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
Related
I'm trying to install sf package from source to run it with latest version of geos/gdal/proj which were installed by homebrew. I'm using an Apple Silicon M1 computer with MacOS BigSur 11.3. and it seems that my issues are linked to this new Apple silicon chip. If any of you already faced the issue and could share some tips that'd be great.
Here is my command in R :
install_github("r-spatial/sf", configure.args = c("--with-proj-lib=/opt/homebrew/bin/", "--with-gdal-config=/opt/homebrew/bin/gdal-config", "--with-geos-config=/opt/homebrew/bin/geos-config"))
and the response is
Downloading GitHub repo r-spatial/sf#HEAD
✓ checking for file ‘/private/var/folders/50/g22y7v993hq6m6r4m3mm05_r0000gn/T/Rtmp5KWH5H/remotesc7c51a94ebf/r-spatial-sf-c99226b/DESCRIPTION’ (418ms)
─ preparing ‘sf’:
✓ checking DESCRIPTION meta-information ...
─ cleaning src
─ running ‘cleanup’
─ checking for LF line-endings in source and make files and shell scripts (629ms)
─ checking for empty or unneeded directories
─ building ‘sf_0.9-9.tar.gz’
* installing *source* package ‘sf’ ...
** using staged installation
configure: CC: clang -mmacosx-version-min=10.13
configure: CXX: clang++ -mmacosx-version-min=10.13 -std=gnu++11
configure: gdal-config set to /opt/homebrew/bin/gdal-config
checking gdal-config exists... yes
checking gdal-config executable... yes
checking gdal-config usability... yes
configure: GDAL: 3.2.2
checking GDAL version >= 2.0.1... yes
checking for gcc... clang -mmacosx-version-min=10.13
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 clang -mmacosx-version-min=10.13 accepts -g... yes
checking for clang -mmacosx-version-min=10.13 option to accept ISO C89... none needed
checking how to run the C preprocessor... clang -mmacosx-version-min=10.13 -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
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
ld: warning: ignoring file /opt/homebrew/Cellar/gdal/3.2.2_4/lib/libgdal.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
Undefined symbols for architecture x86_64:
"_GDALAllRegister", referenced from:
_main in gdal_test-e29770.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
ld: warning: directory not found for option '-L/opt/homebrew/Cellar/libdap/3.20.7/lib64'
ld: library not found for -lcrypto
clang: error: linker command failed with exit code 1 (use -v to see invocation)
configure: Install failure: compilation and/or linkage problems.
configure: error: GDALAllRegister not found in libgdal.
ERROR: configuration failed for package ‘sf’
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/sf’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/sf’
Warning message:
In i.p(...) :
installation of package ‘/var/folders/50/g22y7v993hq6m6r4m3mm05_r0000gn/T//Rtmp5KWH5H/filec7c4271077b/sf_0.9-9.tar.gz’ had non-zero exit status
When I try to do the same for rgdal I get the same result. And if I do it with rgeos, I get the similar error:
...
checking geos: linking with libgeos_c... no
checking geos: linking with -L/opt/homebrew/Cellar/geos/3.9.1/lib -lgeos_c -lgeos -lm... no
ld: warning: ignoring file /opt/homebrew/Cellar/geos/3.9.1/lib/libgeos_c.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /opt/homebrew/Cellar/geos/3.9.1/lib/libgeos.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
...
I'm a bit new at this so let me know if you need more info.
Thanks,
I've had sf and rproj working on mac forever, and still working since upgrading to Catalina / R 3.6.2.
I tried to install the latest version of sf (0.9.0), both from CRAN and the dev version, and get errors both ways, configure: error: libproj not found in standard or given locations.
I've gone through and removed every last trace of gdal and proj on my computer, uninstalled both, reinstalled, and still same issue. And now, trying to install older versions of sf (0.8.1) that I know worked on my computer also fails. Absolutely stumped here!
GDAL 2.4.4, released 2020/01/08
R v3.6.2
macOS 10.15.3
configure: CC: clang
configure: CXX: clang++ -std=gnu++11
checking for gdal-config... /usr/local/bin/gdal-config
checking gdal-config usability... yes
configure: GDAL: 2.4.4
checking GDAL version >= 2.0.1... yes
checking for gcc... clang
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 clang accepts -g... yes
checking for clang option to accept ISO C89... none needed
checking how to run the C preprocessor... clang -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/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... yes
checking GDAL: /usr/local/Cellar/gdal/2.4.4_2/share/gdal/pcs.csv readable... yes
checking GDAL: checking whether PROJ is available for linking:... yes
checking GDAL: checking whether PROJ is available fur running:... yes
configure: GDAL: 2.4.4
checking proj.h usability... yes
checking proj.h presence... yes
checking for proj.h... yes
checking PROJ: checking whether PROJ and sqlite3 are available for linking:... no
configure: error: libproj not found in standard or given locations.
for rgdal...
* installing *source* package ‘rgdal’ ...
** package ‘rgdal’ successfully unpacked and MD5 sums checked
** using staged installation
configure: R_HOME: /Library/Frameworks/R.framework/Resources
configure: CC: clang
configure: CXX: clang++ -std=gnu++11
configure: C++11 support available
configure: rgdal: 1.4-7
checking for /usr/bin/svnversion... yes
configure: svn revision: 845
checking for gdal-config... /usr/local/bin/gdal-config
checking gdal-config usability... yes
configure: GDAL: 2.4.4
checking C++11 support for GDAL >= 2.3.0... yes
checking GDAL version >= 1.11.4... yes
checking GDAL version <= 2.5 or >= 3.0... yes
checking gdal: linking with --libs only... yes
checking GDAL: gdal-config data directory readable... yes
checking GDAL: /usr/local/Cellar/gdal/2.4.4_2/share/gdal/pcs.csv readable... yes
configure: pkg-config proj not available
set PKG_CONFIG_PATH to the directory containing proj.pc
configure: PROJ version not determined using pkg-config proj
configure: proj CPP flags: -I/usr/local/Cellar/gdal/2.4.4_2/include
configure: PROJ LIBS: -lproj
checking PROJ header API:... proj_api.h
checking proj_api.h presence and usability... no
configure: error: proj_api.h not found in standard or given locations.
ERROR: configuration failed for package ‘rgdal’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rgdal
Finally found a solution after many hours of digging here if anyone else comes across this problem.
A solution that works for me. I have posted it in:
https://biostatsr.blogspot.com/2021/05/install-sf-from-github-source-in-macosx.html
In terminal. You must have MacBrew installed. If not, use:
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
Then
brew install proj
brew install gdal
brew install geos
sudo R
Then in R:
library("devtools")
install_github("r-spatial/sf", configure.args = "--with-proj-include=/usr/local/include --with-proj-lib=/usr/local/lib")
And...
packageVersion("sf")
[1] ‘0.9.9’
I have some trouble installing Rcplex on linux.
I tried:
R CMD INSTALL --configure-args="
--with-cplex-dir='/opt/ibm/ILOG/CPLEX_Studio129/cplex'" Rcplex_0.3-3.tar.gz
then I get this error:
* installing *source* package ‘Rcplex’ ...
** package ‘Rcplex’ successfully unpacked and MD5 sums checked
checking for gawk... gawk
checking for gcc... gcc -std=gnu99
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ANSI C... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for egrep... grep -E
checking for ANSI C header files... no
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking ilcplex/cplex.h usability... yes
checking ilcplex/cplex.h presence... yes
checking for ilcplex/cplex.h... yes
checking for library containing CPXversion... no
configure: error: Could not link CPLEX library using -L/opt/ibm/ILOG/CPLEX_Studio129/cplex/lib/x86-64_linux/static_pic -l$(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 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.
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