I am having issues in installing the samr package in R v3.4 MacOS sierra. I get this warning message:
"Package which is only available in source form, and may need compilation of
C/C++/Fortran: ‘samr’
Do you want to attempt to install these from sources?
y/n: y
installing the source package ‘samr’
trying URL 'https://cran.rstudio.com/src/contrib/samr_2.0.tar.gz'
Content type 'application/x-gzip' length 36702 bytes (35 KB)
==================================================
downloaded 35 KB
* installing *source* package ‘samr’ ...
** libs
gfortran -fPIC -g -O2 -c rankcol.f -o rankcol.o
make: gfortran: No such file or directory
make: *** [rankcol.o] Error 1
ERROR: compilation failed for package ‘samr’
* removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/samr’
Warning in install.packages :
installation of package ‘samr’ had non-zero exit status
Does anybody has an idea to overcome this?
Thanks so much, I dwonloaded gofortran for macOs sierra https://gcc.gnu.org/wiki/GFortranBinaries#MacOS and it seems to work now
Related
I have R 4.2.1 and the latest R studio build 554 on a macOS Monterey.
I am trying to install monocle3 using the following :
BiocManager::install('monocle3')
I get a really long error message
BiocManager::install("monocle3")
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details
replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.15 (BiocManager 1.30.19), R 4.2.1 (2022-06-23)
Installing package(s) 'monocle3'
Old packages: 'processx', 'ps', 'tm', 'zip'
Update all/some/none? [a/s/n]:
a
There are binary versions available but the source versions are later:
binary source needs_compilation
processx 3.7.0 3.8.0 TRUE
ps 1.7.1 1.7.2 TRUE
tm 0.7-8 0.7-9 TRUE
zip 2.2.1 2.2.2 TRUE
Do you want to install from sources the packages which need compilation? (Yes/no/cancel) yes
installing the source packages ‘processx’, ‘ps’, ‘tm’, ‘zip’
trying URL 'https://cran.rstudio.com/src/contrib/processx_3.8.0.tar.gz'
Content type 'application/x-gzip' length 162539 bytes (158 KB)
==================================================
downloaded 158 KB
trying URL 'https://cran.rstudio.com/src/contrib/ps_1.7.2.tar.gz'
Content type 'application/x-gzip' length 129096 bytes (126 KB)
==================================================
downloaded 126 KB
trying URL 'https://cran.rstudio.com/src/contrib/tm_0.7-9.tar.gz'
Content type 'application/x-gzip' length 638649 bytes (623 KB)
==================================================
downloaded 623 KB
trying URL 'https://cran.rstudio.com/src/contrib/zip_2.2.2.tar.gz'
Content type 'application/x-gzip' length 103404 bytes (100 KB)
==================================================
downloaded 100 KB
* installing *source* package ‘ps’ ...
** package ‘ps’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -Wall -g -O2 -L/usr/local/lib -Wall px.c -o px
px.c:6:10: fatal error: 'unistd.h' file not found
#include <unistd.h>
^~~~~~~~~~
1 error generated.
make: *** [Makevars:11: px] Error 1
ERROR: compilation failed for package ‘ps’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/ps’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/ps’
* installing *source* package ‘tm’ ...
** package ‘tm’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/RcppCommon.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp/r/headers.h:62:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:100:
In file included from /Users/osman/opt/miniconda3/bin/../include/c++/v1/cmath:305:
/Users/osman/opt/miniconda3/bin/../include/c++/v1/math.h:301:15: fatal error: 'math.h' file not found
#include_next <math.h>
^~~~~~~~
1 error generated.
make: *** [/Library/Frameworks/R.framework/Resources/etc/Makeconf:175: RcppExports.o] Error 1
ERROR: compilation failed for package ‘tm’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/tm’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/tm’
* installing *source* package ‘zip’ ...
** package ‘zip’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -Wall -g -O2 miniz.c zip.c unixutils.c tools/cmdzip.c -o tools/cmdzip
In file included from miniz.c:27:
./miniz.h:156:10: fatal error: 'time.h' file not found
#include <time.h>
^~~~~~~~
1 error generated.
make: *** [Makevars:9: tools/cmdzip] Error 1
ERROR: compilation failed for package ‘zip’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/zip’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/zip’
* installing *source* package ‘processx’ ...
** package ‘processx’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -Wall -g -O2 -L/usr/local/lib -Wall tools/px.c -o tools/px
tools/px.c:11:10: fatal error: 'unistd.h' file not found
#include <unistd.h>
^~~~~~~~~~
1 error generated.
make: *** [Makevars:14: tools/px] Error 1
ERROR: compilation failed for package ‘processx’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/processx’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/processx’
The downloaded source packages are in
‘/private/var/folders/ps/3jjkc4kj1y98mzlpdm3wp5dm0000gn/T/RtmpNbTlti/downloaded_packages’
Warning messages:
1: package ‘monocle3’ is not available for Bioconductor version '3.15'
A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
2: In install.packages(update[instlib == l, "Package"], l, repos = repos, :
installation of package ‘ps’ had non-zero exit status
3: In install.packages(update[instlib == l, "Package"], l, repos = repos, :
installation of package ‘tm’ had non-zero exit status
4: In install.packages(update[instlib == l, "Package"], l, repos = repos, :
installation of package ‘zip’ had non-zero exit status
5: In install.packages(update[instlib == l, "Package"], l, repos = repos, :
installation of package ‘processx’ had non-zero exit status
so I tried installing 'processx', 'ps', 'tm', 'zip' individually and now I get the following message:
Warning message:
package ‘monocle3’ is not available for Bioconductor version '3.15'
A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
Any idea for how to fix this issue?
I expected the installation to go through but it did not
When I get errors installing a package what I usually do is going to the first package that didn't install properly and try and install it in a different way, and I do the same for the others.
Other mac users had similar issue installing the ps package as you can see in this github issues here https://github.com/r-lib/ps/issues/55
they solved the problem by installing ps package via anaconda:
https://anaconda.org/conda-forge/r-ps
My aim is to install the R package "quantreg". In R Studio, I therefore type
install.packages("quantreg")
R Studio then prints:
binary source needs_compilation
quantreg 5.85 5.88 TRUE
Do you want to install from sources the package which needs compilation? (Yes/no/cancel)
I consequently write "Yes" and hit enter. The installation then fails with the following output:
installing the source package ‘quantreg’
trying URL 'https://cran.rstudio.com/src/contrib/quantreg_5.88.tar.gz'
Content type 'application/x-gzip' length 1016964 bytes (993 KB)
==================================================
downloaded 993 KB
* installing *source* package ‘quantreg’ ...
** package ‘quantreg’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gfortran -fPIC -Wall -g -O2 -c akj.f -o akj.o
make: gfortran: No such file or directory
make: *** [akj.o] Error 1
ERROR: compilation failed for package ‘quantreg’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/quantreg’
Warning in install.packages :
installation of package ‘quantreg’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/bl/yxw71y6n3ksbktr_vmp65h1m0000gn/T/Rtmpc1SB0G/downloaded_packages’
I am on Mac OS 12.3.1 Monterey and use R version 3.6.3. I use this old version of R (instead of an up-to-date one) because it is required in combination with another program that I use. Therefore, I cannot use newer versions of R.
What could be a possible fix for my problem, so that R installs quantreg without failing?
I am trying to install sf package in R, but it returns error and unable to install the package.
The warning message said
installation of package ‘sf’ had non-zero exit status.
Would you please advise me on how to install the package? I am using Windows with R version 3.6.1.
Platform: x86_64-w64-mingw32/x64 (64-bit)
Below is the all messages:
> install.packages("sf")
Installing package into ‘C:/Users/***/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)
also installing the dependencies ‘wk’, ‘s2’, ‘units’
There are binary versions available but the source versions are later:
binary source needs_compilation
wk 0.4.1 0.5.0 TRUE
s2 1.0.4 1.0.7 TRUE
units 0.7-1 0.7-2 TRUE
sf 0.9-8 1.0-4 TRUE
installing the source packages ‘wk’, ‘s2’, ‘units’, ‘sf’
trying URL 'https://cran.rstudio.com/src/contrib/wk_0.5.0.tar.gz'
Content type 'application/x-gzip' length 138686 bytes (135 KB)
downloaded 135 KB
trying URL 'https://cran.rstudio.com/src/contrib/s2_1.0.7.tar.gz'
Content type 'application/x-gzip' length 2235408 bytes (2.1 MB)
downloaded 2.1 MB
trying URL 'https://cran.rstudio.com/src/contrib/units_0.7-2.tar.gz'
Content type 'application/x-gzip' length 855840 bytes (835 KB)
downloaded 835 KB
trying URL 'https://cran.rstudio.com/src/contrib/sf_1.0-4.tar.gz'
Content type 'application/x-gzip' length 3526535 bytes (3.4 MB)
downloaded 3.4 MB
* installing *source* package 'wk' ...
** パッケージ 'wk' の解凍および MD5 サムの検証に成功しました
** using staged installation
** libs
*** arch - i386
c:/Rtools/mingw_32/bin/gcc -I"C:/PROGRA~1/R/R-36~1.1/include" -DNDEBUG -I../inst/include/ -I"C:/Users/***/Documents/R/win-library/3.6/cpp11/include" -O3 -Wall -std=gnu99 -mtune=generic -c bbox-handler.c -o bbox-handler.o
sh: line 1: c:/Rtools/mingw_32/bin/gcc: No such file or directory
make: *** [C:/PROGRA~1/R/R-36~1.1/etc/i386/Makeconf:208: bbox-handler.o] Error 127
ERROR: compilation failed for package 'wk'
* removing 'C:/Users/***/Documents/R/win-library/3.6/wk'
Warning in install.packages :
installation of package ‘wk’ had non-zero exit status
* installing *source* package 'units' ...
** パッケージ 'units' の解凍および MD5 サムの検証に成功しました
** using staged installation
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
*** arch - i386
rm -Rf units.dll RcppExports.o udunits.o
"C:/PROGRA~1/R/R-36~1.1/bin/i386/Rscript.exe" "../tools/winlibs.R"
mkdir -p ../inst
rm -Rf ../inst/share
cp -r ../windows/udunits-2.2.20/share ../inst/
c:/Rtools/mingw_32/bin/g++ -I"C:/PROGRA~1/R/R-36~1.1/include" -DNDEBUG -DUDUNITS2_DIR=0 -I../windows/udunits-2.2.20/include -I"C:/Program Files/R/R-3.6.1/library/Rcpp/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
sh: line 1: c:/Rtools/mingw_32/bin/g++: No such file or directory
make: *** [C:/PROGRA~1/R/R-36~1.1/etc/i386/Makeconf:215: RcppExports.o] Error 127
ERROR: compilation failed for package 'units'
* removing 'C:/Users/***/Documents/R/win-library/3.6/units'
Warning in install.packages :
installation of package ‘units’ had non-zero exit status
ERROR: dependency 'wk' is not available for package 's2'
* removing 'C:/Users/***/Documents/R/win-library/3.6/s2'
Warning in install.packages :
installation of package ‘s2’ had non-zero exit status
ERROR: dependencies 's2', 'units' are not available for package 'sf'
* removing 'C:/Users/***/Documents/R/win-library/3.6/sf'
Warning in install.packages :
installation of package ‘sf’ had non-zero exit status
The downloaded source packages are in
‘C:\Users\***\AppData\Local\Temp\RtmpuiUgtA\downloaded_packages’
I specified the package's url as below, but it returns error as well;
> install.packages("https://cran.r-project.org/src/contrib/sf_1.0-4.tar.gz", repos=NULL)
Installing package into ‘C:/Users/***/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)
trying URL 'https://cran.r-project.org/src/contrib/sf_1.0-4.tar.gz'
Content type 'application/x-gzip' length 3526535 bytes (3.4 MB)
downloaded 3.4 MB
ERROR: dependencies 's2', 'units' are not available for package 'sf'
* removing 'C:/Users/***/Documents/R/win-library/3.6/sf'
Warning in install.packages :
installation of package ‘C:/Users/***/AppData/Local/Temp/RtmpuiUgtA/downloaded_packages/sf_1.0-4.tar.gz’ had non-zero exit status
I am trying to install the package pathview in R version 4.0.0. I first installed biocmanager without issue then used this command as directed:
BiocManager::install("pathview")
However it failed to install with the following error:
BiocManager::install("pathview")
'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details
replacement repositories:
CRAN: https://cran.csiro.au
Bioconductor version 3.12 (BiocManager 1.30.16), R 4.0.0 (2020-04-24)
Installing package(s) 'pathview'
also installing the dependencies ‘RSQLite’, ‘AnnotationDbi’, ‘org.Hs.eg.db’
trying URL 'https://cran.csiro.au/src/contrib/RSQLite_2.2.7.tar.gz'
Content type 'application/x-gzip' length 3616162 bytes (3.4 MB)
==================================================
downloaded 3.4 MB
trying URL 'https://bioconductor.org/packages/3.12/bioc/src/contrib/AnnotationDbi_1.52.0.tar.gz'
Content type 'application/x-gzip' length 4338642 bytes (4.1 MB)
==================================================
downloaded 4.1 MB
trying URL 'https://bioconductor.org/packages/3.12/data/annotation/src/contrib/org.Hs.eg.db_3.12.0.tar.gz'
Content type 'application/x-gzip' length 83225518 bytes (79.4 MB)
==================================================
downloaded 79.4 MB
trying URL 'https://bioconductor.org/packages/3.12/bioc/src/contrib/pathview_1.30.1.tar.gz'
Content type 'application/x-gzip' length 2192604 bytes (2.1 MB)
==================================================
downloaded 2.1 MB
* installing *source* package ‘RSQLite’ ...
** package ‘RSQLite’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
icpc -std=gnu++11 -I"/apps/R/4.0.0/lib64/R/include" -DNDEBUG -I. -Ivendor -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/home/590/mr8122/R/x86_64-pc-linux-gnu-library/4.0/plogr/include' -I'/home/590/mr8122/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c DbColumn.cpp -o DbColumn.o
In file included from vendor/boost/container/stable_vector.hpp(68),
from RSQLite.h(14),
from pch.h(1),
from DbColumn.cpp(1):
vendor/boost/container/vector.hpp(2705): warning #2196: routine is both "inline" and "noinline"
BOOST_CONTAINER_NOINLINE iterator priv_insert_forward_range_no_capacity
^
In file included from vendor/boost/container/stable_vector.hpp(68),
from RSQLite.h(14),
from pch.h(1),
from DbColumn.cpp(1):
vendor/boost/container/vector.hpp(2722): warning #2196: routine is both "inline" and "noinline"
BOOST_CONTAINER_NOINLINE iterator priv_insert_forward_range_no_capacity
^
In file included from vendor/boost/preprocessor/control/while.hpp(323),
from vendor/boost/preprocessor/arithmetic/add.hpp(60),
from vendor/boost/mpl/aux_/preprocessor/def_params_tail.hpp(66),
from vendor/boost/mpl/aux_/na_spec.hpp(28),
from vendor/boost/mpl/if.hpp(19),
from vendor/boost/ptr_container/detail/default_deleter.hpp(15),
from vendor/boost/ptr_container/detail/static_move_ptr.hpp(23),
from vendor/boost/ptr_container/detail/reversible_ptr_container.hpp(22),
from vendor/boost/ptr_container/ptr_sequence_adapter.hpp(20),
from vendor/boost/ptr_container/ptr_vector.hpp(20),
from RSQLite.h(15),
from pch.h(1),
from DbColumn.cpp(1):
vendor/boost/preprocessor/list/fold_left.hpp(341): catastrophic error: cannot open source file "boost/preprocessor/list/detail/edg/fold_left.hpp"
# include <boost/preprocessor/list/detail/edg/fold_left.hpp>
^
compilation aborted for DbColumn.cpp (code 4)
make: *** [/apps/R/4.0.0/lib64/R/etc/Makeconf:176: DbColumn.o] Error 4
ERROR: compilation failed for package ‘RSQLite’
* removing ‘/home/590/mr8122/R/x86_64-pc-linux-gnu-library/4.0/RSQLite’
ERROR: dependency ‘RSQLite’ is not available for package ‘AnnotationDbi’
* removing ‘/home/590/mr8122/R/x86_64-pc-linux-gnu-library/4.0/AnnotationDbi’
ERROR: dependency ‘AnnotationDbi’ is not available for package ‘org.Hs.eg.db’
* removing ‘/home/590/mr8122/R/x86_64-pc-linux-gnu-library/4.0/org.Hs.eg.db’
ERROR: dependencies ‘AnnotationDbi’, ‘org.Hs.eg.db’ are not available for package ‘pathview’
* removing ‘/home/590/mr8122/R/x86_64-pc-linux-gnu-library/4.0/pathview’
The downloaded source packages are in
‘/scratch/ki16/mr8122/tmp/RtmpYxgwWN/downloaded_packages’
Installation paths not writeable, unable to update packages
path: /apps/R/4.0.0/lib64/R/library
packages:
boot, class, cluster, codetools, foreign, KernSmooth, lattice, MASS,
Matrix, mgcv, nlme, nnet, spatial, survival
Warning messages:
1: In .inet_warning(msg) :
installation of package ‘RSQLite’ had non-zero exit status
2: In .inet_warning(msg) :
installation of package ‘AnnotationDbi’ had non-zero exit status
3: In .inet_warning(msg) :
installation of package ‘org.Hs.eg.db’ had non-zero exit status
4: In .inet_warning(msg) :
installation of package ‘pathview’ had non-zero exit status
Does anyone know why this might be failing?
RSQLite is failing to find Boost. I recommend installing Boost from source and then re-attempting the R package install.
I was originally seeing this error when installing biomaRt with BiocManager. After installing Boost, I was successfully able to install RSQLite. Depending on your system and installation, it may require further manipulation of your library paths to allow R to find your new Boost install.
I am trying to install tsoutliers library in R where only the source is available and it doesn't has a CRAN package available. Also, KFKSDS in one of the dependencies that have to be installed, again, it is source code version available only.
I used brew to have gsl installed but when I tried to install KFKSDS, it still errorred out. On the other side, I installed gsl, gsl-devel, KFKSDS and tsoutliers easily on the redhat server. Can anyone show me how can I installed it successfully on my Mac. I am using R 3.1.1 which is not cutting edge but should be good enough, I guess.
> install.packages("KFKSDS", type="source")
trying URL 'http://cran.rstudio.com/src/contrib/KFKSDS_1.5.tar.gz'
Content type 'application/x-gzip' length 30272 bytes (29 Kb)
opened URL
==================================================
downloaded 29 Kb
* installing *source* package ‘KFKSDS’ ...
** package ‘KFKSDS’ successfully unpacked and MD5 sums checked
** libs
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c KF-deriv.cpp -o KF-deriv.o
In file included from /usr/include/c++/4.2.1/bits/locale_facets.h:1539,
from /usr/include/c++/4.2.1/bits/basic_ios.h:44,
from /usr/include/c++/4.2.1/ios:50,
from /usr/include/c++/4.2.1/ostream:45,
from /usr/include/c++/4.2.1/iterator:70,
from /usr/include/c++/4.2.1/numeric:67,
from KFKSDS.h:12,
from KF-deriv.cpp:1:
/usr/include/c++/4.2.1/bits/codecvt.h:219:45: error: macro "length" passed 4 arguments, but takes just 1
In file included from /usr/include/c++/4.2.1/bits/locale_facets.h:1539,
from /usr/include/c++/4.2.1/bits/basic_ios.h:44,
from /usr/include/c++/4.2.1/ios:50,
from /usr/include/c++/4.2.1/ostream:45,
from /usr/include/c++/4.2.1/iterator:70,
from /usr/include/c++/4.2.1/numeric:67,
from KFKSDS.h:12,
from KF-deriv.cpp:1:
/usr/include/c++/4.2.1/bits/codecvt.h:218: error: expected ‘;’ before ���const’
/usr/include/c++/4.2.1/bits/codecvt.h:222: error: expected `;' before ‘int’
make: *** [KF-deriv.o] Error 1
ERROR: compilation failed for package ‘KFKSDS’
* removing ‘/Library/Frameworks/R.framework/Versions/3.1/Resources/library/KFKSDS’
Warning in install.packages :
installation of package ‘KFKSDS’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/d2/ffftfj193ng339zrc3jbdv75m9ssv9/T/RtmpgJshhe/downloaded_packages’