I am a bit new to RStudio, I had the previous version but I uninstalled it to install the latest version but when I try to install any package (I try to install tidyverse as an example) it does not install and what appears is the following:
Installing package into ‘/home/edgardo/R/x86_64-pc-linux-gnu-library/4.1’
(as ‘lib’ is unspecified)
also installing the dependencies ‘broom’, ‘haven’, ‘modelr’, ‘readr’, ‘feather’, ‘testthat’
trying URL 'https://cloud.r-project.org/src/contrib/broom_0.7.9.tar.gz'
Content type 'application/x-gzip' length 631606 bytes (616 KB)
==================================================
downloaded 616 KB
trying URL 'https://cloud.r-project.org/src/contrib/haven_2.4.3.tar.gz'
Content type 'application/x-gzip' length 296805 bytes (289 KB)
==================================================
downloaded 289 KB
trying URL 'https://cloud.r-project.org/src/contrib/modelr_0.1.8.tar.gz'
Content type 'application/x-gzip' length 121333 bytes (118 KB)
==================================================
downloaded 118 KB
trying URL 'https://cloud.r-project.org/src/contrib/readr_2.0.1.tar.gz'
Content type 'application/x-gzip' length 517944 bytes (505 KB)
==================================================
downloaded 505 KB
trying URL 'https://cloud.r-project.org/src/contrib/feather_0.3.5.tar.gz'
Content type 'application/x-gzip' length 73812 bytes (72 KB)
==================================================
downloaded 72 KB
trying URL 'https://cloud.r-project.org/src/contrib/testthat_3.0.4.tar.gz'
Content type 'application/x-gzip' length 688142 bytes (672 KB)
==================================================
downloaded 672 KB
trying URL 'https://cloud.r-project.org/src/contrib/tidyverse_1.3.1.tar.gz'
Content type 'application/x-gzip' length 702779 bytes (686 KB)
==================================================
downloaded 686 KB
* installing *source* package ‘broom’ ...
** package ‘broom’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (broom)
ERROR: failed to lock directory ‘/home/edgardo/R/x86_64-pc-linux-gnu-library/4.1’ for modifying
Try removing ‘/home/edgardo/R/x86_64-pc-linux-gnu-library/4.1/00LOCK-readr’
Warning in install.packages :
installation of package ‘readr’ had non-zero exit status
* installing *source* package ‘feather’ ...
** package ‘feather’ successfully unpacked and MD5 sums checked
** using staged installation
Platform is little endian. Good.
** libs
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I. -I'/home/edgardo/R/x86_64-pc-linux-gnu-library/4.1/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-QwogzP/r-base-4.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I. -I'/home/edgardo/R/x86_64-pc-linux-gnu-library/4.1/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-QwogzP/r-base-4.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c feather-read.cpp -o feather-read.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I. -I'/home/edgardo/R/x86_64-pc-linux-gnu-library/4.1/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-QwogzP/r-base-4.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c feather-types.cpp -o feather-types.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I. -I'/home/edgardo/R/x86_64-pc-linux-gnu-library/4.1/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-QwogzP/r-base-4.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c feather-write.cpp -o feather-write.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I. -I'/home/edgardo/R/x86_64-pc-linux-gnu-library/4.1/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-QwogzP/r-base-4.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c feather/buffer.cc -o feather/buffer.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I. -I'/home/edgardo/R/x86_64-pc-linux-gnu-library/4.1/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-QwogzP/r-base-4.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c feather/feather-c.cc -o feather/feather-c.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I. -I'/home/edgardo/R/x86_64-pc-linux-gnu-library/4.1/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-QwogzP/r-base-4.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c feather/io.cc -o feather/io.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I. -I'/home/edgardo/R/x86_64-pc-linux-gnu-library/4.1/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-QwogzP/r-base-4.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c feather/metadata.cc -o feather/metadata.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I. -I'/home/edgardo/R/x86_64-pc-linux-gnu-library/4.1/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-QwogzP/r-base-4.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c feather/reader.cc -o feather/reader.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I. -I'/home/edgardo/R/x86_64-pc-linux-gnu-library/4.1/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-QwogzP/r-base-4.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c feather/status.cc -o feather/status.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I. -I'/home/edgardo/R/x86_64-pc-linux-gnu-library/4.1/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-QwogzP/r-base-4.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c feather/types.cc -o feather/types.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I. -I'/home/edgardo/R/x86_64-pc-linux-gnu-library/4.1/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-QwogzP/r-base-4.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c feather/writer.cc -o feather/writer.o
ar rcs libfeather.a feather/buffer.o feather/feather-c.o feather/io.o feather/metadata.o feather/reader.o feather/status.o feather/types.o feather/writer.o
g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o feather.so RcppExports.o feather-read.o feather-types.o feather-write.o -L. -lfeather -L/usr/lib/R/lib -lR
installing to /home/edgardo/R/x86_64-pc-linux-gnu-library/4.1/00LOCK-feather/00new/feather/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 (feather)
* installing *source* package ‘testthat’ ...
** package ‘testthat’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-QwogzP/r-base-4.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-QwogzP/r-base-4.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c reassign.c -o reassign.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-QwogzP/r-base-4.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c test-catch.cpp -o test-catch.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-QwogzP/r-base-4.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c test-example.cpp -o test-example.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-QwogzP/r-base-4.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c test-runner.cpp -o test-runner.o
g++ -std=gnu++14 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o testthat.so init.o reassign.o test-catch.o test-example.o test-runner.o -L/usr/lib/R/lib -lR
installing to /home/edgardo/R/x86_64-pc-linux-gnu-library/4.1/00LOCK-testthat/00new/testthat/libs
** R
** inst
** byte-compile and prepare package for lazy loading
This repeats for an indefinite period of time which I have to stop it but it never installs the package, I am on Ubuntu 20.04 operating system.
Related
Dear Stackflow Community,
I'm trying to install the R "curl" package from source using a specialized R CMD INSTALL script on Debian 11 x86_64 machine. The source package downloads and build fine but when the linker tries to link libcurl to the source package, the linker can't seem to find my libcurl package and the build fails. I've read others have had similar issues with not being able to local the libcurl package and have followed all prior suggested solutions (including ensuring I have the appropriate libcurl developement files downloaded from Debian distribution as noted in the resultant error message). R itself is installed and runs fine and can install packages from CRAN, but I need a source build for a special project.
Any suggestions? Thanks!
Here is the output of my attempt to build libcurl from source:
It's arguably tricky, but it helps to step back:
There is an CRAN package called curl. If you look at its CRAN page you will notice the hint SystemRequirements: libcurl: libcurl-devel (rpm) or libcurl4-openssl-dev (deb)
Because on Unix / Linux system there is an (extremely popular, widely used) library called curl and on Debian you get it as a run-time via the libcurl* package (with different ssl implementations).
And to build against the (C language) curl library (as opposed to the R package) you need (as the package says) the development package libcurl4-openssl-dev
Because this is hard, "we" (as Debian developers) also try to give you binary Debian package of the key CRAN packages. I think we up to a bit over 1000 of thousand of those (out of 18.7 thousand CRAN packages). So do
sudo apt install r-cran-curl
and you will get a pre-compiled curl package for CRAN along with whatever run-time dependencies your system does not (yet) have (R, the libcurl* I mentioned etc)
Edit Full log in a Docker session using Debian testing (as that is how I build Rocker's r-base image that is also the officual r-base):
edd#rob:~$ docker run --rm -ti rocker/r-base bash
root#31cda2e7378e:/# apt update -qq
70 packages can be upgraded. Run 'apt list --upgradable' to see them.
root#31cda2e7378e:/# apt install libcurl4-openssl-dev
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
Suggested packages:
libcurl4-doc libidn11-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev libssl-dev
The following NEW packages will be installed:
libcurl4-openssl-dev
0 upgraded, 1 newly installed, 0 to remove and 70 not upgraded.
Need to get 463 kB of archives.
After this operation, 1,732 kB of additional disk space will be used.
Get:1 http://deb.debian.org/debian testing/main amd64 libcurl4-openssl-dev amd64 7.85.0-1 [463 kB]
Fetched 463 kB in 0s (9,482 kB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package libcurl4-openssl-dev:amd64.
(Reading database ... 18520 files and directories currently installed.)
Preparing to unpack .../libcurl4-openssl-dev_7.85.0-1_amd64.deb ...
Unpacking libcurl4-openssl-dev:amd64 (7.85.0-1) ...
Setting up libcurl4-openssl-dev:amd64 (7.85.0-1) ...
root#31cda2e7378e:/# root#31cda2e7378e:/# Rscript -e 'install.packages("curl")'
Installing package into ‘/usr/local/lib/R/site-library’ (as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/curl_4.3.3.tar.gz' Content type 'application/x-gzip' length 670416 bytes (654 KB)
================================================== downloaded 654 KB
* installing *source* package ‘curl’ ...
** package ‘curl’ successfully unpacked and MD5 sums checked ** using staged installation
Found pkg-config cflags and libs! Using PKG_CFLAGS=-I/usr/include/x86_64-linux-gnu
Using PKG_LIBS=-lcurl
** libs
rm -f curl.so callbacks.o curl.o download.o escape.o fetch.o form.o getdate.o handle.o ieproxy.o init.o interrupt.o multi.o nslookup.o reflist.o split.o ssl.o typechecking.o utils.o version.o winidn.o writer.o
gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-J8F88F/r-base-4.2.1=. -fstack-protector-strong -Wform
at -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c callbacks.c -o callbacks.o
gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-J8F88F/r-base-4.2.1=. -fstack-protector-strong -Wform
at -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c curl.c -o curl.o
gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-J8F88F/r-base-4.2.1=. -fstack-protector-strong -Wform
at -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c download.c -o download.o
gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-J8F88F/r-base-4.2.1=. -fstack-protector-strong -Wform
at -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c escape.c -o escape.o
gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-J8F88F/r-base-4.2.1=. -fstack-protector-strong -Wform
at -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fetch.c -o fetch.o
gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-J8F88F/r-base-4.2.1=. -fstack-protector-strong -Wform
at -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c form.c -o form.o
gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-J8F88F/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c getdate.c -o getdate.o
gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-J8F88F/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c handle.c -o handle.o
gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-J8F88F/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ieproxy.c -o ieproxy.o
gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-J8F88F/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c init.c -o init.o
gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-J8F88F/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c interrupt.c -o interrupt.o
gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-J8F88F/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c multi.c -o multi.o
gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-J8F88F/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c nslookup.c -o nslookup.o
gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-J8F88F/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c reflist.c -o reflist.o
gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-J8F88F/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c split.c -o split.o
gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-J8F88F/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ssl.c -o ssl.o
gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-J8F88F/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c typechecking.c -o typechecking.o
gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-J8F88F/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c utils.c -o utils.o
gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-J8F88F/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c version.c -o version.o
gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-J8F88F/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c winidn.c -o winidn.o
gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-J8F88F/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c writer.c -o writer.o
gcc -shared -L/usr/lib/R/lib -Wl,-z,relro -o curl.so callbacks.o curl.o download.o escape.o fetch.o form.o getdate.o handle.o ieproxy.o init.o interrupt.o multi.o nslookup.o reflist.o split.o ssl.o typechecking.o utils.o version.o winidn.o writer.o -lcurl -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/00LOCK-curl/00new/curl/libs
** 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
** 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 (curl)
The downloaded source packages are in
‘/tmp/RtmpORcfhX/downloaded_packages’
root#31cda2e7378e:/#
I understand you are compiling R packages to WASM using webR. The R curl package is a wrapper for the libcurl C library. So in order to build a wasm version of this package, you probably first need to figure out how to get a wasm port of libcurl.
This won't be an easy task because WASM doesn't have IO capabilities. I think the only networking that a wasm module can do by interacting with the JavaScript code that it was loaded from, and that limits you to fetch/websockets. I don't see right now how libcurl could be ported to wasm, but maybe I am wrong.
But in short: I'm afraid it is impossible currently to compile the curl package, or other R packages requiring advanced networking, in webR right now. The webR port itself is patched to use XHR (ajax requests) for download.file() in order to support install.packages() and so on, but this is only a small subset of the capabilities of libcurl.
I have recently upgraded the institute workstations to Debian 10. Since the R version got bumped to 3.5.2 (from 3.3) I have removed my ~/R directory and was just going to install the new packages.
This is the R version that I have:
R version 3.5.2 (2018-12-20) -- "Eggshell Igloo"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
Doing install.packages('jsonlite') got me asked whether I want to create a new user library and the installation went through.
When trying to install ggplot2, it fails on the package vctrs:
begin installing package vctrs
* installing *source* package 'purrr' ...
** package 'purrr' successfully unpacked and MD5 sums checked
** libs
make[1]: Entering directory '/tmp/RtmpCnH2Uv/R.INSTALL291734261852/purrr/src'
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 backports.c -o backports.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 coerce.c -o coerce.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 conditions.c -o conditions.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 flatten.c -o flatten.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 init.c -o init.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 map.c -o map.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 pluck.c -o pluck.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 transpose.c -o transpose.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 utils.c -o utils.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-z,relro -o purrr.so backports.o coerce.o conditions.o flatten.o init.o map.o pluck.o transpose.o utils.o -L/usr/lib/R/lib -lR
make[1]: Leaving directory '/tmp/RtmpCnH2Uv/R.INSTALL291734261852/purrr/src'
installing to /home/ueding/R/x86_64-pc-linux-gnu-library/3.5/purrr/libs
** R
** 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
* DONE (purrr)
make: *** [Makefile:97: vctrs.ts] Error 1
* installing *source* package 'Rcpp' ...
* DONE (BH)
make: Target 'all' not remade because of errors.
* installing *source* package 'vctrs' ...
** package 'vctrs' successfully unpacked and MD5 sums checked
** libs
make[1]: Entering directory '/tmp/Rtmp1l6SSj/R.INSTALL294b78e8c200/vctrs/src'
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 arg-counter.c -o arg-counter.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 arg.c -o arg.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 bind.c -o bind.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 c.c -o c.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 cast.c -o cast.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 compare.c -o compare.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 conditions.c -o conditions.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 dictionary.c -o dictionary.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 equal.c -o equal.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 fields.c -o fields.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 growable.c -o growable.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 hash.c -o hash.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 init.c -o init.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 names.c -o names.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 proxy.c -o proxy.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 size-common.c -o size-common.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 size.c -o size.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 slice-array.c -o slice-array.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 slice-assign.c -o slice-assign.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 slice.c -o slice.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 type-data-frame.c -o type-data-frame.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 type-info.c -o type-info.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 type.c -o type.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 type2-dispatch.c -o type2-dispatch.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 type2.c -o type2.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 unspecified.c -o unspecified.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 utils-dispatch.c -o utils-dispatch.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 utils.c -o utils.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-z,relro -o vctrs.so arg-counter.o arg.o bind.o c.o cast.o compare.o conditions.o dictionary.o equal.o fields.o growable.o hash.o init.o names.o proxy.o size-common.o size.o slice-array.o slice-assign.o slice.o type-data-frame.o type-info.o type.o type2-dispatch.o type2.o unspecified.o utils-dispatch.o utils.o -L/usr/lib/R/lib -lR
make[1]: Leaving directory '/tmp/Rtmp1l6SSj/R.INSTALL294b78e8c200/vctrs/src'
installing to /home/ueding/R/x86_64-pc-linux-gnu-library/3.5/vctrs/libs
** R
** 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
Error: package or namespace load failed for 'vctrs':
.onLoad failed in loadNamespace() for 'vctrs', details:
call: loadNamespace(name)
error: there is no package called 'backports'
Error: loading failed
Execution halted
ERROR: loading failed
* removing '/home/ueding/R/x86_64-pc-linux-gnu-library/3.5/vctrs'
cat: pillar.out: No such file or directory
cat: tibble.out: No such file or directory
cat: dplyr.out: No such file or directory
The downloaded source packages are in
'/tmp/RtmpPpOmW2/make_packages'
Warning message:
In install.packages("dplyr") : installation of one or more packages failed,
probably 'vctrs', 'pillar', 'tibble', 'dplyr'
Installing backports manually works well:
trying URL 'https://cloud.r-project.org/src/contrib/backports_1.1.4.tar.gz'
Content type 'application/x-gzip' length 13859 bytes (13 KB)
==================================================
downloaded 13 KB
* installing *source* package 'backports' ...
** package 'backports' successfully unpacked and MD5 sums checked
** libs
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 dotsElt.c -o dotsElt.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 dotsLength.c -o dotsLength.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 init.c -o init.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-z,relro -o backports.so dotsElt.o dotsLength.o init.o -L/usr/lib/R/lib -lR
installing to /home/ueding/R/x86_64-pc-linux-gnu-library/3.5/backports/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (backports)
The downloaded source packages are in
'/tmp/Rtmpg7Vaw9/downloaded_packages'
Then trying to install dplyr again failes with a similar error message:
Error: package or namespace load failed for 'vctrs':
.onLoad failed in loadNamespace() for 'vctrs', details:
call: loadNamespace(name)
error: there is no package called 'backports'
Error: loading failed
Execution halted
ERROR: loading failed
* removing '/home/ueding/R/x86_64-pc-linux-gnu-library/3.5/vctrs'
I do not really see what I could do fix that. How can I get all these packages installed?
The problem was that although the environment variable R_LIBS_USER was set the .libPaths() did not contain it. A call to .libPath('nonexistant/path') was in my ~/.Rprofile such that neither user library ended up in my search path. Installing packages into a directory which is not in the search path will lead to such errors.
I am trying to install the tidyverse package, during installation package "callr" returned an error, so i tried to diagnose the issue by seprately installing it,
While doing so, its dependency "processx" returned an installation error. I tried searching online for the error but without no avail.
Here is the installation log.
>install.packages("callr")
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
also installing the dependency ‘processx’
trying URL 'https://cloud.r-project.org/src/contrib/processx_3.2.1.tar.gz'
Content type 'application/x-gzip' length 101057 bytes (98 KB)
==================================================
downloaded 98 KB
trying URL 'https://cloud.r-project.org/src/contrib/callr_3.1.1.tar.gz'
Content type 'application/x-gzip' length 41273 bytes (40 KB)
==================================================
downloaded 40 KB
* installing *source* package ‘processx’ ...
** package ‘processx’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-QoNLjt/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall tools/px.c -o tools/px
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-QoNLjt/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g supervisor/supervisor.c supervisor/utils.c \
-o supervisor/supervisor
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-QoNLjt/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-QoNLjt/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c poll.c -o poll.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-QoNLjt/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c processx-connection.c -o processx-connection.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-QoNLjt/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c processx-vector.c -o processx-vector.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-QoNLjt/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c create-time.c -o create-time.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-QoNLjt/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c base64.c -o base64.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-QoNLjt/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c unix/childlist.c -o unix/childlist.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-QoNLjt/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c unix/connection.c -o unix/connection.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-QoNLjt/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c unix/processx.c -o unix/processx.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-QoNLjt/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c unix/sigchld.c -o unix/sigchld.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-QoNLjt/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c unix/utils.c -o unix/utils.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-QoNLjt/r-base-3.5.2=. -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 -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-z,relro -o processx.so init.o poll.o processx-connection.o processx-vector.o create-time.o base64.o unix/childlist.o unix/connection.o unix/processx.o unix/sigchld.o unix/utils.o unix/named_pipe.o -L/usr/lib/R/lib -lR
installing via 'install.libs.R' to /usr/local/lib/R/site-library/processx
** R
** inst
** byte-compile and prepare 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: ps::ps_handle()
error: Unknown errorfs_error0NA
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/usr/local/lib/R/site-library/processx’
ERROR: dependency ‘processx’ is not available for package ‘callr’
* removing ‘/usr/local/lib/R/site-library/callr’
The downloaded source packages are in
‘/tmp/RtmpcOOSxJ/downloaded_packages’
Warning messages:
1: In install.packages("callr") :
installation of package ‘processx’ had non-zero exit status
2: In install.packages("callr") :
installation of package ‘callr’ had non-zero exit status
>
I dont know if this is the right place to post this, but if you can help me, i would be very grateful.
Thank you in advance.
Also here are my info:
sessionInfo()
R version 3.5.2 (2018-12-20)
Platform: arm-unknown-linux-gnueabihf (32-bit)
Running under: Debian GNU/Linux buster/sid
Matrix products: default
BLAS: /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3.8.0
LAPACK: /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3.8.0
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
[4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_3.5.2 tools_3.5.2 ps_1.3.0
I am sorry, and thank you for your valuable time.
The problem exists because i think the way my system is installed, no process can acess any files in /proc.
And as to why, took me some tinkering to figure that by myself (not very good with systems).
here is a link to the relevant issue
Anyways, there does not seem to be any problem with processx, so i can close this thread, i suppose, and once again thank you for your valuable time.
I've been trying various suggestions on the many threads discussing how to install rgdal onto Ubuntu 16.04, and am still having trouble.
Here's where I've gotten to, after many false attempts. I tried the answer here (trouble in installing rgdal on ubuntu 16.04):
sudo add-apt-repository -y ppa:ubuntugis/ubuntugis-unstable
sudo apt update
sudo apt install gdal-bin python-gdal python3-gdal libgdal1-dev
This mostly worked, except that for libgdal1-dev, my package manager says the available version is 1.11.3, and that seemed to be giving me difficulties (not sure I can replicate at this stage), so I used Synaptic to uninstall that package and to install libgdal-dev instead, which had been flagged by Synaptic.
So at this point, according to Synaptic, when I do a search for "gdal", the installed files that show up are gdal-bin, gdal-data, libgdal-dev, libgdal20, python-gdal, and python3-gdal.
At this point, when I open R and run install.packages("rgdal"), this is what I get back:
Installing package into ‘/home/[username]/R/x86_64-pc-linux-gnu-library/3.4’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/rgdal_1.3-4.tar.gz'
Content type 'application/x-gzip' length 1664774 bytes (1.6 MB)
==================================================
downloaded 1.6 MB
* installing *source* package ‘rgdal’ ...
** package ‘rgdal’ successfully unpacked and MD5 sums checked
configure: R_HOME: /usr/lib/R
configure: CC: gcc -std=gnu99
configure: CXX: g++
configure: C++11 support available
configure: rgdal: 1.3-4
checking for /usr/bin/svnversion... no
configure: svn revision: 766
checking for gdal-config... /usr/bin/gdal-config
checking gdal-config usability... yes
configure: GDAL: 2.2.2
checking GDAL version >= 1.11.4... yes
checking gdal: linking with --libs only... yes
checking GDAL: /usr/share/gdal/2.2/pcs.csv readable... yes
configure: pkg-config proj exists, will use it
configure: PROJ version: 4.9.2
checking proj_api.h presence and usability... yes
checking PROJ version >= 4.8.0... yes
checking projects.h presence and usability... yes
checking PROJ.4: epsg found and readable... yes
checking PROJ.4: conus found and readable... yes
configure: Package CPP flags: -I/usr/include/gdal
configure: Package LIBS: -L/usr/lib -lgdal -lproj
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I/usr/include/gdal -I"/home/[username]/R/x86_64-pc-linux-gnu-library/3.4/sp/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c OGR_write.cpp -o OGR_write.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I/usr/include/gdal -I"/home/[username]/R/x86_64-pc-linux-gnu-library/3.4/sp/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gdal-bindings.cpp -o gdal-bindings.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include/gdal -I"/home/[username]/R/x86_64-pc-linux-gnu-library/3.4/sp/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 -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include/gdal -I"/home/[username]/R/x86_64-pc-linux-gnu-library/3.4/sp/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c inverser.c -o inverser.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include/gdal -I"/home/[username]/R/x86_64-pc-linux-gnu-library/3.4/sp/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c local_stubs.c -o local_stubs.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I/usr/include/gdal -I"/home/[username]/R/x86_64-pc-linux-gnu-library/3.4/sp/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ogr_geom.cpp -o ogr_geom.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include/gdal -I"/home/[username]/R/x86_64-pc-linux-gnu-library/3.4/sp/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ogr_polygons.c -o ogr_polygons.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I/usr/include/gdal -I"/home/[username]/R/x86_64-pc-linux-gnu-library/3.4/sp/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ogr_proj.cpp -o ogr_proj.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I/usr/include/gdal -I"/home/[username]/R/x86_64-pc-linux-gnu-library/3.4/sp/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ogrdrivers.cpp -o ogrdrivers.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I/usr/include/gdal -I"/home/[username]/R/x86_64-pc-linux-gnu-library/3.4/sp/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ogrsource.cpp -o ogrsource.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I/usr/include/gdal -I"/home/[username]/R/x86_64-pc-linux-gnu-library/3.4/sp/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c projectit.cpp -o projectit.o
g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o rgdal.so OGR_write.o gdal-bindings.o init.o inverser.o local_stubs.o ogr_geom.o ogr_polygons.o ogr_proj.o ogrdrivers.o ogrsource.o projectit.o -L/usr/lib -lgdal -lproj -L/usr/lib/R/lib -lR
installing to /home/[username]/R/x86_64-pc-linux-gnu-library/3.4/rgdal/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Error: package or namespace load failed for ‘rgdal’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/home/[username]/R/x86_64-pc-linux-gnu-library/3.4/rgdal/libs/rgdal.so':
/home/[username]/R/x86_64-pc-linux-gnu-library/3.4/rgdal/libs/rgdal.so: undefined symbol: _ZN10OGRFeature17GetFieldAsIntegerEi
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/[username]/R/x86_64-pc-linux-gnu-library/3.4/rgdal’
The downloaded source packages are in
‘/tmp/Rtmpuc6qcT/downloaded_packages’
Warning message:
In install.packages("rgdal") :
installation of package ‘rgdal’ had non-zero exit status
I did a search for the error message, and found this question (Cannot install rgdal package in R on RHEL6, unable to load shared object rgdal.so), so tried running
ldconfig -c "echo '/usr/local/lib' >> /etc/ld.so.conf.d/R-dependencies-x86_64.conf"
but it doesn't seem to do anything and I'm still getting the same error message when I try to install rgdal.
Where do I go from here?
I'm on Ubuntu 18.04 but I just got the same problem (exact same error log) the solution for me was to link rgdal to a custom built of gdal. I was lucky enough that for other reason I already had a copy of GDAL (git master) built from source in /usr/local/gdal. So to install rgdal from source all i needed was to:
wget https://cran.r-project.org/src/contrib/rgdal_1.3-4.tar.gz
sudo R CMD INSTALL --configure-args=--with-gdal-config=/usr/local/gdal/bin/gdal-config rgdal_1.3-4.tar.gz
If you go this path, make sure your gdal installation has all the projection data installed in the expected location, mine wasn't so I had to add an extra step:
sudo cp -r /path/to/gdal-src-code/gdal/data/* /usr/local/gdal/share/gdal/
please help me in this. I tried installing Rcpp using
sudo apt-get install r-cran-rcpp
and from R-Studio and got the same error:
> install.packages("Rcpp", dependencies=TRUE)
Installing package into ‘/home/sukumar/R/x86_64-pc-linux-gnu-library/3.3’
(as ‘lib’ is unspecified)
also installing the dependency ‘highlight’
trying URL 'http://cran.rstudio.com/src/contrib/highlight_0.4.7.tar.gz'
Content type 'application/x-gzip' length 356443 bytes (348 KB)
==================================================
downloaded 348 KB
trying URL 'http://cran.rstudio.com/src/contrib/Rcpp_0.12.9.tar.gz'
Content type 'application/x-gzip' length 2372283 bytes (2.3 MB)
==================================================
downloaded 2.3 MB
* installing *source* package ‘highlight’ ...
** package ‘highlight’ successfully unpacked and MD5 sums checked
** libs
g++ -I/usr/share/R/include -DNDEBUG -I. -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ASBeautifier.cpp -o ASBeautifier.o
g++ -I/usr/share/R/include -DNDEBUG -I. -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ASEnhancer.cpp -o ASEnhancer.o
g++ -I/usr/share/R/include -DNDEBUG -I. -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ASFormatter.cpp -o ASFormatter.o
g++ -I/usr/share/R/include -DNDEBUG -I. -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ASResource.cpp -o ASResource.o
g++ -I/usr/share/R/include -DNDEBUG -I. -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ASStreamIterator.cpp -o ASStreamIterator.o
g++ -I/usr/share/R/include -DNDEBUG -I. -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c Matcher.cpp -o Matcher.o
g++ -I/usr/share/R/include -DNDEBUG -I. -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c Pattern.cpp -o Pattern.o
g++ -I/usr/share/R/include -DNDEBUG -I. -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ansigenerator.cpp -o ansigenerator.o
g++ -I/usr/share/R/include -DNDEBUG -I. -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c bbcodegenerator.cpp -o bbcodegenerator.o
g++ -I/usr/share/R/include -DNDEBUG -I. -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c codegenerator.cpp -o codegenerator.o
g++ -I/usr/share/R/include -DNDEBUG -I. -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c configurationreader.cpp -o configurationreader.o
g++ -I/usr/share/R/include -DNDEBUG -I. -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ctagsreader.cpp -o ctagsreader.o
g++ -I/usr/share/R/include -DNDEBUG -I. -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c datadir.cpp -o datadir.o
g++ -I/usr/share/R/include -DNDEBUG -I. -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c documentstyle.cpp -o documentstyle.o
g++ -I/usr/share/R/include -DNDEBUG -I. -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c elementstyle.cpp -o elementstyle.o
g++ -I/usr/share/R/include -DNDEBUG -I. -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c highlight_wrapper.cpp -o highlight_wrapper.o
g++ -I/usr/share/R/include -DNDEBUG -I. -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c htmlgenerator.cpp -o htmlgenerator.o
g++ -I/usr/share/R/include -DNDEBUG -I. -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c languagedefinition.cpp -o languagedefinition.o
g++ -I/usr/share/R/include -DNDEBUG -I. -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c latexgenerator.cpp -o latexgenerator.o
g++ -I/usr/share/R/include -DNDEBUG -I. -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c platform_fs.cpp -o platform_fs.o
g++ -I/usr/share/R/include -DNDEBUG -I. -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c preformatter.cpp -o preformatter.o
g++ -I/usr/share/R/include -DNDEBUG -I. -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c render.cpp -o render.o
g++ -I/usr/share/R/include -DNDEBUG -I. -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c rtfgenerator.cpp -o rtfgenerator.o
g++ -I/usr/share/R/include -DNDEBUG -I. -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c stringtools.cpp -o stringtools.o
g++ -I/usr/share/R/include -DNDEBUG -I. -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c stylecolour.cpp -o stylecolour.o
g++ -I/usr/share/R/include -DNDEBUG -I. -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c svggenerator.cpp -o svggenerator.o
g++ -I/usr/share/R/include -DNDEBUG -I. -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c texgenerator.cpp -o texgenerator.o
g++ -I/usr/share/R/include -DNDEBUG -I. -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c xhtmlgenerator.cpp -o xhtmlgenerator.o
g++ -I/usr/share/R/include -DNDEBUG -I. -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c xmlgenerator.cpp -o xmlgenerator.o
g++ -I/usr/share/R/include -DNDEBUG -I. -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c xterm256generator.cpp -o xterm256generator.o
g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o highlight.so ASBeautifier.o ASEnhancer.o ASFormatter.o ASResource.o ASStreamIterator.o Matcher.o Pattern.o ansigenerator.o bbcodegenerator.o codegenerator.o configurationreader.o ctagsreader.o datadir.o documentstyle.o elementstyle.o highlight_wrapper.o htmlgenerator.o languagedefinition.o latexgenerator.o platform_fs.o preformatter.o render.o rtfgenerator.o stringtools.o stylecolour.o svggenerator.o texgenerator.o xhtmlgenerator.o xmlgenerator.o xterm256generator.o -L/usr/lib/R/lib -lR
installing to /home/sukumar/R/x86_64-pc-linux-gnu-library/3.3/highlight/libs
** R
** 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 '/home/sukumar/R/x86_64-pc-linux-gnu-library/3.3/highlight/libs/highlight.so':
/home/sukumar/R/x86_64-pc-linux-gnu-library/3.3/highlight/libs/highlight.so: undefined symbol: _ZTVN10__cxxabiv117__class_type_infoE
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/sukumar/R/x86_64-pc-linux-gnu-library/3.3/highlight’
Warning in install.packages :
installation of package ‘highlight’ had non-zero exit status
* installing *source* package ‘Rcpp’ ...
** package ‘Rcpp’ successfully unpacked and MD5 sums checked
** libs
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c Date.cpp -o Date.o
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c Module.cpp -o Module.o
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c Rcpp_init.cpp -o Rcpp_init.o
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c api.cpp -o api.o
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c attributes.cpp -o attributes.o
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c barrier.cpp -o barrier.o
g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o Rcpp.so Date.o Module.o Rcpp_init.o api.o attributes.o barrier.o -L/usr/lib/R/lib -lR
installing to /home/sukumar/R/x86_64-pc-linux-gnu-library/3.3/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/sukumar/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/libs/Rcpp.so':
/home/sukumar/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/libs/Rcpp.so: undefined symbol: _ZTVN10__cxxabiv120__si_class_type_infoE
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/sukumar/R/x86_64-pc-linux-gnu-library/3.3/Rcpp’
Warning in install.packages :
installation of package ‘Rcpp’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpsPMzSK/downloaded_packages’
> install.packages("Rcpp", dependencies=TRUE)
Installing package into ‘/home/sukumar/R/x86_64-pc-linux-gnu-library/3.3’
(as ‘lib’ is unspecified)
also installing the dependency ‘highlight’
trying URL 'http://cran.rstudio.com/src/contrib/highlight_0.4.7.tar.gz'
Content type 'application/x-gzip' length 356443 bytes (348 KB)
==================================================
downloaded 348 KB
trying URL 'http://cran.rstudio.com/src/contrib/Rcpp_0.12.9.tar.gz'
Content type 'application/x-gzip' length 2372283 bytes (2.3 MB)
==================================================
downloaded 2.3 MB
* installing *source* package ‘highlight’ ...
** package ‘highlight’ successfully unpacked and MD5 sums checked
** libs
g++ -I/usr/share/R/include -DNDEBUG -I. -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ASBeautifier.cpp -o ASBeautifier.o
g++ -I/usr/share/R/include -DNDEBUG -I. -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ASEnhancer.cpp -o ASEnhancer.o
g++ -I/usr/share/R/include -DNDEBUG -I. -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ASFormatter.cpp -o ASFormatter.o
g++ -I/usr/share/R/include -DNDEBUG -I. -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ASResource.cpp -o ASResource.o
g++ -I/usr/share/R/include -DNDEBUG -I. -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ASStreamIterator.cpp -o ASStreamIterator.o
g++ -I/usr/share/R/include -DNDEBUG -I. -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c Matcher.cpp -o Matcher.o
g++ -I/usr/share/R/include -DNDEBUG -I. -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c Pattern.cpp -o Pattern.o
g++ -I/usr/share/R/include -DNDEBUG -I. -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ansigenerator.cpp -o ansigenerator.o
g++ -I/usr/share/R/include -DNDEBUG -I. -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c bbcodegenerator.cpp -o bbcodegenerator.o
g++ -I/usr/share/R/include -DNDEBUG -I. -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c codegenerator.cpp -o codegenerator.o
g++ -I/usr/share/R/include -DNDEBUG -I. -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c configurationreader.cpp -o configurationreader.o
g++ -I/usr/share/R/include -DNDEBUG -I. -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ctagsreader.cpp -o ctagsreader.o
g++ -I/usr/share/R/include -DNDEBUG -I. -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c datadir.cpp -o datadir.o
g++ -I/usr/share/R/include -DNDEBUG -I. -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c documentstyle.cpp -o documentstyle.o
g++ -I/usr/share/R/include -DNDEBUG -I. -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c elementstyle.cpp -o elementstyle.o
g++ -I/usr/share/R/include -DNDEBUG -I. -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c highlight_wrapper.cpp -o highlight_wrapper.o
g++ -I/usr/share/R/include -DNDEBUG -I. -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c htmlgenerator.cpp -o htmlgenerator.o
g++ -I/usr/share/R/include -DNDEBUG -I. -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c languagedefinition.cpp -o languagedefinition.o
g++ -I/usr/share/R/include -DNDEBUG -I. -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c latexgenerator.cpp -o latexgenerator.o
g++ -I/usr/share/R/include -DNDEBUG -I. -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c platform_fs.cpp -o platform_fs.o
g++ -I/usr/share/R/include -DNDEBUG -I. -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c preformatter.cpp -o preformatter.o
g++ -I/usr/share/R/include -DNDEBUG -I. -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c render.cpp -o render.o
g++ -I/usr/share/R/include -DNDEBUG -I. -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c rtfgenerator.cpp -o rtfgenerator.o
g++ -I/usr/share/R/include -DNDEBUG -I. -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c stringtools.cpp -o stringtools.o
g++ -I/usr/share/R/include -DNDEBUG -I. -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c stylecolour.cpp -o stylecolour.o
g++ -I/usr/share/R/include -DNDEBUG -I. -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c svggenerator.cpp -o svggenerator.o
g++ -I/usr/share/R/include -DNDEBUG -I. -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c texgenerator.cpp -o texgenerator.o
g++ -I/usr/share/R/include -DNDEBUG -I. -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c xhtmlgenerator.cpp -o xhtmlgenerator.o
g++ -I/usr/share/R/include -DNDEBUG -I. -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c xmlgenerator.cpp -o xmlgenerator.o
g++ -I/usr/share/R/include -DNDEBUG -I. -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c xterm256generator.cpp -o xterm256generator.o
g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o highlight.so ASBeautifier.o ASEnhancer.o ASFormatter.o ASResource.o ASStreamIterator.o Matcher.o Pattern.o ansigenerator.o bbcodegenerator.o codegenerator.o configurationreader.o ctagsreader.o datadir.o documentstyle.o elementstyle.o highlight_wrapper.o htmlgenerator.o languagedefinition.o latexgenerator.o platform_fs.o preformatter.o render.o rtfgenerator.o stringtools.o stylecolour.o svggenerator.o texgenerator.o xhtmlgenerator.o xmlgenerator.o xterm256generator.o -L/usr/lib/R/lib -lR
installing to /home/sukumar/R/x86_64-pc-linux-gnu-library/3.3/highlight/libs
** R
** 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 '/home/sukumar/R/x86_64-pc-linux-gnu-library/3.3/highlight/libs/highlight.so':
/home/sukumar/R/x86_64-pc-linux-gnu-library/3.3/highlight/libs/highlight.so: undefined symbol: _ZTVN10__cxxabiv117__class_type_infoE
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/sukumar/R/x86_64-pc-linux-gnu-library/3.3/highlight’
Warning in install.packages :
installation of package ‘highlight’ had non-zero exit status
* installing *source* package ‘Rcpp’ ...
** package ‘Rcpp’ successfully unpacked and MD5 sums checked
** libs
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c Date.cpp -o Date.o
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c Module.cpp -o Module.o
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c Rcpp_init.cpp -o Rcpp_init.o
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c api.cpp -o api.o
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c attributes.cpp -o attributes.o
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c barrier.cpp -o barrier.o
g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o Rcpp.so Date.o Module.o Rcpp_init.o api.o attributes.o barrier.o -L/usr/lib/R/lib -lR
installing to /home/sukumar/R/x86_64-pc-linux-gnu-library/3.3/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/sukumar/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/libs/Rcpp.so':
/home/sukumar/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/libs/Rcpp.so: undefined symbol: _ZTVN10__cxxabiv120__si_class_type_infoE
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/sukumar/R/x86_64-pc-linux-gnu-library/3.3/Rcpp’
Warning in install.packages :
installation of package ‘Rcpp’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpsPMzSK/downloaded_packages’
This version of Rcpp is not installed via apt-get as a binary, but rather from source: /home/sukumar/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/libs/Rcpp.so.
The error message undefined symbol: _ZTVN10__cxxabiv120__si_class_type_infoE suggests you have mismatched compilers -- and older and a newer C++ compiler.
I would recommend you delete this version (ie do rm -r ~/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/), and make sure you do not have another version installed. Then installation from source should work just fine.
You generally have a choice of using the prebuilt versions available with Ubuntu 14.04. Or you could upgrade Ubuntu to version 16.04, or even 16.10. All versions should have working Rcpp versions -- and installation from source should also work just fine if you have working and consistent versions of the required tools (ie g++).