I am having trouble updating several packages in rStudio. My Macbook is up to date and my rStudio is also up to date.
Please help me figure out how to fix it.
Kind Regards
Here is a snippit of my rStudio terminal trying to update the "dplyr" package
>install.packages("dplyr")
There is a binary version available but the source version is later:
binary source needs_compilation
dplyr 0.8.0.1 0.8.5 TRUE
Do you want to install from sources the package which needs compilation?
y/n: y
installing the source package ‘dplyr’
trying URL 'https://cran.rstudio.com/src/contrib/dplyr_0.8.5.tar.gz'
Content type 'application/x-gzip' length 1378766 bytes (1.3 MB)
==================================================
downloaded 1.3 MB
* installing *source* package ‘dplyr’ ...
** package ‘dplyr’ successfully unpacked and MD5 sums checked
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include -DRCPP_DEFAULT_INCLUDE_CALL=false -DCOMPILING_DPLYR -DRCPP_USING_UTF8_ERROR_STRING -DRCPP_USE_UNWIND_PROTECT -DBOOST_NO_AUTO_PTR -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -\ ^
1 warning and 5 errors generated.
make: *** [RcppExports.o] Error 1
ERROR: compilation failed for package ‘dplyr’
* removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/dplyr’
Warning in install.packages :
installation of package ‘dplyr’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/p5/7cr4ncpx38s_0trbs9966_8w0000gn/T/RtmpHMQzDX/downloaded_packages’
>
Related
I am trying to install the R package brms on my Ubuntu 22.04 LTS computer. My R version is 4.2.2 and I am using RStudio RStudio 2022.07.2 "Spotted Wakerobin".
rstan is installed and I have successfully verified the installation. My stan version is 2.21.0.
When I try installing brms in RStudio this is the output:
> install.packages("brms")
Installing package into ‘/home/iplank/R/x86_64-pc-linux-gnu-library/4.2’
(as ‘lib’ is unspecified)
also installing the dependencies ‘bayesplot’, ‘shinystan’, ‘bridgesampling’, ‘nleqslv’
trying URL 'https://cloud.r-project.org/src/contrib/bayesplot_1.10.0.tar.gz'
Content type 'application/x-gzip' length 4993447 bytes (4.8 MB)
==================================================
downloaded 4.8 MB
trying URL 'https://cloud.r-project.org/src/contrib/shinystan_2.6.0.tar.gz'
Content type 'application/x-gzip' length 2399890 bytes (2.3 MB)
==================================================
downloaded 2.3 MB
trying URL 'https://cloud.r-project.org/src/contrib/bridgesampling_1.1-2.tar.gz'
Content type 'application/x-gzip' length 1679600 bytes (1.6 MB)
==================================================
downloaded 1.6 MB
trying URL 'https://cloud.r-project.org/src/contrib/nleqslv_3.3.3.tar.gz'
Content type 'application/x-gzip' length 84686 bytes (82 KB)
==================================================
downloaded 82 KB
trying URL 'https://cloud.r-project.org/src/contrib/brms_2.18.0.tar.gz'
Content type 'application/x-gzip' length 4486548 bytes (4.3 MB)
==================================================
downloaded 4.3 MB
* installing *source* package ‘bayesplot’ ...
** package ‘bayesplot’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error in element_line(linewidth = 0.3) :
unused argument (linewidth = 0.3)
Error: unable to load R code in package ‘bayesplot’
Execution halted
ERROR: lazy loading failed for package ‘bayesplot’
* removing ‘/home/iplank/R/x86_64-pc-linux-gnu-library/4.2/bayesplot’
Warning in install.packages :
installation of package ‘bayesplot’ had non-zero exit status
* installing *source* package ‘bridgesampling’ ...
** package ‘bridgesampling’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (bridgesampling)
* installing *source* package ‘nleqslv’ ...
** package ‘nleqslv’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/Rcpp/include/" -I"/usr/lib/R/site-library/RcppEigen/include/" -I"/usr/lib/R/site-library/RcppEigen/include/unsupported" -I"/usr/lib/R/site-library/BH/include" -I"/usr/lib/R/site-library/StanHeaders/include/src/" -I"/usr/lib/R/site-library/StanHeaders/include/" -I"/usr/lib/R/site-library/RcppParallel/include/" -I"/home/iplank/R/x86_64-pc-linux-gnu-library/4.2/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/usr/lib/R/site-library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -fpic -g -O2 -ffile-prefix-map=/build/r-base-Faorqz/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c init.c -o init.o
In file included from /usr/lib/R/site-library/RcppEigen/include/Eigen/Core:88,
from /usr/lib/R/site-library/RcppEigen/include/Eigen/Dense:1,
from /usr/lib/R/site-library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13,
from <command-line>:
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name ‘namespace’
628 | namespace Eigen {
| ^~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:17: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘{’ token
628 | namespace Eigen {
| ^
In file included from /usr/lib/R/site-library/RcppEigen/include/Eigen/Dense:1,
from /usr/lib/R/site-library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13,
from <command-line>:
/usr/lib/R/site-library/RcppEigen/include/Eigen/Core:96:10: fatal error: complex: No such file or directory
96 | #include <complex>
| ^~~~~~~~~
compilation terminated.
make: *** [/usr/lib/R/etc/Makeconf:169: init.o] Error 1
ERROR: compilation failed for package ‘nleqslv’
* removing ‘/home/iplank/R/x86_64-pc-linux-gnu-library/4.2/nleqslv’
Warning in install.packages :
installation of package ‘nleqslv’ had non-zero exit status
ERROR: dependency ‘bayesplot’ is not available for package ‘shinystan’
* removing ‘/home/iplank/R/x86_64-pc-linux-gnu-library/4.2/shinystan’
Warning in install.packages :
installation of package ‘shinystan’ had non-zero exit status
ERROR: dependencies ‘bayesplot’, ‘shinystan’, ‘nleqslv’ are not available for package ‘brms’
* removing ‘/home/iplank/R/x86_64-pc-linux-gnu-library/4.2/brms’
Warning in install.packages :
installation of package ‘brms’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpS56F1Q/downloaded_packages’
There seems to be a problem when installing bayesplot but I'm not sure how to solve it.
Does anyone have any suggestions?
Just in case someon encounters the same problem:
I installed devtools to be able to install bayesplot directly from github using:
install_github("stan-dev/bayesplot", dependencies = TRUE, build_vignettes = FALSE)
This only worked for me after installing all the packages that throw compilation errors in R directly and not in RStudio.
After bayesplot was installed, I was able to install brms.
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.