I've been using R and Rstudio for a while now on a PC with ubuntu 20.04 and have always been able to install whatever package I need. In fact, I can still install most packages, both via install.packages and BiocManager. I have installed R-base-dev and can install most packages from CRAN just fine.
The other day I wanted to install the package "NormalyzerDE" and was also asked if I wanted to update two old packages, "nloptr" and "dplyr".
As you can see below, "NormalyzerDE" fails because the first two dependencies fail, one with the error:
* installing *source* package ‘terra’ ...
** package ‘terra’ successfully unpacked and MD5 sums checked
** using staged installation
Rscript execution error: No such file or directory
./configure: line 2060: test: =: unary operator expected
./configure: line 2064: test: too many arguments
./configure: line 2067: test: too many arguments
configure: CC: gcc
configure: CXX: g++ -std=gnu++11
checking for gdal-config... no
no
configure: error: gdal-config not found or not executable.
ERROR: configuration failed for package ‘terra’
* removing ‘/home/emil/R/x86_64-pc-linux-gnu-library/4.2/terra’
And the other with the error:
* installing *source* package ‘polyclip’ ...
** package ‘polyclip’ successfully unpacked and MD5 sums checked
** using staged installation
Rscript execution error: No such file or directory
compiling under C++11
checking whether the C++ compiler works... no
configure: error: in `/tmp/RtmpL9dO8R/R.INSTALL683312b8a63e4/polyclip':
configure: error: C++ compiler cannot create executables
See `config.log' for more details
ERROR: configuration failed for package ‘polyclip’
* removing ‘/home/emil/R/x86_64-pc-linux-gnu-library/4.2/polyclip’
Finally, "dplyr" updates just fine, but "nloptr" fails with the error:
* installing *source* package ‘nloptr’ ...
** package ‘nloptr’ successfully unpacked and MD5 sums checked
** using staged installation
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C++... yes
checking whether g++ -std=gnu++14 accepts -g... yes
checking for g++ -std=gnu++14 option to enable C++11 features... none needed
checking how to run the C++ preprocessor... g++ -std=gnu++14 -E
checking whether the compiler supports GNU C++... (cached) yes
checking whether g++ -std=gnu++14 accepts -g... (cached) yes
checking for g++ -std=gnu++14 option to enable C++11 features... (cached) none needed
checking for pkg-config... /usr/bin/pkg-config
checking if pkg-config knows NLopt... yes
checking for pkg-config checking NLopt version... insufficient: NLopt 2.7.0 or later is preferred.
checking for cmake... /usr/bin/cmake
Rscript execution error: No such file or directory
using NLopt via local cmake build on
Rscript execution error: No such file or directory
set CMAKE_BIN=/usr/bin/cmake
Rscript execution error: No such file or directory
mv: cannot stat 'nlopt-2.7.1': No such file or directory
set CC=gcc
set CFLAGS= -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2
set CXX=g++
set CXXFLAGS=-std=gnu++11 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2
set LDFLAGS=-Wl,-Bsymbolic-functions -Wl,-z,relro
Rscript execution error: No such file or directory
Rscript execution error: No such file or directory
CMake Error: The source directory "/tmp/RtmpU9IvGD/R.INSTALL684e27f439022/nloptr/src/nlopt-src" does not exist.
Specify --help for usage, or press the help button on the CMake GUI.
make: *** No targets specified and no makefile found. Stop.
make: *** No rule to make target 'install'. Stop.
mv: cannot stat 'nlopt/lib*': No such file or directory
cp: cannot stat 'nlopt/include/*': No such file or directory
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I'/home/emil/R/x86_64-pc-linux-gnu-library/4.2/testthat/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c init_nloptr.c -o init_nloptr.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I'/home/emil/R/x86_64-pc-linux-gnu-library/4.2/testthat/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c nloptr.c -o nloptr.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I'/home/emil/R/x86_64-pc-linux-gnu-library/4.2/testthat/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c test-C-API.cpp -o test-C-API.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I'/home/emil/R/x86_64-pc-linux-gnu-library/4.2/testthat/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c test-runner.cpp -o test-runner.o
g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o nloptr.so init_nloptr.o nloptr.o test-C-API.o test-runner.o -llapack -lblas -lgfortran -lm -lquadmath nlopt/lib/libnlopt.a -L/usr/lib/R/lib -lR
g++: error: nlopt/lib/libnlopt.a: No such file or directory
make: *** [/usr/share/R/share/make/shlib.mk:10: nloptr.so] Error 1
ERROR: compilation failed for package ‘nloptr’
* removing ‘/home/emil/R/x86_64-pc-linux-gnu-library/4.2/nloptr’
* restoring previous ‘/home/emil/R/x86_64-pc-linux-gnu-library/4.2/nloptr’
I've looked around quite a bit for the answer and have made sure to have R-base-dev and build-essentials installed and have tried to set CMAKE_BIN=/usr/bin/cmake in the bash terminal, but nothing seems to be working and I can't find any answers online.
Does anyone know what to do?
Full output:
> BiocManager::install("NormalyzerDE")
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details
replacement repositories:
CRAN: https://cloud.r-project.org
Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.1 (2022-06-23)
Installing package(s) 'NormalyzerDE'
also installing the dependencies ‘terra’, ‘polyclip’, ‘raster’, ‘ggforce’
trying URL 'https://cloud.r-project.org/src/contrib/terra_1.6-7.tar.gz'
Content type 'application/x-gzip' length 689703 bytes (673 KB)
==================================================
downloaded 673 KB
trying URL 'https://cloud.r-project.org/src/contrib/polyclip_1.10-0.tar.gz'
Content type 'application/x-gzip' length 79619 bytes (77 KB)
==================================================
downloaded 77 KB
trying URL 'https://cloud.r-project.org/src/contrib/raster_3.5-29.tar.gz'
Content type 'application/x-gzip' length 577629 bytes (564 KB)
==================================================
downloaded 564 KB
trying URL 'https://cloud.r-project.org/src/contrib/ggforce_0.3.4.tar.gz'
Content type 'application/x-gzip' length 860656 bytes (840 KB)
==================================================
downloaded 840 KB
trying URL 'https://bioconductor.org/packages/3.15/bioc/src/contrib/NormalyzerDE_1.14.0.tar.gz'
Content type 'application/x-gzip' length 1085633 bytes (1.0 MB)
==================================================
downloaded 1.0 MB
* installing *source* package ‘terra’ ...
** package ‘terra’ successfully unpacked and MD5 sums checked
** using staged installation
Rscript execution error: No such file or directory
./configure: line 2060: test: =: unary operator expected
./configure: line 2064: test: too many arguments
./configure: line 2067: test: too many arguments
configure: CC: gcc
configure: CXX: g++ -std=gnu++11
checking for gdal-config... no
no
configure: error: gdal-config not found or not executable.
ERROR: configuration failed for package ‘terra’
* removing ‘/home/emil/R/x86_64-pc-linux-gnu-library/4.2/terra’
* installing *source* package ‘polyclip’ ...
** package ‘polyclip’ successfully unpacked and MD5 sums checked
** using staged installation
Rscript execution error: No such file or directory
compiling under C++11
checking whether the C++ compiler works... no
configure: error: in `/tmp/RtmpL9dO8R/R.INSTALL683312b8a63e4/polyclip':
configure: error: C++ compiler cannot create executables
See `config.log' for more details
ERROR: configuration failed for package ‘polyclip’
* removing ‘/home/emil/R/x86_64-pc-linux-gnu-library/4.2/polyclip’
ERROR: dependency ‘terra’ is not available for package ‘raster’
* removing ‘/home/emil/R/x86_64-pc-linux-gnu-library/4.2/raster’
ERROR: dependency ‘polyclip’ is not available for package ‘ggforce’
* removing ‘/home/emil/R/x86_64-pc-linux-gnu-library/4.2/ggforce’
ERROR: dependencies ‘raster’, ‘ggforce’ are not available for package ‘NormalyzerDE’
* removing ‘/home/emil/R/x86_64-pc-linux-gnu-library/4.2/NormalyzerDE’
The downloaded source packages are in
‘/tmp/Rtmppq0Ahj/downloaded_packages’
Installation paths not writeable, unable to update packages
path: /usr/lib/R/library
packages:
MASS, spatial
path: /usr/lib/R/site-library
packages:
gtable, rlang, tibble
Old packages: 'dplyr', 'nloptr'
Update all/some/none? [a/s/n]:
a
trying URL 'https://cloud.r-project.org/src/contrib/dplyr_1.0.10.tar.gz'
Content type 'application/x-gzip' length 884984 bytes (864 KB)
==================================================
downloaded 864 KB
trying URL 'https://cloud.r-project.org/src/contrib/nloptr_2.0.3.tar.gz'
Content type 'application/x-gzip' length 2219877 bytes (2.1 MB)
==================================================
downloaded 2.1 MB
* installing *source* package ‘dplyr’ ...
** package ‘dplyr’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c chop.cpp -o chop.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c filter.cpp -o filter.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c funs.cpp -o funs.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c group_by.cpp -o group_by.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c group_data.cpp -o group_data.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c imports.cpp -o imports.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c init.cpp -o init.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c mask.cpp -o mask.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c mutate.cpp -o mutate.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c slice.cpp -o slice.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c summarise.cpp -o summarise.o
g++ -std=gnu++14 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o dplyr.so chop.o filter.o funs.o group_by.o group_data.o imports.o init.o mask.o mutate.o slice.o summarise.o -L/usr/lib/R/lib -lR
installing to /home/emil/R/x86_64-pc-linux-gnu-library/4.2/00LOCK-dplyr/00new/dplyr/libs
** R
** data
*** moving datasets to lazyload DB
** 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
** 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 (dplyr)
* installing *source* package ‘nloptr’ ...
** package ‘nloptr’ successfully unpacked and MD5 sums checked
** using staged installation
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C++... yes
checking whether g++ -std=gnu++14 accepts -g... yes
checking for g++ -std=gnu++14 option to enable C++11 features... none needed
checking how to run the C++ preprocessor... g++ -std=gnu++14 -E
checking whether the compiler supports GNU C++... (cached) yes
checking whether g++ -std=gnu++14 accepts -g... (cached) yes
checking for g++ -std=gnu++14 option to enable C++11 features... (cached) none needed
checking for pkg-config... /usr/bin/pkg-config
checking if pkg-config knows NLopt... yes
checking for pkg-config checking NLopt version... insufficient: NLopt 2.7.0 or later is preferred.
checking for cmake... /usr/bin/cmake
Rscript execution error: No such file or directory
using NLopt via local cmake build on
Rscript execution error: No such file or directory
set CMAKE_BIN=/usr/bin/cmake
Rscript execution error: No such file or directory
mv: cannot stat 'nlopt-2.7.1': No such file or directory
set CC=gcc
set CFLAGS= -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2
set CXX=g++
set CXXFLAGS=-std=gnu++11 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2
set LDFLAGS=-Wl,-Bsymbolic-functions -Wl,-z,relro
Rscript execution error: No such file or directory
Rscript execution error: No such file or directory
CMake Error: The source directory "/tmp/RtmpU9IvGD/R.INSTALL684e27f439022/nloptr/src/nlopt-src" does not exist.
Specify --help for usage, or press the help button on the CMake GUI.
make: *** No targets specified and no makefile found. Stop.
make: *** No rule to make target 'install'. Stop.
mv: cannot stat 'nlopt/lib*': No such file or directory
cp: cannot stat 'nlopt/include/*': No such file or directory
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I'/home/emil/R/x86_64-pc-linux-gnu-library/4.2/testthat/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c init_nloptr.c -o init_nloptr.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I'/home/emil/R/x86_64-pc-linux-gnu-library/4.2/testthat/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c nloptr.c -o nloptr.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I'/home/emil/R/x86_64-pc-linux-gnu-library/4.2/testthat/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c test-C-API.cpp -o test-C-API.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I'/home/emil/R/x86_64-pc-linux-gnu-library/4.2/testthat/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c test-runner.cpp -o test-runner.o
g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o nloptr.so init_nloptr.o nloptr.o test-C-API.o test-runner.o -llapack -lblas -lgfortran -lm -lquadmath nlopt/lib/libnlopt.a -L/usr/lib/R/lib -lR
g++: error: nlopt/lib/libnlopt.a: No such file or directory
make: *** [/usr/share/R/share/make/shlib.mk:10: nloptr.so] Error 1
ERROR: compilation failed for package ‘nloptr’
* removing ‘/home/emil/R/x86_64-pc-linux-gnu-library/4.2/nloptr’
* restoring previous ‘/home/emil/R/x86_64-pc-linux-gnu-library/4.2/nloptr’
The downloaded source packages are in
‘/tmp/Rtmppq0Ahj/downloaded_packages’
Warning messages:
1: In install.packages(...) :
installation of package ‘terra’ had non-zero exit status
2: In install.packages(...) :
installation of package ‘polyclip’ had non-zero exit status
3: In install.packages(...) :
installation of package ‘raster’ had non-zero exit status
4: In install.packages(...) :
installation of package ‘ggforce’ had non-zero exit status
5: In install.packages(...) :
installation of package ‘NormalyzerDE’ had non-zero exit status
6: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, :
installation of package ‘nloptr’ had non-zero exit status
UPDATE
Thanks for the fast replies!
which cmake yields /usr/bin/cmake (the same is true for make) and ls -la /usr/bin/cmake yields -rwxr-xr-x 1 root root 5944072 feb 6 2020 /usr/bin/cmake. Changing the ownership with chown to me did not solve the issue. gdal-config was indeed not installed and after installing it, terra installs properly! (I also had to install libobdc1 and unixobdc-dev to make it work). However, polyclip and nloptr still does not install properly. Something seems to be wrong with the c++ compiler?
UPDATED OUTPUT
> BiocManager::install("NormalyzerDE")
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details
replacement repositories:
CRAN: https://cloud.r-project.org
Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.1 (2022-06-23)
Installing package(s) 'NormalyzerDE'
also installing the dependencies ‘polyclip’, ‘ggforce’
trying URL 'https://cloud.r-project.org/src/contrib/polyclip_1.10-0.tar.gz'
Content type 'application/x-gzip' length 79619 bytes (77 KB)
==================================================
downloaded 77 KB
trying URL 'https://cloud.r-project.org/src/contrib/ggforce_0.3.4.tar.gz'
Content type 'application/x-gzip' length 860656 bytes (840 KB)
==================================================
downloaded 840 KB
trying URL 'https://bioconductor.org/packages/3.15/bioc/src/contrib/NormalyzerDE_1.14.0.tar.gz'
Content type 'application/x-gzip' length 1085633 bytes (1.0 MB)
==================================================
downloaded 1.0 MB
* installing *source* package ‘polyclip’ ...
** package ‘polyclip’ successfully unpacked and MD5 sums checked
** using staged installation
Rscript execution error: No such file or directory
compiling under C++11
checking whether the C++ compiler works... no
configure: error: in `/tmp/RtmpULM1t8/R.INSTALLe17e7b8b5788/polyclip':
configure: error: C++ compiler cannot create executables
See `config.log' for more details
ERROR: configuration failed for package ‘polyclip’
* removing ‘/home/emil/R/x86_64-pc-linux-gnu-library/4.2/polyclip’
ERROR: dependency ‘polyclip’ is not available for package ‘ggforce’
* removing ‘/home/emil/R/x86_64-pc-linux-gnu-library/4.2/ggforce’
ERROR: dependency ‘ggforce’ is not available for package ‘NormalyzerDE’
* removing ‘/home/emil/R/x86_64-pc-linux-gnu-library/4.2/NormalyzerDE’
The downloaded source packages are in
‘/tmp/RtmpAV94Sg/downloaded_packages’
Installation paths not writeable, unable to update packages
path: /usr/lib/R/library
packages:
MASS, spatial
path: /usr/lib/R/site-library
packages:
gtable, rlang, tibble
Old packages: 'nloptr'
Update all/some/none? [a/s/n]:
a
trying URL 'https://cloud.r-project.org/src/contrib/nloptr_2.0.3.tar.gz'
Content type 'application/x-gzip' length 2219877 bytes (2.1 MB)
==================================================
downloaded 2.1 MB
* installing *source* package ‘nloptr’ ...
** package ‘nloptr’ successfully unpacked and MD5 sums checked
** using staged installation
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C++... yes
checking whether g++ -std=gnu++14 accepts -g... yes
checking for g++ -std=gnu++14 option to enable C++11 features... none needed
checking how to run the C++ preprocessor... g++ -std=gnu++14 -E
checking whether the compiler supports GNU C++... (cached) yes
checking whether g++ -std=gnu++14 accepts -g... (cached) yes
checking for g++ -std=gnu++14 option to enable C++11 features... (cached) none needed
checking for pkg-config... /usr/bin/pkg-config
checking if pkg-config knows NLopt... yes
checking for pkg-config checking NLopt version... insufficient: NLopt 2.7.0 or later is preferred.
checking for cmake... /usr/bin/cmake
Rscript execution error: No such file or directory
using NLopt via local cmake build on
Rscript execution error: No such file or directory
set CMAKE_BIN=/usr/bin/cmake
Rscript execution error: No such file or directory
mv: cannot stat 'nlopt-2.7.1': No such file or directory
set CC=gcc
set CFLAGS= -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2
set CXX=g++
set CXXFLAGS=-std=gnu++11 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2
set LDFLAGS=-Wl,-Bsymbolic-functions -Wl,-z,relro
Rscript execution error: No such file or directory
Rscript execution error: No such file or directory
CMake Error: The source directory "/tmp/Rtmpcdneyf/R.INSTALLe3b819d8bc7f/nloptr/src/nlopt-src" does not exist.
Specify --help for usage, or press the help button on the CMake GUI.
make: *** No targets specified and no makefile found. Stop.
make: *** No rule to make target 'install'. Stop.
mv: cannot stat 'nlopt/lib*': No such file or directory
cp: cannot stat 'nlopt/include/*': No such file or directory
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I'/home/emil/R/x86_64-pc-linux-gnu-library/4.2/testthat/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c init_nloptr.c -o init_nloptr.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I'/home/emil/R/x86_64-pc-linux-gnu-library/4.2/testthat/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c nloptr.c -o nloptr.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I'/home/emil/R/x86_64-pc-linux-gnu-library/4.2/testthat/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c test-C-API.cpp -o test-C-API.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I'/home/emil/R/x86_64-pc-linux-gnu-library/4.2/testthat/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c test-runner.cpp -o test-runner.o
g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o nloptr.so init_nloptr.o nloptr.o test-C-API.o test-runner.o -llapack -lblas -lgfortran -lm -lquadmath nlopt/lib/libnlopt.a -L/usr/lib/R/lib -lR
g++: error: nlopt/lib/libnlopt.a: No such file or directory
make: *** [/usr/share/R/share/make/shlib.mk:10: nloptr.so] Error 1
ERROR: compilation failed for package ‘nloptr’
* removing ‘/home/emil/R/x86_64-pc-linux-gnu-library/4.2/nloptr’
* restoring previous ‘/home/emil/R/x86_64-pc-linux-gnu-library/4.2/nloptr’
The downloaded source packages are in
‘/tmp/RtmpAV94Sg/downloaded_packages’
Warning messages:
1: In install.packages(...) :
installation of package ‘polyclip’ had non-zero exit status
2: In install.packages(...) :
installation of package ‘ggforce’ had non-zero exit status
3: In install.packages(...) :
installation of package ‘NormalyzerDE’ had non-zero exit status
4: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, :
installation of package ‘nloptr’ had non-zero exit status