I'm trying to install one R package with MacOSX with the command:
install_github("yuanzhongshang/PMR")
But there is an error:
Downloading GitHub repo yuanzhongshang/PMR#HEAD
✓ checking for file
─ preparing ‘PMR’:
✓ checking DESCRIPTION meta-information ...
─ cleaning src
─ installing the package to process help pages
-----------------------------------
─ installing *source* package ‘PMR’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -Wall -pedantic -fdiagnostics-color=always -c EstimateVC_1.cpp -o EstimateVC_1.o
clang: error: unsupported option '-fopenmp'
make: *** [EstimateVC_1.o] Error 1
ERROR: compilation failed for package ‘PMR’
─ removing
How can I solve it?
Related
when installing a R package from github
install_github("DataSlingers/ExclusiveLasso")
I get the error messages:
* installing *source* package 'ExclusiveLasso' ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/include" -DNDEBUG -I'D:/R-4.2.2/library/Rcpp/include' -I'D:/R-4.2.2/library/RcppArmadillo/include' -I"D:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ExclusiveLasso.cpp -o ExclusiveLasso.o
In file included from D:/R-4.2.2/library/Rcpp/include/RcppCommon.h:30,
from D:/R-4.2.2/library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25,
from D:/R-4.2.2/library/RcppArmadillo/include/RcppArmadillo.h:29,
from ExclusiveLasso.cpp:23:
D:/R-4.2.2/library/Rcpp/include/Rcpp/r/headers.h:66:10: fatal error: R.h: No such file or directory
66 | #include <R.h>
| ^~~~~
compilation terminated.
make: *** [D:/R-4.2.2/etc/x64/Makeconf:260：ExclusiveLasso.o] 错误 1
ERROR: compilation failed for package 'ExclusiveLasso'
* removing 'D:/R-4.2.2/library/ExclusiveLasso'
I know where my R.h at, and I tried change
#include <R.h>
into
#include <D:/R-4.2.2/include>,
but there's too many files and errors like this
It seems that I should tell the g++ where to find D:/R-4.2.2/include, can someone guide me whether I should do that or what should I do.
I's using:
R version 4.2.2 (2022-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Using vscode
Works fine here on Ubuntu 22.10. Note in the log below how it uses -I"/usr/share/R/include" (which is something R itself adds) to point to R's headers. So to me it looks like your R installation is at fault because the src/Makevars.win in that repo is very standard and mostly likely correct.
edd#rob:~$ installGithub.r DataSlingers/ExclusiveLasso # wrapper around install_github()
Using github PAT from envvar GITHUB_PAT
Downloading GitHub repo DataSlingers/ExclusiveLasso#HEAD
Skipping 1 packages ahead of CRAN: Rcpp
── R CMD build ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
✔ checking for file ‘/tmp/remotes2ac86f2646632b/DataSlingers-ExclusiveLasso-ed6b729/DESCRIPTION’ ...
─ preparing ‘ExclusiveLasso’:
✔ checking DESCRIPTION meta-information ...
─ cleaning src
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ building ‘ExclusiveLasso_0.0.tar.gz’
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
* installing *source* package ‘ExclusiveLasso’ ...
** using staged installation
** libs
ccache g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -fpic -g -O3 -Wall -pipe -pedantic -Wno-ignored-attributes -c ExclusiveLasso.cpp -o ExclusiveLasso.o
ccache g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -fpic -g -O3 -Wall -pipe -pedantic -Wno-ignored-attributes -c RcppExports.cpp -o RcppExports.o
ccache g++ -std=gnu++11 -Wl,-S -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o ExclusiveLasso.so ExclusiveLasso.o RcppExports.o -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
if test -e "/usr/bin/strip" & test -e "/bin/uname" & [[ `uname` == "Linux" ]] ; then /usr/bin/strip --strip-debug *.o *.so; fi
if test -e "/usr/bin/strip" & test -e "/bin/uname" & [[ `uname` == "Darwin" ]] ; then /usr/bin/strip -S *.o *.so; fi
installing to /usr/local/lib/R/site-library/00LOCK-ExclusiveLasso/00new/ExclusiveLasso/libs
** R
** 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
** 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 (ExclusiveLasso)
edd#rob:~$
Looking at your installation attempt confirms that because you have
g++ -std=gnu++11 -I"/include"
so R does not figure out where its installation is. Normally you should have
edd#rob:~$ R RHOME
/usr/lib/R
edd#rob:~$
but I suspect that too is borked at your end.
I just started R. I am on a M1 BigSur Mac.
I have tried several packages, but I could not install anyone of them.
for example, swirl
> install.packages("swirl")
trying URL 'https://cran.rstudio.com/src/contrib/swirl_2.4.5.tar.gz'
Content type 'application/x-gzip' length 108847 bytes (106 KB)
==================================================
downloaded 106 KB
* installing *source* package ‘swirl’ ...
** package ‘swirl’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/opt/homebrew/Cellar/r/4.1.0/lib/R/library/stringi/libs/stringi.so':
dlopen(/opt/homebrew/Cellar/r/4.1.0/lib/R/library/stringi/libs/stringi.so, 6): no suitable image found. Did find:
/opt/homebrew/Cellar/r/4.1.0/lib/R/library/stringi/libs/stringi.so: mach-o, but wrong architecture
/opt/homebrew/Cellar/r/4.1.0/lib/R/library/stringi/libs/stringi.so: mach-o, but wrong architecture
Calls: <Anonymous> ... namespaceImport -> loadNamespace -> library.dynam -> dyn.load
Execution halted
ERROR: lazy loading failed for package ‘swirl’
* removing ‘/opt/homebrew/Cellar/r/4.1.0/lib/R/library/swirl’
Warning in install.packages :
installation of package ‘swirl’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/t6/qy2rcbdx0g9_fv98q1g48v_h0000gn/T/RtmpDAcI28/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
tidyverse it has been repeating the following output but it does not complete a proper installation.
* installing *source* package ‘cpp11’ ...
** package ‘cpp11’ successfully unpacked and MD5 sums checked
** using staged installation
** 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 (cpp11)
* installing *source* package ‘Rcpp’ ...
** package ‘Rcpp’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
clang++ -std=gnu++14 -I"/opt/homebrew/Cellar/r/4.1.0/lib/R/include" -DNDEBUG -I../inst/include/ -I/opt/homebrew/opt/gettext/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/xz/include -I/opt/homebrew/include -fPIC -g -O2 -c api.cpp -o api.o
clang++ -std=gnu++14 -I"/opt/homebrew/Cellar/r/4.1.0/lib/R/include" -DNDEBUG -I../inst/include/ -I/opt/homebrew/opt/gettext/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/xz/include -I/opt/homebrew/include -fPIC -g -O2 -c attributes.cpp -o attributes.o
clang++ -std=gnu++14 -I"/opt/homebrew/Cellar/r/4.1.0/lib/R/include" -DNDEBUG -I../inst/include/ -I/opt/homebrew/opt/gettext/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/xz/include -I/opt/homebrew/include -fPIC -g -O2 -c barrier.cpp -o barrier.o
clang++ -std=gnu++14 -I"/opt/homebrew/Cellar/r/4.1.0/lib/R/include" -DNDEBUG -I../inst/include/ -I/opt/homebrew/opt/gettext/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/xz/include -I/opt/homebrew/include -fPIC -g -O2 -c date.cpp -o date.o
clang++ -std=gnu++14 -I"/opt/homebrew/Cellar/r/4.1.0/lib/R/include" -DNDEBUG -I../inst/include/ -I/opt/homebrew/opt/gettext/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/xz/include -I/opt/homebrew/include -fPIC -g -O2 -c module.cpp -o module.o
clang++ -std=gnu++14 -I"/opt/homebrew/Cellar/r/4.1.0/lib/R/include" -DNDEBUG -I../inst/include/ -I/opt/homebrew/opt/gettext/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/xz/include -I/opt/homebrew/include -fPIC -g -O2 -c rcpp_init.cpp -o rcpp_init.o
clang++ -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/opt/homebrew/Cellar/r/4.1.0/lib/R/lib -L/opt/homebrew/opt/gettext/lib -L/opt/homebrew/opt/readline/lib -L/opt/homebrew/opt/xz/lib -L/opt/homebrew/lib -o Rcpp.so api.o attributes.o barrier.o date.o module.o rcpp_init.o -L/opt/homebrew/Cellar/r/4.1.0/lib/R/lib -lR -lintl -Wl,-framework -Wl,CoreFoundation
I tried install.package('swirl', type='mac.binary').
It forces a successful installation but it gives the following error when I call library("swirl"):
Error: package or namespace load failed for ‘swirl’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/opt/homebrew/Cellar/r/4.1.0/lib/R/library/stringi/libs/stringi.so':
dlopen(/opt/homebrew/Cellar/r/4.1.0/lib/R/library/stringi/libs/stringi.so, 6): no suitable image found. Did find:
/opt/homebrew/Cellar/r/4.1.0/lib/R/library/stringi/libs/stringi.so: mach-o, but wrong architecture
/opt/homebrew/Cellar/r/4.1.0/lib/R/library/stringi/libs/stringi.so: mach-o, but wrong architecture
Have followed the processes outlined on the Github repo.
Have tried installed blotter first and then quantstrat. Doesnt work
Have then moved to installing all dependencies first.
install.packages("FinancialInstrument",repos="https://github.com/braverock/FinancialInstrument")
When trying to install from Github using devtools get the following error.
devtools::install_github("braverock/blotter")
Downloading GitHub repo braverock/blotter#master
✓ checking for file ‘/private/var/folders/_8/zy8__ntx5cx0_lnbybvfjhsr0000gp/T/Rtmp0wtY3O/remotes2547e2faf85/braverock-blotter-67be2c8/DESCRIPTION’ (400ms)
─ preparing ‘blotter’:
✓ checking DESCRIPTION meta-information ...
─ cleaning src
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ looking to see if a ‘data/datalist’ file should be added
─ building ‘blotter_0.14.8.tar.gz’
installing source package ‘blotter’ ...
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c calcPosAvgCost.c -o calcPosAvgCost.o
calcPosAvgCost.c:31:12: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
if(abs(d_PrevPosQty) > abs(d_PosQty[i])){
^
calcPosAvgCost.c:31:12: note: use function 'fabs' instead
if(abs(d_PrevPosQty) > abs(d_PosQty[i])){
^~~
fabs
calcPosAvgCost.c:31:32: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
if(abs(d_PrevPosQty) > abs(d_PosQty[i])){
^
calcPosAvgCost.c:31:32: note: use function 'fabs' instead
if(abs(d_PrevPosQty) > abs(d_PosQty[i])){
^~~
fabs
2 warnings generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c init.c -o init.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 blotter.so calcPosAvgCost.o init.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-blotter/00new/blotter/libs
** R
** data
** demo
** byte-compile and prepare package for lazy loading
Error: (converted from warning) package ‘quantmod’ was built under R version 3.6.2
Execution halted
ERROR: lazy loading failed for package ‘blotter’
removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/blotter’
Error: Failed to install 'blotter' from GitHub:
(converted from warning) installation of package ‘/var/folders/_8/zy8__ntx5cx0_lnbybvfjhsr0000gp/T//Rtmp0wtY3O/file25475cac4c09/blotter_0.14.8.tar.gz’ had non-zero exit status
I fixed the issue using Sys.setenv(R_REMOTES_NO_ERRORS_FROM_WARNINGS=TRUE) from https://github.com/r-lib/remotes/issues/434
I am trying to install ggplot package in R but I got the following error
install.packages('ggplot2',dependencies = TRUE)
* installing *source* package ‘gdtools’ ...
** package ‘gdtools’ successfully unpacked and MD5 sums checked
Using PKG_CFLAGS=-I/usr/local/opt/cairo/include/cairo
Using PKG_LIBS=-L/usr/local/opt/cairo/lib -lcairo
** libs
clang++ -I/usr/local/Cellar/r/3.3.1_2/R.framework/Resources/include -DNDEBUG -I/usr/local/opt/cairo/include/cairo -I../inst/include/ -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -I/usr/local/include -I"/usr/local/lib/R/3.3/site-library/Rcpp/include" -fPIC -g -O2 -c CairoContext.cpp -o CairoContext.o
clang++ -I/usr/local/Cellar/r/3.3.1_2/R.framework/Resources/include -DNDEBUG -I/usr/local/opt/cairo/include/cairo -I../inst/include/ -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -I/usr/local/include -I"/usr/local/lib/R/3.3/site-library/Rcpp/include" -fPIC -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -I/usr/local/Cellar/r/3.3.1_2/R.framework/Resources/include -DNDEBUG -I/usr/local/opt/cairo/include/cairo -I../inst/include/ -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -I/usr/local/include -I"/usr/local/lib/R/3.3/site-library/Rcpp/include" -fPIC -g -O2 -c font_metrics.cpp -o font_metrics.o
In file included from font_metrics.cpp:3:
/usr/local/opt/cairo/include/cairo/cairo-ft.h:46:10: fatal error: 'ft2build.h'
file not found
#include <ft2build.h>
^
1 error generated.
make: *** [font_metrics.o] Error 1
ERROR: compilation failed for package ‘gdtools’
* removing ‘/usr/local/lib/R/3.3/site-library/gdtools’
* installing *source* package ‘ggplot2’ ...
** package ‘ggplot2’ successfully unpacked and MD5 sums checked
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ggplot2)
ERROR: dependency ‘gdtools’ is not available for package ‘svglite’
* removing ‘/usr/local/lib/R/3.3/site-library/svglite’
The downloaded source packages are in
‘/private/var/folders/mm/8gjs_s_s01x3_qr4xrdky88c0000gn/T/RtmpwQObj5/downloaded_packages’
Warning messages:
1: In install.packages("ggplot2", dependencies = TRUE) :
installation of package ‘gdtools’ had non-zero exit status
2: In install.packages("ggplot2", dependencies = TRUE) :
installation of package ‘svglite’ had non-zero exit status
I installed R by following the instruction in this page: Installing R with Homebrew
brew tap homebrew/science
brew install Caskroom/cask/xquartz
brew install r
Can anyone shed me some light on this? thanks so much!
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.