无法安装 R 包：CMake 错误
cannot install R package: CMake errorr
我正在尝试安装 factoextra，但我在 CMake 部分卡住了，特别是错误，例如：
CMake Error: The source directory "/tmp/..." does not exist.
（当我尝试安装其依赖项时也是如此：nloptr、pbkrtest、lme4、car、rstatix、FactoMineR , ggpubr )
有什么想法吗？
谢谢
ps:
- R 版本 4.0.0
- centos 7
日志的最后一部分：
CMake Error: The source directory "/tmp/RtmpgJySdf/R.INSTALL20c31df42f6/nloptr/src/nlopt-build" does not exist.
Specify --help for usage, or press the help button on the CMake GUI.
Unknown argument -j
Unknown argument 2
Usage: cmake --build <dir> [options] [-- [native-options]]
Options:
<dir> = Project binary directory to be built.
--target <tgt> = Build <tgt> instead of default targets.
--config <cfg> = For multi-configuration tools, choose <cfg>.
--clean-first = Build target 'clean' first, then build.
(To clean only, use --target 'clean'.)
--use-stderr = Don't merge stdout/stderr output and pass the
original stdout/stderr handles to the native
tool so it can use the capabilities of the
calling terminal (e.g. colored output).
-- = Pass remaining options to the native tool.
CMake Error: The source directory "/tmp/RtmpgJySdf/R.INSTALL20c31df42f6/nloptr/src/nlopt" does not exist.
Specify --help for usage, or press the help button on the CMake GUI.
cp: cannot stat 'nlopt/include/*': No such file or directory
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I"/opt/R/4.0.0/lib/R/include" -DNDEBUG -I../inst/include -I'/opt/R/4.0.0/lib/R/library/testthat/include' -I/usr/local/include -fpic -g -O2 -c init_nloptr.c -o init_nloptr.o
gcc -std=gnu99 -I"/opt/R/4.0.0/lib/R/include" -DNDEBUG -I../inst/include -I'/opt/R/4.0.0/lib/R/library/testthat/include' -I/usr/local/include -fpic -g -O2 -c nloptr.c -o nloptr.o
g++ -std=gnu++11 -I"/opt/R/4.0.0/lib/R/include" -DNDEBUG -I../inst/include -I'/opt/R/4.0.0/lib/R/library/testthat/include' -I/usr/local/include -fpic -g -O2 -c test-C-API.cpp -o test-C-API.o
g++ -std=gnu++11 -I"/opt/R/4.0.0/lib/R/include" -DNDEBUG -I../inst/include -I'/opt/R/4.0.0/lib/R/library/testthat/include' -I/usr/local/include -fpic -g -O2 -c test-runner.cpp -o test-runner.o
g++ -std=gnu++11 -shared -L/opt/R/4.0.0/lib/R/lib -L/usr/local/lib -o nloptr.so init_nloptr.o nloptr.o test-C-API.o test-runner.o -L/opt/R/4.0.0/lib/R/lib -lRlapack -L/opt/R/4.0.0/lib/R/lib -lRblas -lgfortran -lm -lquadmath -Lnlopt/lib -lnlopt -L/opt/R/4.0.0/lib/R/lib -lR
/bin/ld: cannot find -lnlopt
collect2: error: ld returned 1 exit status
make: *** [nloptr.so] Error 1
ERROR: compilation failed for package ‘nloptr’
* removing ‘/opt/R/4.0.0/lib/R/library/nloptr’
ERROR: dependency ‘nloptr’ is not available for package ‘lme4’
* removing ‘/opt/R/4.0.0/lib/R/library/lme4’
ERROR: dependency ‘lme4’ is not available for package ‘pbkrtest’
* removing ‘/opt/R/4.0.0/lib/R/library/pbkrtest’
ERROR: dependencies ‘pbkrtest’, ‘lme4’ are not available for package ‘car’
* removing ‘/opt/R/4.0.0/lib/R/library/car’
ERROR: dependency ‘car’ is not available for package ‘rstatix’
* removing ‘/opt/R/4.0.0/lib/R/library/rstatix’
ERROR: dependency ‘car’ is not available for package ‘FactoMineR’
* removing ‘/opt/R/4.0.0/lib/R/library/FactoMineR’
ERROR: dependency ‘rstatix’ is not available for package ‘ggpubr’
* removing ‘/opt/R/4.0.0/lib/R/library/ggpubr’
ERROR: dependencies ‘FactoMineR’, ‘ggpubr’ are not available for package ‘factoextra’
* removing ‘/opt/R/4.0.0/lib/R/library/factoextra’
The downloaded source packages are in
‘/tmp/Rtmp98DJqK/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning messages:
1: In install.packages("factoextra") :
installation of package ‘nloptr’ had non-zero exit status
2: In install.packages("factoextra") :
installation of package ‘lme4’ had non-zero exit status
3: In install.packages("factoextra") :
installation of package ‘pbkrtest’ had non-zero exit status
4: In install.packages("factoextra") :
installation of package ‘car’ had non-zero exit status
5: In install.packages("factoextra") :
installation of package ‘rstatix’ had non-zero exit status
6: In install.packages("factoextra") :
installation of package ‘FactoMineR’ had non-zero exit status
7: In install.packages("factoextra") :
installation of package ‘ggpubr’ had non-zero exit status
8: In install.packages("factoextra") :
installation of package ‘factoextra’ had non-zero exit status
我通过 sudo apt-get install libnlopt-dev 解决了这个问题。
所以，
我想我终于明白了！
factoextra（或更好，nloptr）目前需要 组合
- R v. >= 4（centos 未试用！）
- cmake v. >= 3 (yum install cmake3 -- 归功于 https://github.com/astamm/nloptr/issues/104#issuecomment-1034229550)
在Ubuntu中从源安装cmake v3.20.2，它将解决问题：
sudo apt install build-essential libssl-dev
wget https://github.com/Kitware/CMake/releases/download/v3.20.2/cmake-3.20.2.tar.gz
tar -zxvf cmake-3.20.2.tar.gz
cd cmake-3.20.2
./bootstrap
make
sudo make install
我正在尝试安装 factoextra，但我在 CMake 部分卡住了，特别是错误，例如：
CMake Error: The source directory "/tmp/..." does not exist.
（当我尝试安装其依赖项时也是如此：nloptr、pbkrtest、lme4、car、rstatix、FactoMineR , ggpubr )
有什么想法吗？
谢谢
ps:
- R 版本 4.0.0
- centos 7
日志的最后一部分：
CMake Error: The source directory "/tmp/RtmpgJySdf/R.INSTALL20c31df42f6/nloptr/src/nlopt-build" does not exist.
Specify --help for usage, or press the help button on the CMake GUI.
Unknown argument -j
Unknown argument 2
Usage: cmake --build <dir> [options] [-- [native-options]]
Options:
<dir> = Project binary directory to be built.
--target <tgt> = Build <tgt> instead of default targets.
--config <cfg> = For multi-configuration tools, choose <cfg>.
--clean-first = Build target 'clean' first, then build.
(To clean only, use --target 'clean'.)
--use-stderr = Don't merge stdout/stderr output and pass the
original stdout/stderr handles to the native
tool so it can use the capabilities of the
calling terminal (e.g. colored output).
-- = Pass remaining options to the native tool.
CMake Error: The source directory "/tmp/RtmpgJySdf/R.INSTALL20c31df42f6/nloptr/src/nlopt" does not exist.
Specify --help for usage, or press the help button on the CMake GUI.
cp: cannot stat 'nlopt/include/*': No such file or directory
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I"/opt/R/4.0.0/lib/R/include" -DNDEBUG -I../inst/include -I'/opt/R/4.0.0/lib/R/library/testthat/include' -I/usr/local/include -fpic -g -O2 -c init_nloptr.c -o init_nloptr.o
gcc -std=gnu99 -I"/opt/R/4.0.0/lib/R/include" -DNDEBUG -I../inst/include -I'/opt/R/4.0.0/lib/R/library/testthat/include' -I/usr/local/include -fpic -g -O2 -c nloptr.c -o nloptr.o
g++ -std=gnu++11 -I"/opt/R/4.0.0/lib/R/include" -DNDEBUG -I../inst/include -I'/opt/R/4.0.0/lib/R/library/testthat/include' -I/usr/local/include -fpic -g -O2 -c test-C-API.cpp -o test-C-API.o
g++ -std=gnu++11 -I"/opt/R/4.0.0/lib/R/include" -DNDEBUG -I../inst/include -I'/opt/R/4.0.0/lib/R/library/testthat/include' -I/usr/local/include -fpic -g -O2 -c test-runner.cpp -o test-runner.o
g++ -std=gnu++11 -shared -L/opt/R/4.0.0/lib/R/lib -L/usr/local/lib -o nloptr.so init_nloptr.o nloptr.o test-C-API.o test-runner.o -L/opt/R/4.0.0/lib/R/lib -lRlapack -L/opt/R/4.0.0/lib/R/lib -lRblas -lgfortran -lm -lquadmath -Lnlopt/lib -lnlopt -L/opt/R/4.0.0/lib/R/lib -lR
/bin/ld: cannot find -lnlopt
collect2: error: ld returned 1 exit status
make: *** [nloptr.so] Error 1
ERROR: compilation failed for package ‘nloptr’
* removing ‘/opt/R/4.0.0/lib/R/library/nloptr’
ERROR: dependency ‘nloptr’ is not available for package ‘lme4’
* removing ‘/opt/R/4.0.0/lib/R/library/lme4’
ERROR: dependency ‘lme4’ is not available for package ‘pbkrtest’
* removing ‘/opt/R/4.0.0/lib/R/library/pbkrtest’
ERROR: dependencies ‘pbkrtest’, ‘lme4’ are not available for package ‘car’
* removing ‘/opt/R/4.0.0/lib/R/library/car’
ERROR: dependency ‘car’ is not available for package ‘rstatix’
* removing ‘/opt/R/4.0.0/lib/R/library/rstatix’
ERROR: dependency ‘car’ is not available for package ‘FactoMineR’
* removing ‘/opt/R/4.0.0/lib/R/library/FactoMineR’
ERROR: dependency ‘rstatix’ is not available for package ‘ggpubr’
* removing ‘/opt/R/4.0.0/lib/R/library/ggpubr’
ERROR: dependencies ‘FactoMineR’, ‘ggpubr’ are not available for package ‘factoextra’
* removing ‘/opt/R/4.0.0/lib/R/library/factoextra’
The downloaded source packages are in
‘/tmp/Rtmp98DJqK/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning messages:
1: In install.packages("factoextra") :
installation of package ‘nloptr’ had non-zero exit status
2: In install.packages("factoextra") :
installation of package ‘lme4’ had non-zero exit status
3: In install.packages("factoextra") :
installation of package ‘pbkrtest’ had non-zero exit status
4: In install.packages("factoextra") :
installation of package ‘car’ had non-zero exit status
5: In install.packages("factoextra") :
installation of package ‘rstatix’ had non-zero exit status
6: In install.packages("factoextra") :
installation of package ‘FactoMineR’ had non-zero exit status
7: In install.packages("factoextra") :
installation of package ‘ggpubr’ had non-zero exit status
8: In install.packages("factoextra") :
installation of package ‘factoextra’ had non-zero exit status
我通过 sudo apt-get install libnlopt-dev 解决了这个问题。
所以，
我想我终于明白了！
factoextra（或更好，nloptr）目前需要 组合
- R v. >= 4（centos 未试用！）
- cmake v. >= 3 (yum install cmake3 -- 归功于 https://github.com/astamm/nloptr/issues/104#issuecomment-1034229550)
在Ubuntu中从源安装cmake v3.20.2，它将解决问题：
sudo apt install build-essential libssl-dev
wget https://github.com/Kitware/CMake/releases/download/v3.20.2/cmake-3.20.2.tar.gz
tar -zxvf cmake-3.20.2.tar.gz
cd cmake-3.20.2
./bootstrap
make
sudo make install