[英]Unable to install a package on R
I'm getting an issue when I try to install Bioconductor for R. I've searched everywhere for solutions however nothing is really working for me.当我尝试为 R 安装 Bioconductor 时遇到了一个问题。我到处寻找解决方案,但是没有任何东西对我有用。 Please, any advice?
请问,有什么建议吗?
The downloaded binary packages are in
/var/folders/74/y92tqhzj0l98l6syjjl7vtcr0000gn/T//RtmpNYOkbZ/downloaded_packages
Old packages: 'nlme'
Update all/some/none? [a/s/n]:
a
Warning: unable to access index for repository https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6:
cannot open URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/PACKAGES'
Package which is only available in source form, and may need compilation of
C/C++/Fortran: ‘nlme’
Do you want to attempt to install these from sources? (Yes/no/cancel) Yes
installing the source package ‘nlme’
trying URL 'https://cran.rstudio.com/src/contrib/nlme_3.1-144.tar.gz'
Content type 'application/x-gzip' length 778660 bytes (760 KB)
==================================================
downloaded 760 KB
* installing *source* package ‘nlme’ ...
** package ‘nlme’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gfortran -fPIC -Wall -g -O2 -c chol.f -o chol.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c corStruct.c -o corStruct.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c gnls.c -o gnls.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c init.c -o init.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c matrix.c -o matrix.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c nlOptimizer.c -o nlOptimizer.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c nlme.c -o nlme.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c nlmefit.c -o nlmefit.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c pdMat.c -o pdMat.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c pythag.c -o pythag.o
gfortran -fPIC -Wall -g -O2 -c rs.f -o rs.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o nlme.so chol.o corStruct.o gnls.o init.o matrix.o nlOptimizer.o nlme.o nlmefit.o pdMat.o pythag.o rs.o -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0'
ld: warning: directory not found for option '-L/usr/local/gfortran/lib'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [nlme.so] Error 1
ERROR: compilation failed for package ‘nlme’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/nlme’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/nlme’
The downloaded source packages are in
‘/private/var/folders/74/y92tqhzj0l98l6syjjl7vtcr0000gn/T/RtmpNYOkbZ/downloaded_packages’
Warning message:
In install.packages(update[instlib == l, "Package"], l, repos = repos, :
installation of package ‘nlme’ had non-zero exit status
I've tried to reinstall R and it didn't work.我试过重新安装R,但没有用。
The code I am using to install bioconductor is:我用来安装 bioconductor 的代码是:
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(version = "3.10")
I had the same problem.我有同样的问题。 This happens since I updated to R4.0.
这是因为我更新到 R4.0。 I've seen that in Mac (and maybe Windows) can be related to missing Rtools .
我已经看到在 Mac(也许是 Windows)中可能与缺少 Rtools相关。 In Linux, I tried to install the package from other mirrors (this solved my problem in the past), but no success.
在Linux中,我尝试从其他镜像安装包(这解决了我过去的问题),但没有成功。 Finally, I realized that the initial error is "make: gfortran: No such file or directory"
最后,我意识到最初的错误是“make: gfortran: No such file or directory”
Therefore, I installed gcc & gcc-fortran and that solved it!因此,我安装了 gcc & gcc-fortran 并解决了它!
In Manjaro, Arch linux:在 Manjaro 中,Arch linux:
pacman -S gcc
pacman -S gcc-fortran
In Debian or Ubuntu should be:在 Debian 或 Ubuntu 中应该是:
sudo apt update
sudo apt install build-essential
sudo apt-get install manpages-dev
gcc --version
Check here for more information:在这里查看更多信息:
因为现在新版本的Bioconductor是BiocManager,尝试使用这个: install.packages("BiocManager")
Apparently, it is trying to install package nlme
as a dependency and fails doing that.显然,它试图将包
nlme
作为依赖项安装,但失败了。 Did you try installing that one manually before installing Bioconductor ?在安装 Bioconductor 之前,您是否尝试过手动安装那个? That could give us more info on the issue.
这可以为我们提供有关该问题的更多信息。
Just as a heads up for someone who encounters similar issue.就像提醒遇到类似问题的人一样。 I was presented with a choice of installing a binary or compiling from scratch.
我可以选择安装二进制文件或从头开始编译。 As I chose compilation option, it was failing to install
nlme
.当我选择编译选项时,它无法安装
nlme
。 However, installation of binary was successful and there was a minor version difference between the source and the binary.但是,二进制文件安装成功,源代码和二进制文件之间存在细微的版本差异。
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