installing source package ‘deldir’ ...
package ‘deldir’ successfully unpacked and MD5 sums checked
using staged installation
** libs
Error in if (nzchar(SHLIB_LIBADD)) SHLIB_LIBADD else character() :
argument is of length zero
installing source package ‘minqa’ ...
package ‘minqa’ successfully unpacked and MD5 sums checked
using staged installation
** libs
Error in if (nzchar(SHLIB_LIBADD)) SHLIB_LIBADD else character() :
argument is of length zero
installing source package ‘RcppEigen’ ...
package ‘RcppEigen’ successfully unpacked and MD5 sums checked
using staged installation
** libs
Error in if (nzchar(SHLIB_LIBADD)) SHLIB_LIBADD else character() :
argument is of length zero
installing source package ‘png’ ...
package ‘png’ successfully unpacked and MD5 sums checked
using staged installation
** libs
Error in if (nzchar(SHLIB_LIBADD)) SHLIB_LIBADD else character() :
argument is of length zero
installing source package ‘jpeg’ ...
package ‘jpeg’ successfully unpacked and MD5 sums checked
using staged installation
** libs
Error in if (nzchar(SHLIB_LIBADD)) SHLIB_LIBADD else character() :
argument is of length zero
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 /groups/itay_mayrose/halabikeren/miniconda3/envs/ppn/bin/x86_64-conda-linux-gnu-c++ accepts -g... yes
checking for /groups/itay_mayrose/halabikeren/miniconda3/envs/ppn/bin/x86_64-conda-linux-gnu-c++ option to enable C++11 features... none needed
checking how to run the C++ preprocessor... /groups/itay_mayrose/halabikeren/miniconda3/envs/ppn/bin/x86_64-conda-linux-gnu-c++ -E
checking whether the compiler supports GNU C++... (cached) yes
checking whether /groups/itay_mayrose/halabikeren/miniconda3/envs/ppn/bin/x86_64-conda-linux-gnu-c++ accepts -g... (cached) yes
checking for /groups/itay_mayrose/halabikeren/miniconda3/envs/ppn/bin/x86_64-conda-linux-gnu-c++ 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/local/bin/cmake
using NLopt via local cmake build on x86_64
set CMAKE_BIN=/usr/local/bin/cmake
set CC=/groups/itay_mayrose/halabikeren/miniconda3/envs/ppn/bin/x86_64-conda-linux-gnu-cc
set CFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /groups/itay_mayrose/halabikeren/miniconda3/envs/ppn/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /groups/itay_mayrose/halabikeren/miniconda3/envs/ppn/include
set CXX=
set CXXFLAGS= -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /groups/itay_mayrose/halabikeren/miniconda3/envs/ppn/include
set LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/groups/itay_mayrose/halabikeren/miniconda3/envs/ppn/lib -Wl,-rpath-link,/groups/itay_mayrose/halabikeren/miniconda3/envs/ppn/lib -L/groups/itay_mayrose/halabikeren/miniconda3/envs/ppn/lib
Could not detect C++ compiler with R CMD config.
CMake Error at CMakeLists.txt:15 (cmake_minimum_required):
CMake 3.2 or higher is required. You are running version 2.8.12.2
-- Configuring incomplete, errors occurred!
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
Error in if (nzchar(SHLIB_LIBADD)) SHLIB_LIBADD else character() :
argument is of length zero
installing source package ‘RcppArmadillo’ ...
package ‘RcppArmadillo’ 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 /groups/itay_mayrose/halabikeren/miniconda3/envs/ppn/bin/x86_64-conda-linux-gnu-c++ accepts -g... yes
checking for /groups/itay_mayrose/halabikeren/miniconda3/envs/ppn/bin/x86_64-conda-linux-gnu-c++ option to enable C++11 features... none needed
checking how to run the C++ preprocessor... /groups/itay_mayrose/halabikeren/miniconda3/envs/ppn/bin/x86_64-conda-linux-gnu-c++ -E
checking whether the compiler supports GNU C++... (cached) yes
checking whether /groups/itay_mayrose/halabikeren/miniconda3/envs/ppn/bin/x86_64-conda-linux-gnu-c++ accepts -g... (cached) yes
checking for /groups/itay_mayrose/halabikeren/miniconda3/envs/ppn/bin/x86_64-conda-linux-gnu-c++ option to enable C++11 features... (cached) none needed
checking whether we have a suitable tempdir... /tmp
checking whether R CMD SHLIB can already compile programs using OpenMP... no
checking whether g++ version is sufficient... yes, with OpenMP as version 10.3.0
checking for macOS... no
checking LAPACK_LIBS... system LAPACK found
checking for OpenMP... R was not built as a library
missing
configure: creating ./config.status
config.status: creating inst/include/RcppArmadillo/config/RcppArmadilloConfigGenerated.h
config.status: creating src/Makevars
** libs
Error in if (nzchar(SHLIB_LIBADD)) SHLIB_LIBADD else character() :
argument is of length zero
removing ‘/groups/itay_mayrose/halabikeren/miniconda3/envs/ppn/lib/R/library/RcppArmadillo’
ERROR: dependencies ‘deldir’, ‘RcppEigen’ are not available for package ‘interp’
removing ‘/groups/itay_mayrose/halabikeren/miniconda3/envs/ppn/lib/R/library/interp’
ERROR: dependencies ‘minqa’, ‘nloptr’, ‘RcppEigen’ are not available for package ‘lme4’
removing ‘/groups/itay_mayrose/halabikeren/miniconda3/envs/ppn/lib/R/library/lme4’
ERROR: dependencies ‘png’, ‘jpeg’, ‘interp’ are not available for package ‘latticeExtra’
removing ‘/groups/itay_mayrose/halabikeren/miniconda3/envs/ppn/lib/R/library/latticeExtra’
ERROR: dependencies ‘lme4’, ‘nloptr’, ‘latticeExtra’, ‘RcppArmadillo’ are not available for package ‘phyr’
The downloaded source packages are in
‘/tmp/RtmpEVxjR2/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
There were 11 warnings (use warnings() to see them)
The package has not been installed:
library("phyr")
Error in library("phyr") : there is no package called ‘phyr’
Hi,
I am trying to install the package in a linux environment using: options(repos = c( phyr = 'https://daijiang.r-universe.dev', CRAN = 'https://cloud.r-project.org')) install.packages('phyr')
And I get an error:
-- Configuring incomplete, errors occurred! 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 Error in if (nzchar(SHLIB_LIBADD)) SHLIB_LIBADD else character() : argument is of length zero
The downloaded source packages are in ‘/tmp/RtmpEVxjR2/downloaded_packages’ Updating HTML index of packages in '.Library' Making 'packages.html' ... done There were 11 warnings (use warnings() to see them)
The package has not been installed:
The problem is not reproducible in Windows
Cheers!