M2芯片的MAC下载Rstudio的WGCNA

最近新换了电脑，之前下载的R包也要重新下载了。

目录

GO.db包的出错

GO.db包的解决办法

impute包的安装出错信息

impute包的解决办法

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GO.db包的出错

 最开始是想下载WGCNA这个包，结果依赖包GO.db下载失败，那就单独下载这个包吧。

BiocManager::install("GO.db")

警告

Warning: 无法在貯藏處https://bioconductor.org/packages/3.15/bioc/bin/macosx/big-sur-arm64/contrib/4.2中读写索引:   无法打开URL'https://bioconductor.org/packages/3.15/bioc/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES' Warning: 无法在貯藏處https://bioconductor.org/packages/3.15/data/annotation/bin/macosx/big-sur-arm64/contrib/4.2中读写索引:   无法打开URL'https://bioconductor.org/packages/3.15/data/annotation/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES' Warning: 无法在貯藏處https://bioconductor.org/packages/3.15/data/experiment/bin/macosx/big-sur-arm64/contrib/4.2中读写索引:   无法打开URL'https://bioconductor.org/packages/3.15/data/experiment/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES' Warning: 无法在貯藏處https://bioconductor.org/packages/3.15/workflows/bin/macosx/big-sur-arm64/contrib/4.2中读写索引:   无法打开URL'https://bioconductor.org/packages/3.15/workflows/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES' Warning: 无法在貯藏處https://bioconductor.org/packages/3.15/books/bin/macosx/big-sur-arm64/contrib/4.2中读写索引:   无法打开URL'https://bioconductor.org/packages/3.15/books/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES' Packages which are only available in source form, and may need compilation of   C/C++/Fortran: ‘zlibbioc’ ‘XVector’ ‘Biostrings’ ‘Biobase’ ‘IRanges’   ‘S4Vectors’

提示信息：Do you want to attempt to install these from sources? (Yes/no/cancel) Yes

错误信息没有记录了

GO.db包的解决办法

解决方法：打开Rstudio客户端之后，弹出安装git的提示框，选择下载安装，然后在提示信息那里继续输入Yes，就可以成功下载了。（如果弹不出来这个窗口，试着在终端输入git，系统就会检测到你有下载git的意向，窗口就弹出来啦）

impute包的安装出错信息

BiocManager::install("impute")

然后依次下载依赖包，直到impute下载的时候出现错误

'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details replacement repositories:    

CRAN: https://cran.rstudio.com/

Warning: unable to access index for repository https://cran.rstudio.com/src/contrib:   download from 'https://cran.rstudio.com/src/contrib/PACKAGES' failed

Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.1 (2022-06-23) Installing package(s) 'impute'

Warning: unable to access index for repository https://bioconductor.org/packages/3.15/bioc/bin/macosx/big-sur-arm64/contrib/4.2:   cannot open URL 'https://bioconductor.org/packages/3.15/bioc/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES'

Warning: unable to access index for repository https://bioconductor.org/packages/3.15/data/annotation/bin/macosx/big-sur-arm64/contrib/4.2:   cannot open URL 'https://bioconductor.org/packages/3.15/data/annotation/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES'

Warning: unable to access index for repository https://bioconductor.org/packages/3.15/data/experiment/bin/macosx/big-sur-arm64/contrib/4.2:   cannot open URL 'https://bioconductor.org/packages/3.15/data/experiment/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES'

Warning: unable to access index for repository https://bioconductor.org/packages/3.15/workflows/bin/macosx/big-sur-arm64/contrib/4.2:   cannot open URL 'https://bioconductor.org/packages/3.15/workflows/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.15/books/bin/macosx/big-sur-arm64/contrib/4.2:   cannot open URL 'https://bioconductor.org/packages/3.15/books/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES' Package which is only available in source form, and may need compilation of   C/C++/Fortran: ‘impute’

Do you want to attempt to install these from sources? (Yes/no/cancel) Yes

  installing the source package ‘impute’ trying URL 'https://bioconductor.org/packages/3.15/bioc/src/contrib/impute_1.70.0.tar.gz' Content type 'application/x-gzip' length 641570 bytes (626 KB) ================================================== downloaded 626 KB * installing *source* package ‘impute’ ... ** using staged installation ** libs /opt/R/arm64/bin/gfortran -mtune=native -fno-optimize-sibling-calls  -fPIC  -Wall -g -O2  -c knnimpute.f -o knnimpute.o

make: /opt/R/arm64/bin/gfortran: No such file or directory

make: *** [knnimpute.o]

Error 1 ERROR: compilation failed for package ‘impute’ * removing ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/impute’

The downloaded source packages are in     ‘/private/var/folders/1s/yly4nc8s1879mc8svmcl97_r0000gn/T/RtmpsWEPMD/downloaded_packages’

Warning message: In install.packages(...) :   installation of package ‘impute’ had non-zero exit status

就是编译出错了嘛。

然后参考这里

https://blog.csdn.net/qq_31550269/article/details/123942579

但是我需要的gfortran包的版本不一样，R4.2的需要最新版的编译包！！！

clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o impute.so knnimpute.o -L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1 -L/opt/R/arm64/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation

我需要20.6.0的

impute包的解决办法

想办法下载20.6.0的包

Tools - R for Mac OS X - developer's page - GNU Fortan for Xcode

在这里下载最新版，然后打开终端

tar fxz gfortran-12.0.1-20220312-is-darwin20-arm64.tar.xz -C /

解压好之后，在R重新下载impute

出现各种提示，都需要去隐私设置里面点击一下仍然允许。（我这里就是每一个包都要允许一下）

 然后重复下载就没问题了！

> library(WGCNA)

Attaching package: ‘WGCNA’

The following object is masked from ‘package:stats’:

    cor