I am new with CDO, and wanted to use it to merge several netcdf files on the time variable with
cdo mergetime pr_Amon_IITM-ESM_historical_r1i1p1f1_gn_199001-199912.nc pr_Amon_IITM-ESM_historical_r1i1p1f1_gn_201001-201412.nc output.nc
I just installed CDO on Mac following the instructions given here: https://thiagodossantos.com/post/1-mac-science-software/.
I have Version 1.9.9 and it seems to work fine, however it can't open any .nc file I have tried so far.
This is the error message I got:
cdo mergetime: Open failed on >pr_Amon_IITM-ESM_historical_r1i1p1f1_gn_199001-199912.nc<
No such file or directory
This is the Version I am using:
Climate Data Operators version 1.9.9 (https://mpimet.mpg.de/cdo)
System: x86_64-apple-darwin20.1.0
CXX Compiler: /opt/local/bin/g++-mp-10 -pipe -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX11.0.sdk -arch x86_64 -pthread
CXX version : g++-mp-10 (MacPorts gcc10 10.2.0_4) 10.2.0
C Compiler: /opt/local/bin/gcc-mp-10 -pipe -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX11.0.sdk -arch x86_64 -pthread -pthread
C version : gcc-mp-10 (MacPorts gcc10 10.2.0_4) 10.2.0
F77 Compiler: gfortran -pipe -Os -m64
F77 version : GNU Fortran (MacPorts gcc10 10.2.0_4) 10.2.0
Features: 8GB 4threads C++14 Fortran PTHREADS HDF5 NC4/HDF5 OPeNDAP SZ UDUNITS2 PROJ CURL FFTW3 SSE3
Libraries: HDF5/1.12.0 proj/5.2.0 curl/7.74.0
Filetypes: srv ext ieg grb1 grb2 nc1 nc2 nc4 nc4c nc5
CDI library version : 1.9.9
ecCodes library version : 2.19.1
NetCDF library version : 4.7.4 of Jan 28 2021 10:09:27 $
hdf5 library version : 1.12.0
exse library version : 1.4.1
FILE library version : 1.9.1
I've also tried to reinstall it, but it didn't help. Any help is much appreciated!
P.S: I am also new with stack overflow, so please excuse me if I didn't ask the question correctly.
I was experiencing a similar problem, and I fixed it by closing that .nc by calling nc_close("file")-file after performing my calculations.
Related
I'm trying to use packages that require Rcpp in R on my M1 Mac, which I was never able to get up and running after purchasing this computer. I updated it to Monterey in the hope that this would fix some installation issues but it hasn't. I tried running the Rcpp check from this page but I get the following error:
> Rcpp::sourceCpp("~/github/helloworld.cpp")
ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.2.0/11.0.0'
ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [sourceCpp_4.so] Error 1
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I"/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/RcppArmadillo/include" -I"/Users/afredston/github" -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c helloworld.cpp -o helloworld.o
clang++ -arch arm64 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o sourceCpp_4.so helloworld.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.2.0/11.0.0 -L/opt/R/arm64/gfortran/lib -lgfortran -lemutls_w -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
Error in Rcpp::sourceCpp("~/github/helloworld.cpp") :
Error 1 occurred building shared library.
I get that it can't "find" gfortran. I installed this release of gfortran for Monterey. When I type which gfortran into Terminal, it returns /opt/homebrew/bin/gfortran. (Maybe this version of gfortran requires Xcode tools that are too new—it says something about 13.2 and when I run clang --version it says 13.0—but I don't see another release of gfortran for Monterey?)
I also appended /opt/homebrew/bin: to PATH in R so it looks like this now:
> Sys.getenv("PATH")
[1] "/opt/homebrew/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/Library/TeX/texbin:/Applications/RStudio.app/Contents/MacOS/postback"
Other things I checked:
Xcode command line tools is installed (which clang returns /usr/bin/clang).
Files ~/.R/Makevars and ~/.Renviron don't exist.
Here's my session info:
R version 4.1.1 (2021-08-10)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.1
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.1.1 tools_4.1.1 RcppArmadillo_0.10.7.5.0
[4] Rcpp_1.0.7
Background
Currently (2023-02-20), CRAN builds R 4.2 binaries for Apple silicon using Apple clang from Command Line Tools for Xcode 13.1 and using an experimental fork of GNU Fortran 12.
If you obtain R from CRAN (i.e., here), then you need to replicate CRAN's compiler setup on your system before building R packages that contain C/C++/Fortran code from their sources (and before using Rcpp, etc.). This requirement ensures that your package builds are compatible with R itself.
A further complication is the fact that Apple clang doesn't support OpenMP, so you need to do even more work to compile programs that make use of multithreading. You could circumvent the issue by building R itself and all R packages from sources with LLVM clang, which does support OpenMP, but that approach is onerous and "for experts only".
There is another approach that has been tested by a few people, including Simon Urbanek, the maintainer of R for macOS. It is experimental and also "for experts only", but it works on my machine and is much simpler than learning to build R yourself.
Instructions for obtaining a working toolchain
Warning: These come with no warranty and could break at any time. Some level of familiarity with C/C++/Fortran program compilation, Makefile syntax, and Unix shells is assumed. Everyone is encouraged to consult official documentation, which is more likely to be maintained than answers on SO. As usual, sudo at your own risk.
I will try to address compilers and OpenMP support at the same time. I am going to assume that you are starting from nothing. Feel free to skip steps you've already taken, though you might find a fresh start helpful.
I've tested these instructions on a machine running Big Sur, and at least one person has tested them on a machine running Monterey. I would be glad to hear from others.
Download an R 4.2 binary from CRAN here and install. Be sure to select the binary built for Apple silicon.
Run
$ sudo xcode-select --install
in Terminal to install the latest release version of Apple's Command Line Tools for Xcode, which includes Apple clang. You can obtain earlier versions from your browser here. However, the version that you install should not be older than the one that CRAN used to build your R binary.
Download the gfortran binary recommended here and install by unpacking to root:
$ curl -LO https://mac.r-project.org/tools/gfortran-12.0.1-20220312-is-darwin20-arm64.tar.xz
$ sudo tar xvf gfortran-12.0.1-20220312-is-darwin20-arm64.tar.xz -C /
$ sudo ln -sfn $(xcrun --show-sdk-path) /opt/R/arm64/gfortran/SDK
The last command updates a symlink inside of the gfortran installation so that it points to the SDK inside of your Command Line Tools installation.
Download an OpenMP runtime suitable for your Apple clang version here and install by unpacking to root. You can query your Apple clang version with clang --version. For example, I have version 1300.0.29.3, so I did:
$ curl -LO https://mac.r-project.org/openmp/openmp-12.0.1-darwin20-Release.tar.gz
$ sudo tar xvf openmp-12.0.1-darwin20-Release.tar.gz -C /
After unpacking, you should find these files on your system:
/usr/local/lib/libomp.dylib
/usr/local/include/ompt.h
/usr/local/include/omp.h
/usr/local/include/omp-tools.h
Add the following lines to $(HOME)/.R/Makevars, creating the file if necessary.
CPPFLAGS += -I/usr/local/include -Xclang -fopenmp
LDFLAGS += -L/usr/local/lib -lomp
Run R and test that you can compile a program with OpenMP support. For example:
if (!requireNamespace("RcppArmadillo", quietly = TRUE))
install.packages("RcppArmadillo")
Rcpp::sourceCpp(code = '
#include <RcppArmadillo.h>
#ifdef _OPENMP
# include <omp.h>
#endif
// [[Rcpp::depends(RcppArmadillo)]]
// [[Rcpp::export]]
void omp_test()
{
#ifdef _OPENMP
Rprintf("OpenMP threads available: %d\\n", omp_get_max_threads());
#else
Rprintf("OpenMP not supported\\n");
#endif
}
')
omp_test()
OpenMP threads available: 8
If the C++ code fails to compile, or if it compiles without error but you get linker warnings or you find that OpenMP is not supported, then one of us has probably made a mistake. Please report any issues.
References
Everything is a bit scattered:
R Installation and Administration manual [link]
R for macOS Developers page [link]
I resolved this issue by adding a path to the homebrew installation of gfortran to my ~/.R/Makevars following these instructions: https://pat-s.me/transitioning-from-x86-to-arm64-on-macos-experiences-of-an-r-user/#gfortran
I just avoided the issue until MacOS had things working more smoothly. so I either Windows Developer Virtual Machine (VM) or run my code development in another environment. I'm not too impressed with the updated and "faster" chipset, but that it doesn't work with much. Slow to implement and work-a-rounds often are a must.
Tested the following process for making multithread data.table work in a M2 MacBook Pro (macOS Monterey)
Steps are mostly the same with this answer by the user inferator.
Download and install R from CRAN
Download and install RStudio with developer tools
Run the following commands in terminal to install OpenMP
curl -O https://mac.r-project.org/openmp/openmp-12.0.1-darwin20-Release.tar.gz
sudo tar fvxz openmp-12.0.1-darwin20-Release.tar.gz -C /
Add compiler flags to connect clan w/ OpenMP. In terminal, write the following:
cd ~
mkdir .R
nano .R/Makevars
Inside the opened Makevars file paste the following lines. Once finished, hit command+O and then Enter to save. Do a command+X to close the editor.
CPPFLAGS += -Xclang -fopenmp
LDFLAGS += -lomp
Download and run the installer for gfortran by downloading gfortran-ARM-12.1-Monterey.dmg from the respective GitHub repo
This concludes the steps regarding enabling OpenMP and (hopefully) Rcpp in R under a M2 chip system.
Now, for testing that everything works with data.table I did the following
Open RStudio and run
install.packages("data.table", type = "source")
If everything is done correctly, the package should compile without any errors and return the following when running getDTthreads(verbose = TRUE):
OpenMP version (_OPENMP) 201811
omp_get_num_procs() 8
R_DATATABLE_NUM_PROCS_PERCENT unset (default 50)
R_DATATABLE_NUM_THREADS unset
R_DATATABLE_THROTTLE unset (default 1024)
omp_get_thread_limit() 2147483647
omp_get_max_threads() 8
OMP_THREAD_LIMIT unset
OMP_NUM_THREADS unset
RestoreAfterFork true
data.table is using 4 threads with throttle==1024. See ?setDTthreads.
[1] 4
I'm trying to use packages that require Rcpp in R on my M1 Mac, which I was never able to get up and running after purchasing this computer. I updated it to Monterey in the hope that this would fix some installation issues but it hasn't. I tried running the Rcpp check from this page but I get the following error:
> Rcpp::sourceCpp("~/github/helloworld.cpp")
ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.2.0/11.0.0'
ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [sourceCpp_4.so] Error 1
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I"/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/RcppArmadillo/include" -I"/Users/afredston/github" -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c helloworld.cpp -o helloworld.o
clang++ -arch arm64 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o sourceCpp_4.so helloworld.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.2.0/11.0.0 -L/opt/R/arm64/gfortran/lib -lgfortran -lemutls_w -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
Error in Rcpp::sourceCpp("~/github/helloworld.cpp") :
Error 1 occurred building shared library.
I get that it can't "find" gfortran. I installed this release of gfortran for Monterey. When I type which gfortran into Terminal, it returns /opt/homebrew/bin/gfortran. (Maybe this version of gfortran requires Xcode tools that are too new—it says something about 13.2 and when I run clang --version it says 13.0—but I don't see another release of gfortran for Monterey?)
I also appended /opt/homebrew/bin: to PATH in R so it looks like this now:
> Sys.getenv("PATH")
[1] "/opt/homebrew/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/Library/TeX/texbin:/Applications/RStudio.app/Contents/MacOS/postback"
Other things I checked:
Xcode command line tools is installed (which clang returns /usr/bin/clang).
Files ~/.R/Makevars and ~/.Renviron don't exist.
Here's my session info:
R version 4.1.1 (2021-08-10)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.1
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.1.1 tools_4.1.1 RcppArmadillo_0.10.7.5.0
[4] Rcpp_1.0.7
Background
Currently (2023-02-20), CRAN builds R 4.2 binaries for Apple silicon using Apple Clang from Command Line Tools for Xcode 13.1 and using an experimental fork of GNU Fortran 12.
If you obtain R from CRAN (i.e., here), then you need to replicate CRAN's compiler setup on your system before building R packages that contain C/C++/Fortran code from their sources (and before using Rcpp, etc.). This requirement ensures that your package builds are compatible with R itself.
A further complication is the fact that Apple Clang doesn't support OpenMP, so you need to do even more work to compile programs that make use of multithreading. You could circumvent the issue by building R itself, all R packages, and all external libraries from sources with LLVM Clang, which does support OpenMP, but that approach is onerous and "for experts only".
There is another approach that has been tested by a few people, including Simon Urbanek, the maintainer of R for macOS. It is experimental and also "for experts only", but it works on my machine and is much simpler than learning to build R and other libraries yourself.
Instructions for obtaining a working toolchain
Warning: These come with no warranty and could break at any time. Some level of familiarity with C/C++/Fortran program compilation, Makefile syntax, and Unix shells is assumed. Everyone is encouraged to consult official documentation, which is more likely to be maintained than answers on SO. As usual, sudo at your own risk.
I will try to address compilers and OpenMP support at the same time. I am going to assume that you are starting from nothing. Feel free to skip steps you've already taken, though you might find a fresh start helpful.
I've tested these instructions on a machine running Big Sur, but they should also work on Monterey and Ventura.
Download an R 4.2 binary from CRAN here and install. Be sure to select the binary built for Apple silicon.
Run
$ sudo xcode-select --install
in Terminal to install the latest release version of Apple's Command Line Tools for Xcode, which includes Apple Clang. You can obtain earlier versions from your browser here. However, the version that you install should not be older than the one that CRAN used to build your R binary.
Download the GNU Fortran binary provided here and install by unpacking to root:
$ curl -LO https://mac.r-project.org/tools/gfortran-12.0.1-20220312-is-darwin20-arm64.tar.xz
$ sudo tar xvf gfortran-12.0.1-20220312-is-darwin20-arm64.tar.xz -C /
$ sudo ln -sfn $(xcrun --show-sdk-path) /opt/R/arm64/gfortran/SDK
The last command updates a symlink inside of the installation so that it points to the SDK inside of your Command Line Tools installation.
Download an OpenMP runtime suitable for your Apple Clang version here and install by unpacking to root. You can query your Apple Clang version with clang --version. For example, I have version 1300.0.29.3, so I did:
$ curl -LO https://mac.r-project.org/openmp/openmp-12.0.1-darwin20-Release.tar.gz
$ sudo tar xvf openmp-12.0.1-darwin20-Release.tar.gz -C /
After unpacking, you should find these files on your system:
/usr/local/lib/libomp.dylib
/usr/local/include/ompt.h
/usr/local/include/omp.h
/usr/local/include/omp-tools.h
Add the following lines to $(HOME)/.R/Makevars, creating the file if necessary.
CPPFLAGS += -I/usr/local/include -Xclang -fopenmp
LDFLAGS += -L/usr/local/lib -lomp
Test that you are able to use R to compile a C or C++ program with OpenMP support while linking relevant libraries from the GNU Fortran installation (indicated by the -l flags in the output of R CMD CONFIG FLIBS).
The most transparent approach is to use R CMD SHLIB directly. In a temporary directory, create an empty source file omp_test.c and add the following lines:
#ifdef _OPENMP
# include <omp.h>
#endif
#include <Rinternals.h>
SEXP omp_test(void)
{
#ifdef _OPENMP
Rprintf("OpenMP threads available: %d\n", omp_get_max_threads());
#else
Rprintf("OpenMP not supported\n");
#endif
return R_NilValue;
}
Compile it:
$ R CMD SHLIB omp_test.c $(R CMD CONFIG FLIBS)
Then call the compiled C function from R:
$ R -e 'dyn.load("omp_test.so"); invisible(.Call("omp_test"))'
OpenMP threads available: 8
If the compiler or linker throws an error, or if you find that OpenMP is still not supported, then one of us has made a mistake. Please report any issues.
Note that you can implement the same test using Rcpp, if you don't mind installing it:
library(Rcpp)
registerPlugin("flibs", Rcpp.plugin.maker(libs = "$(FLIBS)"))
sourceCpp(code = '
#ifdef _OPENMP
# include <omp.h>
#endif
#include <Rcpp.h>
// [[Rcpp::plugins(flibs)]]
// [[Rcpp::export]]
void omp_test()
{
#ifdef _OPENMP
Rprintf("OpenMP threads available: %d\\n", omp_get_max_threads());
#else
Rprintf("OpenMP not supported\\n");
#endif
return;
}
')
omp_test()
OpenMP threads available: 8
References
Everything is a bit scattered:
R Installation and Administration manual [link]
Writing R Extensions manual [link]
R for macOS Developers web page [link]
I resolved this issue by adding a path to the homebrew installation of gfortran to my ~/.R/Makevars following these instructions: https://pat-s.me/transitioning-from-x86-to-arm64-on-macos-experiences-of-an-r-user/#gfortran
I just avoided the issue until MacOS had things working more smoothly. so I either Windows Developer Virtual Machine (VM) or run my code development in another environment. I'm not too impressed with the updated and "faster" chipset, but that it doesn't work with much. Slow to implement and work-a-rounds often are a must.
Tested the following process for making multithread data.table work in a M2 MacBook Pro (macOS Monterey)
Steps are mostly the same with this answer by the user inferator.
Download and install R from CRAN
Download and install RStudio with developer tools
Run the following commands in terminal to install OpenMP
curl -O https://mac.r-project.org/openmp/openmp-12.0.1-darwin20-Release.tar.gz
sudo tar fvxz openmp-12.0.1-darwin20-Release.tar.gz -C /
Add compiler flags to connect clan w/ OpenMP. In terminal, write the following:
cd ~
mkdir .R
nano .R/Makevars
Inside the opened Makevars file paste the following lines. Once finished, hit command+O and then Enter to save. Do a command+X to close the editor.
CPPFLAGS += -Xclang -fopenmp
LDFLAGS += -lomp
Download and run the installer for gfortran by downloading gfortran-ARM-12.1-Monterey.dmg from the respective GitHub repo
This concludes the steps regarding enabling OpenMP and (hopefully) Rcpp in R under a M2 chip system.
Now, for testing that everything works with data.table I did the following
Open RStudio and run
install.packages("data.table", type = "source")
If everything is done correctly, the package should compile without any errors and return the following when running getDTthreads(verbose = TRUE):
OpenMP version (_OPENMP) 201811
omp_get_num_procs() 8
R_DATATABLE_NUM_PROCS_PERCENT unset (default 50)
R_DATATABLE_NUM_THREADS unset
R_DATATABLE_THROTTLE unset (default 1024)
omp_get_thread_limit() 2147483647
omp_get_max_threads() 8
OMP_THREAD_LIMIT unset
OMP_NUM_THREADS unset
RestoreAfterFork true
data.table is using 4 threads with throttle==1024. See ?setDTthreads.
[1] 4
I am getting the below error on an AWS EC2 instance (I specifically say that as I don't have an issue with this on my Mac):
Error: Command failed: gm convert: No decode delegate for this image format (/tmp/5c5830319d29e4678e8691cd-1549705844271.jpg)
The file does exist just in case that looks to be the suspect.
My config for gm is as follows:
[mw-user#mwServer ~]$ gm version
GraphicsMagick 1.3.31 2018-11-17 Q8 http://www.GraphicsMagick.org/
Copyright (C) 2002-2018 GraphicsMagick Group.
Additional copyrights and licenses apply to this software.
See http://www.GraphicsMagick.org/www/Copyright.html for details.
Feature Support:
Native Thread Safe yes
Large Files (> 32 bit) yes
Large Memory (> 32 bit) yes
BZIP no
DPS no
FlashPix no
FreeType no
Ghostscript (Library) no
JBIG no
JPEG-2000 no
JPEG no
Little CMS no
Loadable Modules no
OpenMP yes (201511)
PNG no
TIFF no
TRIO no
UMEM no
WebP no
WMF no
X11 no
XML no
ZLIB yes
Host type: x86_64-pc-linux-gnu
Configured using the command:
./configure
Final Build Parameters:
CC = gcc
CFLAGS = -fopenmp -g -O2 -Wall -pthread
CPPFLAGS =
CXX = g++
CXXFLAGS = -pthread
LDFLAGS =
LIBS = -lz -lm -lpthread
I am using the Node module:
var gm = require('gm');
gm("/tmp/5c5830319d29e4678e8691cd-1549705844271.jpg")
.resize(450, null)
.write("/tmp/5c5830319d29e4678e8691cd-1549705844271-Resized.jpg", (function(err){
if (err) {
console.log(err);
}
}));
I don't know enough about gm to go anywhere from here. The problem seems like I don't have a "converter" for JPEG. Question is - how does one set this up so it supports most image formats like: jpg, png etc?
Thanks in advance!
You don't say what OS your instance is running, but basically you don't seem to have JPEG support in GraphicsMagick.
So you need to work out what package manager your instance uses and then use that to install libjpeg and libjpeg-dev packages and then probably re-install GraphicsMagick.
Your comment seems to imply your question is broader than the JPEG-support you mention, but the answer is the same. You need to install
libTIFF, libTIFF-dev
libPNG, libPNG-dev
...
and then re-install GraphicsMagick.
I have now been searching the web and tried different methods to get a R library (ctsmr) installed from the source, but without luck. I know it works on Linux and Windows, but have not succeeded on my Mac (OSX v10.12.6) with R v3.3.3.
When I try to install it like this:
install.packages("ctsmr", repo="http://ctsm.info/repo/dev", type="source")
I get the some warnings during the installation process, but the installation finishes.
* installing *source* package ‘ctsmr’ ...
** libs
gfortran-4.8 -fopenmp -fPIC -Wall -g -O2 -c fdf.f90 -o fdf.o
gfortran-4.8: warning: couldn’t understand kern.osversion ‘16.7.0
fdf.f90:19.30:
INTEGER I,ISTOP
1
Warning: Unused variable 'istop' declared at (1)
gfortran-4.8 -fPIC -g -O2 -c matutil.f -o matutil.o
gfortran-4.8: warning: couldn’t understand kern.osversion ‘16.7.0
gfortran-4.8 -fPIC -g -O2 -c opkda1.f -o opkda1.o
...
When I run an example in RStudio (the one that is called "Building 1" on the packages webpage, http://ctsm.info) I get an error message for one of the function from the package. (This error message actually does not show up at the moment, as RStudio just crash when I run the line):
fit <- model$estimate(data=X)
Error in dyn.load(x = m$libfile) :
unable to load shared object '/var/folders/7g/81dqdb9s4qq2r79ncggcv2l40000gn/T//RtmpNoNnQl/model5a613c359b3f.so':
dlopen(/var/folders/7g/81dqdb9s4qq2r79ncggcv2l40000gn/T//RtmpNoNnQl/model5a613c359b3f.so, 6): Symbol not found: _GOMP_parallel_end
Referenced from: /var/folders/7g/81dqdb9s4qq2r79ncggcv2l40000gn/T//RtmpNoNnQl/model5a613c359b3f.so
Expected in: dynamic lookup
It looks a little different if I run the same script in the R application:
fit <- model$estimate(data=X)
*** caught illegal operation ***
address 0x7fffa39b0e97, cause 'illegal opcode'
Trackback:
1: dyn.load(x = m$libfile)
2: CallFunction("ctsmdriver", .self, rho, verbose = verbose)
3: model$estimate(data = X)
So, I am wondering if the package is not installed correctly or if their is a bug in the package (maybe because of the double slashes in the path in the error message).
If I manually go look for the shared object, model5a613c359b3f.so, it actually exist on my computer.
Regarding the gfortran compiler I get the following form the therminal:
~ $ gfortran --version
GNU Fortran (GCC) 6.3.0
Copyright (C) 2016 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
~ $ gcc --version
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 8.1.0 (clang-802.0.42)
Target: x86_64-apple-darwin16.7.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
I would appreciate if someone could tell me if it is a installation error or a bug in the package. And secondly, come up with possible solutions.
I can load the rJava and xlsxjars packages, but I get a "Failed to load JVM" when I execute library(xlsx). Below are my details.
OS Version:
$ sw_vers
ProductName: Mac OS X
ProductVersion: 10.11
BuildVersion: 15A284
Java Version:
$ java -version
java version "1.8.0_65"
Java(TM) SE Runtime Environment (build 1.8.0_65-b17)
Java HotSpot(TM) 64-Bit Server VM (build 25.65-b01, mixed mode)
Java Path:
$ which java
/usr/bin/java
Java Home:
$ /usr/libexec/java_home
/Library/Java/JavaVirtualMachines/jdk1.8.0_65.jdk/Contents/Home
R Version:
$ R --version
R version 3.2.3 (2015-12-10) -- "Wooden Christmas-Tree"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (64-bit)
How I launch R:
$ LD_LIBRARY_PATH=$(/usr/libexec/java_home)/jre/lib/server: open -a RStudio
Loading the rJava and xlsxjars packages successfully:
> library(rJava)
> library(xlsxjars)
Unsuccessfully trying to load the xlsx package:
> library(xlsx)
JavaVM: requested Java version ((null)) not available. Using Java at "" instead.
JavaVM: Failed to load JVM: /bundle/Libraries/libserver.dylib
JavaVM FATAL: Failed to load the jvm library.
Error : .onLoad failed in loadNamespace() for 'xlsx', details:
call: .jinit()
error: JNI_GetCreatedJavaVMs returned -1
Error: package or namespace load failed for ‘xlsx’
R Configuration:
Matts-MacBook-Pro:~ matt$ R CMD javareconf
Java interpreter : /usr/bin/java
Java version : 1.8.0_65
Java home path : /Library/Java/JavaVirtualMachines/jdk1.8.0_65.jdk/Contents/Home/jre
Java compiler : /usr/bin/javac
Java headers gen.: /usr/bin/javah
Java archive tool: /usr/bin/jar
Non-system Java on OS X
trying to compile and link a JNI program
detected JNI cpp flags : -I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/darwin
detected JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/Library/Java/JavaVirtualMachines/jdk1.8.0_65.jdk/Contents/Home/jre/../include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_65.jdk/Contents/Home/jre/../include/darwin -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c conftest.c -o conftest.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o conftest.so conftest.o -L/Library/Java/JavaVirtualMachines/jdk1.8.0_65.jdk/Contents/Home/jre/lib/server -ljvm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
JAVA_HOME : /Library/Java/JavaVirtualMachines/jdk1.8.0_65.jdk/Contents/Home/jre
Java library path: $(JAVA_HOME)/lib/server
JNI cpp flags : -I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/darwin
JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm
Updating Java configuration in /Library/Frameworks/R.framework/Resources
Unfortunately, these symlink tricks didn't help me. However, I found a similar issue on stackoverflow! (where else ;))
This one worked for me by doing the following:
In terminal enter the following to relink Java correctly:
sudo R CMD javareconf
Back in R (or RStudio) install the rJava package from source:
install.packages("rJava",type='source')
Hope, this helps!
I ´ve got also problems with loading packages like openNLP, xlsx, RWeka, ... and got the same error message like you.
But finally this command worked for me on OS X 10.11.3:
sudo ln -s $(/usr/libexec/java_home)/jre/lib/server/libjvm.dylib /usr/local/lib
There might be a problem in the version of Java for which the R xlsx package was built in. Some old software require to install the Java 6 for OS X 10.11 El Capitan, OS X 10.10 Yosemite, OS X 10.9 Mavericks, OS X 10.8 Mountain Lion, and OS X 10.7 Lion.
So you can try to install this old version of Java (Java for OS X 2015-001) at Apple website, link below:
https://support.apple.com/kb/DL1572?locale=pt_BR&viewlocale=en_US
And check if you have a Java SE Development Kit 8. You can download it at Oracle website, link below:
www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html
I was having the same problem and downloading the old version of Java solved it.. I hope this help you!
Basically, just do what is described here:
https://oliverdowling.com.au/2015/10/09/oracles-jre-8-on-mac-os-x-el-capitan/
short version:
d/l Java JRE from oracle as tar file
http://www.oracle.com/technetwork/java/javase/downloads/jre8-downloads-2133155.html
then put this into you terminal (for sudo, your pw is needed):
cd ~/Downloads
tar -xzf `ls -1r jre-*-macosx-x64.tar.gz | head -1`
cd `ls -1rd jre*/ | head -1`
defaults write `pwd`/Contents/Info.plist JavaVM -dict-add 'JVMCapabilities' '<array><string>JNI</string><string>BundledApp</string><string>CommandLine</string></array>'
plutil -convert xml1 Contents/Info.plist
sudo mv `pwd` /Library/Java/JavaVirtualMachines/
mkdir -p Contents/Home/bundle/Libraries
cd Contents/Home/bundle/Libraries
ln -s ../../lib/server/libjvm.dylib libserver.dylib
works fine on my OS X 10.11
For me, MacOS Catalina 10.15.7, it was as simple as installing the current JRE and JDK software (downloaded as .dmg files from the official distributer websites on java.com and oracle.com - No affiliations whatsoever!).
I have also (re-) installed the rJava package, but I don't feel this was necessary. I actually simply did not have Java installed on my computer.
Now the xlsx package loads.