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I am attempting to install MatchIt - an R package - in an Anaconda environment. I keep getting error messages that I just don't understand.
I made sure that I had Rcpp installed in the same Conda environment and that I have Xcode installed on my machine. Still no luck. I was wondering if anyone had a solution.
devtools::install_github('kosukeimai/MatchIt')
Downloading GitHub repo kosukeimai/MatchIt#HEAD
✔ checking for file ‘/private/var/folders/cz/1d4gc7b13dsfknrnbr0tjz580000gn/T/RtmpYISSL1/remotes50d505ff397/kosukeimai-MatchIt-b3032e6/DESCRIPTION’ ...
─ preparing ‘MatchIt’:
✔ checking DESCRIPTION meta-information ...
─ cleaning src
─ installing the package to process help pages
-----------------------------------
─ installing *source* package ‘MatchIt’ ...
** using staged installation
** libs
x86_64-apple-darwin13.4.0-clang++ -std=gnu++11 -I"/opt/anaconda3/envs/pirate/lib/R/include" -DNDEBUG -I'/opt/anaconda3/envs/pirate/lib/R/library/Rcpp/include' -I'/opt/anaconda3/envs/pirate/lib/R/library/RcppProgress/include' -D_FORTIFY_SOURCE=2 -isystem /opt/anaconda3/envs/pirate/include -mmacosx-version-min=10.9 -I/opt/anaconda3/envs/pirate/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -fmessage-length=0 -isystem /opt/anaconda3/envs/pirate/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1630154249442/work=/usr/local/src/conda/r-base-4.1.1 -fdebug-prefix-map=/opt/anaconda3/envs/pirate=/usr/local/src/conda-prefix -Wall -pedantic -c RcppExports.cpp -o RcppExports.o
/bin/sh: x86_64-apple-darwin13.4.0-clang++: command not found
make: *** [RcppExports.o] Error 127
ERROR: compilation failed for package ‘MatchIt’
─ removing ‘/private/var/folders/cz/1d4gc7b13dsfknrnbr0tjz580000gn/T/RtmpeKesPi/Rinst1a5f6063566d/MatchIt’
-----------------------------------
ERROR: package installation failed
Error: Failed to install 'MatchIt' from GitHub:
System command 'R' failed, exit status: 1, stdout + stderr (last 10 lines):
E> * installing *source* package ‘MatchIt’ ...
E> ** using staged installation
E> ** libs
E> x86_64-apple-darwin13.4.0-clang++ -std=gnu++11 -I"/opt/anaconda3/envs/pirate/lib/R/include" -DNDEBUG -I'/opt/anaconda3/envs/pirate/lib/R/library/Rcpp/include' -I'/opt/anaconda3/envs/pirate/lib/R/library/RcppProgress/include' -D_FORTIFY_SOURCE=2 -isystem /opt/anaconda3/envs/pirate/include -mmacosx-version-min=10.9 -I/opt/anaconda3/envs/pirate/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -fmessage-length=0 -isystem /opt/anaconda3/envs/pirate/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1630154249442/work=/usr/local/src/conda/r-base-4.1.1 -fdebug-prefix-map=/opt/anaconda3/envs/pirate=/usr/local/src/conda-prefix -Wall -pedant
I have also looked around on the Conda-forge channel to see if I could just conda install -c conda-forge r-MatchIt but no luck either.
I ended up getting the package to install and compile but I am not exactly sure how.
I deleted then reinstalled Xcode.
I then accessed R in my conda environment via terminal and tried reinstalling the package that way with pgkbuild().
$ conda activate pirate
$ R
> pkgbuild::check_build_tools(devtools::install_github('kosukeimai/MatchIt'), debug = TRUE)
I obviously don't really understand how any of the Clang compiling works, but if this can be useful for someone as clueless as I am, I guess the ole classic of deleting and reinstalling Xcode will do it.
Related
I just updated my R packages packages in RStudio. For the RcppArmadillo package (version 0.11.4.3.1), RStudio warned me that no binary package is available for my system (x86_64, Windows 11) and asked if I wanted to install the source package instead. Since I have RTools installed for just this purpose, I said yes.
The installation succeeded, but a warning was issued that the package "has a configure script" and "probably needs manual configuration".
* installing *source* package 'RcppArmadillo' ...
** package 'RcppArmadillo' successfully unpacked and MD5 sums checked
** using staged installation
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-42~1.2/include" -DNDEBUG -I'C:/.../R/win-library/4.2/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -I../inst/include -I. -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppArmadillo.cpp -o RcppArmadillo.o
g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-42~1.2/include" -DNDEBUG -I'C:/.../R/win-library/4.2/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -I../inst/include -I. -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-42~1.2/include" -DNDEBUG -I'C:/.../R/win-library/4.2/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -I../inst/include -I. -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fastLm.cpp -o fastLm.o
g++ -shared -s -static-libgcc -o RcppArmadillo.dll tmp.def RcppArmadillo.o RcppExports.o fastLm.o -fopenmp -LC:/PROGRA~1/R/R-42~1.2/bin/x64 -lRlapack -LC:/PROGRA~1/R/R-42~1.2/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LC:/PROGRA~1/R/R-42~1.2/bin/x64 -lR
installing to C:/.../R/win-library/4.2/00LOCK-RcppArmadillo/00new/RcppArmadillo/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RcppArmadillo)
My questions are:
Should I be concerned?
How can I tell that the package is working correctly?
If manual configuration is needed, how do I do it?
An aside for the second of those: I'm not using this package directly, and presume that it was installed as a dependency of another package that I used in the past. Since I do not remember which package that may have been (or when I last used it), I can't just dig into my older code, find a script that uses this package, and see if it still works.
Is there such a thing in the R world as automated tests to ensure that a newly-compiled package actually works before it gets installed? I'm a little surprised that this is apparently not done by default.
I apologize in advance if this question has been asked before but I haven't been able to find a suitable answer after days of searching.
I have a package that has a couple of small functions written in C++ using Rcpp (package can be found here). When trying to install this package on Linux systems (both local install and via Github Actions - Ubuntu 18.04, 20.04) the compiling procedure was successful but R cannot load the package because an .so file was not found. Mac and Windows systems work fine and there were no R CMD CHECK issues when tested on these systems.
I was wondering if there is any way to solve this issue? I was thinking of adding something in .Makevars but I don't know what to add.
Thank you so much in advance.
─ installing *source* package ‘CBEA’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I'/__w/_temp/Library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -pedantic -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I'/__w/_temp/Library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -pedantic -c gmeans.cpp -o gmeans.o
g++ -std=gnu++11 -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o CBEA.so RcppExports.o gmeans.o -L/usr/local/lib/R/lib -lR
installing to /tmp/RtmpwFufM0/Rinst8982598ffd0c/00LOCK-CBEA/00new/CBEA/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘CBEA’ in library.dynam(lib, package, package.lib):
shared object ‘cbea.so’ not found
Error: loading failed
Execution halted
ERROR: loading failed
─ removing ‘/tmp/RtmpwFufM0/Rinst8982598ffd0c/CBEA’
Your (generated) NAMESPACE file has two entries referring to the package:
useDynLib(CBEA, .registration = TRUE)
useDynLib(cbea, .registration = TRUE)
Remove the second one (i.e. remove whereever you tell roxygen2 to add it, and you will be fine. The rror message you see and quote indicates a case issue as on Linux, cbea.so is different from CBEA.so (whereas macOS and Windows let you get away with it).
When trying to use ROracle I get the following error message
> library("ROracle")
Error: package or namespace load failed for ‘ROracle’:
package ‘ROracle’ was installed before R 4.0.0: please re-install it
I've installed/downloaded DBI, RTools, oracle isntant client (basic + sdk) and tried following these instructions but it did not work: ROracle install
I'm able to download ROracle just fine (see below) so I'm stumped on what is missing. Do I need to downgrade a version?
> Roracle_path <- "filepath.../ROracle_1.3-2.zip"
> install.packages(Roracle_path, repos = NULL)
Installing package into ‘C:/Users/<my username>/Documents/R/win-library/4.0’
(as ‘lib’ is unspecified)
package ‘ROracle’ successfully unpacked and MD5 sums checked
ROracle_1.3-2.tar.gz which is built for R 3.6.x works also with R 4.x if you install the package from SOURCES.
On Linux systems at first you have to install the Oracle Instant Client basic and SDK:
/home/jovyan/R
unzip instantclient-basic-linux.x64-21.4.0.0.0dbru.zip -d /opt/oracle/
unzip instantclient-sdk-linux.x64-21.4.0.0.0dbru.zip -d /opt/oracle
The linux package libaio1 have to be installed on the system:
apt install -y libaio1
Next, the environment variables must be set:
export PATH="$PATH:/opt/oracle/instantclient_21_4"
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/opt/oracle/instantclient_21_4"
Finally the package can be installed from Sources (use ROracle_1.3-2.tar.gz (sources) but not ROracle_1.3-2_R_x86_64-linux-gnu.tar.gz (binary) ):
R CMD INSTALL --configure-args='--with-oci-lib=/opt/oracle/instantclient_21_4/ --with-oci-inc=/opt/oracle/instantclient_21_4/sdk/include' ROracle_1.3-2.tar.gz
During the installation process you will see that the package will be installed from SOURCES:
* installing to library ‘/opt/conda/lib/R/library’
* installing *source* package ‘ROracle’ ...
** using staged installation
configure: creating ./config.status
config.status: creating src/Makevars
** libs
x86_64-conda-linux-gnu-cc -I"/opt/conda/lib/R/include" -DNDEBUG -I/opt/oracle/instantclient_21_4/sdk/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /opt/conda/include -I/opt/conda/include -Wl,-rpath-link,/opt/conda/lib -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1639563404388/work=/usr/local/src/conda/r-base-4.1.2 -fdebug-prefix-map=/opt/conda=/usr/local/src/conda-prefix -c rodbi.c -o rodbi.o
x86_64-conda-linux-gnu-cc -I"/opt/conda/lib/R/include" -DNDEBUG -I/opt/oracle/instantclient_21_4/sdk/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /opt/conda/include -I/opt/conda/include -Wl,-rpath-link,/opt/conda/lib -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1639563404388/work=/usr/local/src/conda/r-base-4.1.2 -fdebug-prefix-map=/opt/conda=/usr/local/src/conda-prefix -c rooci.c -o rooci.o
x86_64-conda-linux-gnu-cc -shared -L/opt/conda/lib/R/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/opt/conda/lib -Wl,-rpath-link,/opt/conda/lib -L/opt/conda/lib -o ROracle.so rodbi.o rooci.o -L/opt/oracle/instantclient_21_4/ -lclntsh -Wl,-rpath,/opt/oracle/instantclient_21_4/ -L/opt/conda/lib/R/lib -lR
installing to /opt/conda/lib/R/library/00LOCK-ROracle/00new/ROracle/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ROracle)
#
Check the line in the output to see it will be installed from Sources:
* installing *source* package ‘ROracle’ ...
I downgraded to R 3.6.3 and used RTools 35 and now it works.
I am no longer able to compile an R package from source, and this has never been a problem before today. This is what happens:
R CMD build BAMMtools
* checking for file ‘BAMMtools/DESCRIPTION’ ... OK
* preparing ‘BAMMtools’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘BAMMtools_2.1.0.tar.gz’
R CMD INSTALL BAMMtools
* installing to library ‘/usr/local/lib/R/site-library’
* installing *source* package ‘BAMMtools’ ...
** libs
make: Nothing to be done for 'all'.
installing to /usr/local/lib/R/site-library/BAMMtools/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/usr/local/lib/R/site-library/BAMMtools/libs/BAMMtools.so':
/usr/local/lib/R/site-library/BAMMtools/libs/BAMMtools.so: invalid ELF header
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/usr/local/lib/R/site-library/BAMMtools’
* restoring previous ‘/usr/local/lib/R/site-library/BAMMtools’
This does not seem to be a problem with this R package in particular, as I am able to install the package from within R, as:
> install.packages('BAMMtools_2.1.0.tar.gz', repos=NULL)
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
* installing *source* package ‘BAMMtools’ ...
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c cohort_matrix.c -o cohort_matrix.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c dtrates.c -o dtrates.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c jenksBrks.c -o jenksBrks.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c treetraverse.c -o treetraverse.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o BAMMtools.so cohort_matrix.o dtrates.o jenksBrks.o treetraverse.o -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/BAMMtools/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (BAMMtools)
I am running R v3.2.2, under Ubuntu v15.10 wily. I can't think of anything I've done within the last 24 hours that would have this effect, except updating my system with sudo apt-get update/upgrade.
Although this is not too much of a problem for installing the package, I can't run the R CMD check commands either, and this is a problem for development.
Any suggestions or advice would be greatly appreciated! Thanks!
As was found in the comments to the question, thanks to Jack Wasey, the problem was simply that I was running R CMD INSTALL on the name of the source directory, rather than on the built .tar.gz file.
I want to install Rcpp using install.packages("Rcpp"), but it failed.
The error message:
* installing *source* package ‘Rcpp’ ...
** package ‘Rcpp’ successfully unpacked and MD5 sums checked
** libs
g++ -I/usr/local/lib64/R/include -DNDEBUG -I../inst/include/ -I/usr/local/include -fpic -g -O2 -c Date.cpp -o Date.o
g++ -I/usr/local/lib64/R/include -DNDEBUG -I../inst/include/ -I/usr/local/include -fpic -g -O2 -c Module.cpp -o Module.o
g++ -I/usr/local/lib64/R/include -DNDEBUG -I../inst/include/ -I/usr/local/include -fpic -g -O2 -c Rcpp_init.cpp -o Rcpp_init.o
g++ -I/usr/local/lib64/R/include -DNDEBUG -I../inst/include/ -I/usr/local/include -fpic -g -O2 -c api.cpp -o api.o
g++ -I/usr/local/lib64/R/include -DNDEBUG -I../inst/include/ -I/usr/local/include -fpic -g -O2 -c attributes.cpp -o attributes.o
g++ -I/usr/local/lib64/R/include -DNDEBUG -I../inst/include/ -I/usr/local/include -fpic -g -O2 -c barrier.cpp -o barrier.o
g++ -shared -L/usr/local/lib64 -o Rcpp.so Date.o Module.o Rcpp_init.o api.o attributes.o barrier.o
installing to /home/sethbrin/R/x86_64-redhat-linux-gnu-library/3.1/Rcpp/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/home/sethbrin/R/x86_64-redhat-linux-gnu-library/3.1/Rcpp/libs/Rcpp.so':
/home/sethbrin/R/x86_64-redhat-linux-gnu-library/3.1/Rcpp/libs/Rcpp.so: undefined symbol: _ZNSt15basic_streambufIcSt11char_traitsIcEE7seekoffExSt12_Ios_SeekdirSt13_Ios_Openmode
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/sethbrin/R/x86_64-redhat-linux-gnu-library/3.1/Rcpp’
The downloaded source packages are in
‘/tmp/Rtmp6PKB8N/downloaded_packages’
Warning message:
In install.packages("Rcpp") :
installation of package ‘Rcpp’ had non-zero exit status
Then I use
c++fit _ZNSt15basic_streambufIcSt11char_traitsIcEE7seekoffExSt12_Ios_SeekdirSt13_Ios_Openmode
std::basic_streambuf<char, std::char_traits<char> >::seekoff(long long, std::_Ios_Seekdir, std::_Ios_Openmode)
I have searched for some solutions for that. It seems that it is because of the gcc version. But I don't know how to change the gcc version that R uses to compile Rcpp package.
CRAN tests Rcpp just like any other of the (by now) 6700+ package.
You can see the aggregate test report and the test setups includes two Fedora-based machines:
one fedora setup using clang and
one fedora setup using g++.
As such your problems are possibly local, or simply due to using an older setup. In which case the Archive section gives you access to an older version.
I've encountered a similar problem.
And after some searches, here are the solutions to alter the compiler:
1. If you have the root privilege:
I found that the Makeconf file in R directory actually sets all the information that is needed for compilation.
To find the path to it, echo which R in the command line.
e.g. I got like:
/data/apps/R/3.1.2/bin/R
And then the file is in:
/data/apps/R/3.1.2/lib64/R/etc/Makeconf
then sudo edit the file on line CC = XXX and maybe more relative lines.
Problem solved!
2. If you only have local user privilege.
Add your own configurations to ~/.R/Makevars
However, #Dirk is probably right.
For me, I finally solved my problem by adding -Doff_t=__off_t to CFLAGS (My problem was error: unknown type name 'off_t'). And I got the halted error when I manually altered parts of the compilers...