Cannot install roxygen2 on Debian Jessie - r

When I try to install roxygen2 I get:
> sudo Rscript -e 'install.packages("roxygen2", repos="http://mirrors.dotsrc.org/cran/")'
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
trying URL 'http://mirrors.dotsrc.org/cran/src/contrib/roxygen2_5.0.1.tar.gz'
Content type 'text/plain' length 106197 bytes (103 Kb)
opened URL
==================================================
downloaded 103 Kb
* installing *source* package ‘roxygen2’ ...
** package ‘roxygen2’ successfully unpacked and MD5 sums checked
** libs
g++ -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/Rcpp/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o
g++ -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/Rcpp/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c isComplete.cpp -o isComplete.o
g++ -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/Rcpp/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c leadingSpaces.cpp -o leadingSpaces.o
g++ -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/Rcpp/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c parser2.cpp -o parser2.o
parser2.cpp: In function ‘Rcpp::CharacterVector find_includes(std::string)’:
parser2.cpp:165:35: error: too many arguments to function ‘void Rcpp::stop(const string&)’
stop("Failed to open %s", path);
^
In file included from /usr/lib/R/site-library/Rcpp/include/RcppCommon.h:131:0,
from /usr/lib/R/site-library/Rcpp/include/Rcpp.h:27,
from parser2.cpp:1:
/usr/lib/R/site-library/Rcpp/include/Rcpp/exceptions.h:195:17: note: declared here
inline void stop(const std::string& message) {
^
/usr/lib/R/etc/Makeconf:137: recipe for target 'parser2.o' failed
make: *** [parser2.o] Error 1
ERROR: compilation failed for package ‘roxygen2’
* removing ‘/usr/local/lib/R/site-library/roxygen2’
The downloaded source packages are in
‘/tmp/RtmpSn8jzt/downloaded_packages’
Warning message:
In install.packages("roxygen2", repos = "http://mirrors.dotsrc.org/cran/") :
installation of package ‘roxygen2’ had non-zero exit status
I tried several different repos, but result is always the same. Is it a problem with version that got published in repos? What else could I try?

Hadley noticed this problem with other packages and stated on a Github thread that the solution is to use the dev verstion of Rcpp, i.e.
install_github("RcppCore/Rcpp")
So, upgrade Rcpp then fully shutdown all RStudio and R processes, then restart and reinstall roxygen2.

Related

ERROR: compilation failed for package 'kernlab'; appears to fail when running some function 'dcauchy'

I'm getting an error while trying to install kernlab for R. My R version is 3.5.2. My OS is ChromeOS 108.0.5359.58 beta (64-bit), with Debian 10 (buster). Processor is an intel m3-8100Y (64-bit).
The error I'm getting doesn't seem to have been reported when trying to search for either problems with kernlab or dcauchy.c, though if there has been a previous question identical to mine, apologies!
> install.packages("kernlab", type="source")
Installing package into ‘/home/user/R/x86_64-pc-linux-gnu-library/3.5’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/kernlab_0.9-31.tar.gz'
Content type 'application/x-gzip' length 1215549 bytes (1.2 MB)
==================================================
downloaded 1.2 MB
* installing *source* package ‘kernlab’ ...
** package ‘kernlab’ successfully unpacked and MD5 sums checked
** libs
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c brweight.cpp -o brweight.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ctable.cpp -o ctable.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c cweight.cpp -o cweight.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dbreakpt.c -o dbreakpt.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dcauchy.c -o dcauchy.o
dcauchy.c: In function ‘dcauchy’:
dcauchy.c:110:13: error: expected ‘)’ before ‘FCONE’
wa, &inc FCONE);
^~~~~~
)
dcauchy.c:132:67: error: expected ‘)’ before ‘FCONE’
F77_CALL(dsymv)("U", &n, &one, A, &n, s, &inc, &zero, wa, &inc FCONE);
^~~~~~
)
dcauchy.c:156:67: error: expected ‘)’ before ‘FCONE’
F77_CALL(dsymv)("U", &n, &one, A, &n, s, &inc, &zero, wa, &inc FCONE);
^~~~~~
)
make: *** [/usr/lib/R/etc/Makeconf:162: dcauchy.o] Error 1
ERROR: compilation failed for package ‘kernlab’
* removing ‘/home/user/R/x86_64-pc-linux-gnu-library/3.5/kernlab’
The downloaded source packages are in
‘/tmp/RtmpUQr5y3/downloaded_packages’
Warning message:
In install.packages("kernlab", type = "source") :
installation of package ‘kernlab’ had non-zero exit status
I tried searching around for solutions, but nothing seems to have been posted. I would expect kernlab to install properly as it is required for certain parts of the caret package to also work properly, which I am using. Unfortunately, when I run install.packages("kernlab"), I instead get the above error. This includes trying to run R with sudo.
Just in case anyone has this issue in the future, I did manage to get it working. I noticed that I couldn't install kernlab on my Debian WSL on Windows either but it would work in windows Rterm. So one solution is to apparently not use linux.
Once I identified that it seemed to be specifically linux where install.packages("kernlab") failed, I did some googling and saw that kernlab was available on the debian repos.
sudo apt-get install r-cran-kernlab thus did the charm.

sf install on Ubuntu fails - no member named SetAxisMappingStrategy

sf install on Ubuntu 18.04 fails with:
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/gdal -I/usr/include -I'/usr/local/lib/R/site-library/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-J7pprH/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c signed_area.cpp -o signed_area.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/gdal -I/usr/include -I'/usr/local/lib/R/site-library/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-J7pprH/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stars.cpp -o stars.o
stars.cpp: In function ‘void CPL_create(Rcpp::CharacterVector, Rcpp::IntegerVector, Rcpp::NumericVector, Rcpp::CharacterVector, Rcpp::NumericVector, Rcpp::NumericVector)’:
stars.cpp:771:7: error: ‘class OGRSpatialReference’ has no member named ‘SetAxisMappingStrategy’
oSRS.SetAxisMappingStrategy(OAMS_TRADITIONAL_GIS_ORDER);
^~~~~~~~~~~~~~~~~~~~~~
stars.cpp:771:30: error: ‘OAMS_TRADITIONAL_GIS_ORDER’ was not declared in this scope
oSRS.SetAxisMappingStrategy(OAMS_TRADITIONAL_GIS_ORDER);
^~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/R/etc/Makeconf:177: recipe for target 'stars.o' failed
make: *** [stars.o] Error 1
ERROR: compilation failed for package ‘sf’
* removing ‘/usr/local/lib/R/site-library/sf’
The downloaded source packages are in
‘/tmp/RtmpDZ9Qvj/downloaded_packages’
Warning message:
In install.packages("sf") :
installation of package ‘sf’ had non-zero exit status
Any suggestions appreciated.
Solved by installing the development versions (sf_1.0-7) from GitHub with:
library(devtools)
install_github("r-spatial/sf")

fatal error: zlib.h: No such file or directory when install R package

When I trying to install package Rsamtools, I encountered this error:
> BiocManager::install('Rsamtools')
Bioconductor version 3.12 (BiocManager 1.30.12), ?BiocManager::install for help
'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details
replacement repositories:
CRAN: https://cloud.r-project.org
Bioconductor version 3.12 (BiocManager 1.30.12), R 4.0.4 (2021-02-15)
Installing package(s) 'Rsamtools'
also installing the dependency ‘Rhtslib’
trying URL 'https://bioconductor.org/packages/3.12/bioc/src/contrib/Rhtslib_1.22.0.tar.gz'
Content type 'application/x-gzip' length 1472143 bytes (1.4 MB)
==================================================
downloaded 1.4 MB
trying URL 'https://bioconductor.org/packages/3.12/bioc/src/contrib/Rsamtools_2.6.0.tar.gz'
Content type 'application/x-gzip' length 2906572 bytes (2.8 MB)
==================================================
downloaded 2.8 MB
* installing *source* package ‘Rhtslib’ ...
** using non-staged installation via StagedInstall field
** libs
cd "htslib-1.7" && make -f "/usr/lib/R/etc/Makeconf" -f "Makefile.Rhtslib"
make[1]: Entering directory '/tmp/RtmphSYt1J/R.INSTALLc46363cf91e5/Rhtslib/src/htslib-1.7'
Makefile.Rhtslib:128: warning: overriding recipe for target '.c.o'
/usr/lib/R/etc/Makeconf:172: warning: ignoring old recipe for target '.c.o'
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-fhxXXR/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o kfunc.o kfunc.c
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-fhxXXR/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o knetfile.o knetfile.c
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-fhxXXR/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o kstring.o kstring.c
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-fhxXXR/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o bcf_sr_sort.o bcf_sr_sort.c
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-fhxXXR/r-base-4.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o bgzf.o bgzf.c
In file included from bgzf.c:39:
htslib/bgzf.h:35:10: fatal error: zlib.h: No such file or directory
#include <zlib.h>
^~~~~~~~
compilation terminated.
make[1]: *** [Makefile.Rhtslib:128: bgzf.o] Error 1
make[1]: Leaving directory '/tmp/RtmphSYt1J/R.INSTALLc46363cf91e5/Rhtslib/src/htslib-1.7'
make: *** [Makevars.common:24: htslib] Error 2
ERROR: compilation failed for package ‘Rhtslib’
* removing ‘/usr/local/lib/R/site-library/Rhtslib’
ERROR: dependency ‘Rhtslib’ is not available for package ‘Rsamtools’
* removing ‘/usr/local/lib/R/site-library/Rsamtools’
The downloaded source packages are in
‘/tmp/Rtmpq79sQU/downloaded_packages’
Warning messages:
1: In install.packages(...) :
installation of package ‘Rhtslib’ had non-zero exit status
2: In install.packages(...) :
installation of package ‘Rsamtools’ had non-zero exit status
From what I found, the library zlib1g-dev already installed in my computer does not create zlib.h at the folder R running the compile. However, all the solution I found was for compile on bash command, not on R and I don't know how to solve this solution. Can anyone help me, please.

"pcadapt", "installation of package ‘bigutilsr’ had non-zero exit status"

I'm trying to install the pcadapt in RStudio using
> remotes::install_github("bcm-uga/pcadapt")
But it gives me the error installation of package ‘bigutilsr’ had non-zero exit status
Downloading GitHub repo bcm-uga/pcadapt#master
Installing 1 packages: bigutilsr
Installing package into ‘/home/jenifer/R/x86_64-pc-linux-gnu-library/3.5’
(as ‘lib’ is unspecified)
probando la URL 'https://cloud.r-project.org/src/contrib/bigutilsr_0.3.2.tar.gz'
Content type 'application/x-gzip' length 915116 bytes (893 KB)
==================================================
downloaded 893 KB
* installing *source* package ‘bigutilsr’ ...
** package ‘bigutilsr’ successfully unpacked and MD5 sums checked
** libs
g++ -I"/usr/share/R/include" -DNDEBUG -I"/home/jenifer/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o
g++ -I"/usr/share/R/include" -DNDEBUG -I"/home/jenifer/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ogk.cpp -o ogk.o
g++ -I"/usr/share/R/include" -DNDEBUG -I"/home/jenifer/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rollmean.cpp -o rollmean.o
g++ -I"/usr/share/R/include" -DNDEBUG -I"/home/jenifer/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rowSumsSq.cpp -o rowSumsSq.o
g++ -shared -L/usr/lib/R/lib -Wl,-z,relro -o bigutilsr.so RcppExports.o ogk.o rollmean.o rowSumsSq.o -L/usr/lib/R/lib -lR
installing to /home/jenifer/R/x86_64-pc-linux-gnu-library/3.5/bigutilsr/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: S3 methods ‘eigs.matrix’, ‘eigs.dgeMatrix’, ‘eigs.dgCMatrix’, ‘eigs.dgRMatrix’, ‘eigs.dsyMatrix’, ‘eigs.dsCMatrix’, ‘eigs.dsRMatrix’, ‘eigs.function’, ‘eigs_sym.matrix’, ‘eigs_sym.dgeMatrix’, ‘eigs_sym.dgCMatrix’, ‘eigs_sym.dgRMatrix’, ‘eigs_sym.function’, ‘svds.matrix’, ‘svds.dgeMatrix’, ‘svds.dgCMatrix’, ‘svds.dgRMatrix’, ‘svds.dsyMatrix’, ‘svds.dsCMatrix’, ‘svds.dsRMatrix’, ‘svds.function’ were declared in NAMESPACE but not found
Error in library.dynam(lib, package, package.lib) :
shared object ‘RSpectra.so’ not found
ERROR: lazy loading failed for package ‘bigutilsr’
* removing ‘/home/jenifer/R/x86_64-pc-linux-gnu-library/3.5/bigutilsr’
Error: Failed to install 'pcadapt' from GitHub:
(convertido del aviso) installation of package ‘bigutilsr’ had non-zero exit status
>
I've been searching on google and it seems that if gcc isn't set up correctly, then R tries to compile the packages and it fails (https://community.rstudio.com/t/cannot-install-any-packages-non-zero-exit-status/53310), but I don't know if this is the case, and if it is, I don't know how to solve it.
gcc --version
gcc (Debian 8.3.0-6) 8.3.0
I'm also having similar issues while trying to install adegenet, hierfstat, pegas, poppr and other packages but I will put a post about this with moor details somewhere else ins stackoverflow just to keep it simple and to not give place to confussion with the code.
If somebody can help me, I will appreciate it very much
Cheers

Cant install dev-tools package in R

I cant seem to install devtools package in R. I've tried the option with dependencies=True but that fails as well.
I've also tried installing 'ps' as per the error logs below, that seems to install fine. But when I try and install devtools after installing 'ps' it gives me the same error.
Can anyone advise as to how I can fix this?
> install.packages('devtools')
Installing package into ‘/home/user/pq-tool/packrat/lib/x86_64-pc-linux-gnu/3.4.2’
(as ‘lib’ is unspecified)
also installing the dependencies ‘processx’, ‘xopen’, ‘callr’, ‘pkgbuild’, ‘pkgload’, ‘rcmdcheck’
trying URL 'https://cran.rstudio.com/src/contrib/processx_3.2.0.tar.gz'
Content type 'application/x-gzip' length 97959 bytes (95 KB)
==================================================
downloaded 95 KB
trying URL 'https://cran.rstudio.com/src/contrib/xopen_1.0.0.tar.gz'
Content type 'application/x-gzip' length 11221 bytes (10 KB)
==================================================
downloaded 10 KB
trying URL 'https://cran.rstudio.com/src/contrib/callr_3.0.0.tar.gz'
Content type 'application/x-gzip' length 36365 bytes (35 KB)
==================================================
downloaded 35 KB
trying URL 'https://cran.rstudio.com/src/contrib/pkgbuild_1.0.2.tar.gz'
Content type 'application/x-gzip' length 25264 bytes (24 KB)
==================================================
downloaded 24 KB
trying URL 'https://cran.rstudio.com/src/contrib/pkgload_1.0.2.tar.gz'
Content type 'application/x-gzip' length 55605 bytes (54 KB)
==================================================
downloaded 54 KB
trying URL 'https://cran.rstudio.com/src/contrib/rcmdcheck_1.3.2.tar.gz'
Content type 'application/x-gzip' length 1408582 bytes (1.3 MB)
==================================================
downloaded 1.3 MB
trying URL 'https://cran.rstudio.com/src/contrib/devtools_2.0.1.tar.gz'
Content type 'application/x-gzip' length 388953 bytes (379 KB)
==================================================
downloaded 379 KB
* installing *source* package ‘processx’ ...
** package ‘processx’ successfully unpacked and MD5 sums checked
** libs
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall tools/px.c -o tools/px
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g supervisor/supervisor.c supervisor/utils.c \
-o supervisor/supervisor
gcc -I/usr/local/lib/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o
gcc -I/usr/local/lib/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c poll.c -o poll.o
gcc -I/usr/local/lib/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c processx-connection.c -o processx-connection.o
gcc -I/usr/local/lib/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c processx-vector.c -o processx-vector.o
gcc -I/usr/local/lib/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c create-time.c -o create-time.o
gcc -I/usr/local/lib/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c unix/childlist.c -o unix/childlist.o
gcc -I/usr/local/lib/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c unix/connection.c -o unix/connection.o
gcc -I/usr/local/lib/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c unix/processx.c -o unix/processx.o
gcc -I/usr/local/lib/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c unix/sigchld.c -o unix/sigchld.o
gcc -I/usr/local/lib/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c unix/utils.c -o unix/utils.o
gcc -I/usr/local/lib/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c unix/named_pipe.c -o unix/named_pipe.o
gcc -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o processx.so init.o poll.o processx-connection.o processx-vector.o create-time.o unix/childlist.o unix/connection.o unix/processx.o unix/sigchld.o unix/utils.o unix/named_pipe.o -L/usr/local/lib/R/lib -lR
installing via 'install.libs.R' to /home/user/pq-tool/packrat/lib/x86_64-pc-linux-gnu/3.4.2/processx
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Error: package or namespace load failed for ‘processx’:
.onLoad failed in loadNamespace() for 'processx', details:
call: loadNamespace(name)
error: there is no package called ‘ps’
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/user/pq-tool/packrat/lib/x86_64-pc-linux-gnu/3.4.2/processx’
Warning in install.packages :
installation of package ‘processx’ had non-zero exit status
ERROR: dependency ‘processx’ is not available for package ‘xopen’
* removing ‘/home/user/pq-tool/packrat/lib/x86_64-pc-linux-gnu/3.4.2/xopen’
Warning in install.packages :
installation of package ‘xopen’ had non-zero exit status
ERROR: dependency ‘processx’ is not available for package ‘callr’
* removing ‘/home/user/pq-tool/packrat/lib/x86_64-pc-linux-gnu/3.4.2/callr’
Warning in install.packages :
installation of package ‘callr’ had non-zero exit status
ERROR: dependency ‘callr’ is not available for package ‘pkgbuild’
* removing ‘/home/user/pq-tool/packrat/lib/x86_64-pc-linux-gnu/3.4.2/pkgbuild’
Warning in install.packages :
installation of package ‘pkgbuild’ had non-zero exit status
ERROR: dependency ‘pkgbuild’ is not available for package ‘pkgload’
* removing ‘/home/user/pq-tool/packrat/lib/x86_64-pc-linux-gnu/3.4.2/pkgload’
Warning in install.packages :
installation of package ‘pkgload’ had non-zero exit status
ERROR: dependencies ‘callr’, ‘pkgbuild’, ‘xopen’ are not available for package ‘rcmdcheck’
* removing ‘/home/user/pq-tool/packrat/lib/x86_64-pc-linux-gnu/3.4.2/rcmdcheck’
Warning in install.packages :
installation of package ‘rcmdcheck’ had non-zero exit status
ERROR: dependencies ‘callr’, ‘pkgbuild’, ‘pkgload’, ‘rcmdcheck’ are not available for package ‘devtools’
* removing ‘/home/user/pq-tool/packrat/lib/x86_64-pc-linux-gnu/3.4.2/devtools’
Warning in install.packages :
installation of package ‘devtools’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpvzJcng/downloaded_packages’
try this
Sys.setenv(R_INSTALL_STAGED = FALSE)
install.packages("devtools", repos="http://cran.r-project.org", clean=TRUE)

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