sudo yum install libX11-devel
I guess it is the same on CentOS.
I also had to install openGL and GLU libraries.
sudo yum install mesa-libGL mesa-libGL-devel mesa-libGLU mesa-libGLU-devel
sudo yum groupinstall X11
Please could you help me, i try to install this packages in R and my OS is linux ubuntu 15.04
devtools
rjava
but i get some error, for example, when i install devtools
Warning in install.packages :
installation of package ‘git2r’ had non-zero exit status
Warning in install.packages :
installation of package ‘devtools’ had non-zero exit status
and when i install rjava
checking for gcc... gcc -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/wait.h that is POSIX.1 compatible... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for string.h... (cached) yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for unistd.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking whether time.h and sys/time.h may both be included... yes
configure: checking whether gcc -std=gnu99 supports static inline...
yes
checking whether setjmp.h is POSIX.1 compatible... yes
checking whether sigsetjmp is declared... yes
checking whether siglongjmp is declared... yes
checking Java support in R... present:
interpreter : '/usr/bin/java'
archiver : '/usr/bin/jar'
compiler : '/usr/bin/javac'
header prep.: '/usr/bin/javah'
cpp flags : '-I/usr/lib/jvm/java-7-openjdk-i386/jre/../include'
java libs : '-L/usr/lib/jvm/java-7-openjdk-i386/jre/lib/i386/client -ljvm'
checking whether Java run-time works...
Picked up JAVA_TOOL_OPTIONS: -javaagent:/usr/share/java/jayatanaag.jar
yes
checking whether -Xrs is supported...
Picked up JAVA_TOOL_OPTIONS: -javaagent:/usr/share/java/jayatanaag.jar
yes
checking whether JNI programs can be compiled...
configure: error: Cannot compile a simple JNI program. See config.log for details.
Make sure you have Java Development Kit installed and correctly registered in R.
If in doubt, re-run "R CMD javareconf" as root.
ERROR: configuration failed for package ‘rJava’
* removing ‘/home/dave/R/i686-pc-linux-gnu-library/3.1/rJava’
Warning in install.packages :
installation of package ‘rJava’ had non-zero exit status
The downloaded source packages are in
‘/tmp/Rtmp86RnJ1/downloaded_packages’
of course before ask this question i found similar questions on this site, but given advices didn't help me
i used this
sudo apt-get build-dep libxml2-dev
sudo apt-get install r-cran-rjava
what i should do to install needed packages. This problem concern and other packages like jgr,deducer,rweka