R坑一:installation of package ‘org.Mm.eg.db’ had non-zero exit status

使用ChIPseeker做ChIP-Seq注释时,需安装“org.Mm.eg.db”,于是使用以下命令下载安装:


BiocManager::install("org.Mm.eg.db")

结果报错如下:


Bioconductor version 3.8 (BiocManager 1.30.8), ?BiocManager::install for help

Bioconductor version '3.8' is out-of-date; the current release version '3.9' is available with R version

  '3.6'; see https://bioconductor.org/install

Bioconductor version 3.8 (BiocManager 1.30.8), R 3.5.1 (2018-07-02)

Installing package(s) 'org.Mm.eg.db'

installing the source package ‘org.Mm.eg.db’

trying URL 'https://bioconductor.org/packages/3.8/data/annotation/src/contrib/org.Mm.eg.db_3.7.0.tar.gz'

Content type 'application/x-gzip' length 69822781 bytes (66.6 MB)

downloaded 66.6 MB

* installing *source* package 'org.Mm.eg.db' ...

** R

** inst

** byte-compile and prepare package for lazy loading

Error: package or namespace load failed for 'AnnotationDbi' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):

 there is no package called 'RSQLite'

Error : package 'AnnotationDbi' could not be loaded

ERROR: lazy loading failed for package 'org.Mm.eg.db'

* removing 'C:/Users/zhangdengwei/Documents/R/win-library/3.5/org.Mm.eg.db'

In R CMD INSTALL

The downloaded source packages are in

‘C:\Users\zhangdengwei\AppData\Local\Temp\RtmpIDBXB0\downloaded_packages’

Installation path not writeable, unable to update packages: boot, class, cluster, codetools, foreign,

  KernSmooth, lattice, MASS, Matrix, mgcv, nlme, rpart, survival

Old packages: 'digest'

Update all/some/none? [a/s/n]: 

a

  There is a binary version available but the source version is later:

       binary source needs_compilation

digest 0.6.21 0.6.22              TRUE

  Binaries will be installed

trying URL 'https://cran.csiro.au/bin/windows/contrib/3.5/digest_0.6.21.zip'

Content type 'application/zip' length 237366 bytes (231 KB)

downloaded 231 KB

package ‘digest’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in

C:\Users\zhangdengwei\AppData\Local\Temp\RtmpIDBXB0\downloaded_packages

Warning message:

In install.packages(...) :

  installation of package ‘org.Mm.eg.db’ had non-zero exit status

后面去官网问了,有人建议说可能是缓存路径含有中文字符,确认了下不是这个问题,然后在网上查了下,决定使用已下载到本地的包进行安装,使用以下命令:


install.packages("C:\\Users\\zhangdengwei\\AppData\\Local\\Temp\\RtmpIDBXB0\\downloaded_packages\\org.Mm.eg.db_3.7.0.tar.gz")

还是报错....


Installing package into ‘C:/Users/zhangdengwei/Documents/R/win-library/3.5’

(as ‘lib’ is unspecified)

Warning in install.packages :

  package ‘C:\Users\zhangdengwei\AppData\Local\Temp\RtmpIDBXB0\downloaded_packages\org.Mm.eg.db_3.7.0.tar.gz’ is not available (for R version 3.5.1)

不死心,继续试,使用Rstudio菜单栏导入本地模块进行安装,如下

image

Tools中的 Install Packages,然后导入本地安装已下载的压缩包进行安装,继续报错...


> install.packages("C:/Users/zhangdengwei/AppData/Local/Temp/RtmpIDBXB0/downloaded_packages/org.Mm.eg.db_3.7.0.tar.gz", repos = NULL, type = "source")

Installing package into ‘C:/Users/zhangdengwei/Documents/R/win-library/3.5’

(as ‘lib’ is unspecified)

* installing *source* package 'org.Mm.eg.db' ...

** R

** inst

** byte-compile and prepare package for lazy loading

Error: package or namespace load failed for 'AnnotationDbi' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):

 there is no package called 'RSQLite'

Error : package 'AnnotationDbi' could not be loaded

ERROR: lazy loading failed for package 'org.Mm.eg.db'

* removing 'C:/Users/zhangdengwei/Documents/R/win-library/3.5/org.Mm.eg.db'

In R CMD INSTALL

Warning in install.packages :

  installation of package ‘C:/Users/zhangdengwei/AppData/Local/Temp/RtmpIDBXB0/downloaded_packages/org.Mm.eg.db_3.7.0.tar.gz’ had non-zero exit status

不过这次发现上述报错里提到没有RSQLite包,安装


> BiocManager::install("RSQLite")

Bioconductor version 3.8 (BiocManager 1.30.8), R 3.5.1 (2018-07-02)

Installing package(s) 'RSQLite'

trying URL 'https://cran.csiro.au/bin/windows/contrib/3.5/RSQLite_2.1.2.zip'

Content type 'application/zip' length 2267199 bytes (2.2 MB)

downloaded 2.2 MB

package ‘RSQLite’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in

C:\Users\zhangdengwei\AppData\Local\Temp\RtmpIDBXB0\downloaded_packages

Installation path not writeable, unable to update packages: boot, class, cluster, codetools, foreign,

  KernSmooth, lattice, MASS, Matrix, mgcv, nlme, rpart, survival

Old packages: 'digest'

Update all/some/none? [a/s/n]: 

a

  There is a binary version available but the source version is later:

       binary source needs_compilation

digest 0.6.21 0.6.22              TRUE

  Binaries will be installed

trying URL 'https://cran.csiro.au/bin/windows/contrib/3.5/digest_0.6.21.zip'

Content type 'application/zip' length 237366 bytes (231 KB)

downloaded 231 KB

package ‘digest’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in

C:\Users\zhangdengwei\AppData\Local\Temp\RtmpIDBXB0\downloaded_packages

然后再安装


> install.packages("C:/Users/zhangdengwei/AppData/Local/Temp/RtmpIDBXB0/downloaded_packages/org.Mm.eg.db_3.7.0.tar.gz", repos = NULL, type = "source")

Installing package into ‘C:/Users/zhangdengwei/Documents/R/win-library/3.5’

(as ‘lib’ is unspecified)

* installing *source* package 'org.Mm.eg.db' ...

** R

** inst

** byte-compile and prepare package for lazy loading

** help

*** installing help indices

  converting help for package 'org.Mm.eg.db'

    finding HTML links ... 好了

    org.Mm.egACCNUM                         html  

    org.Mm.egALIAS2EG                       html  

    org.Mm.egBASE                           html  

    org.Mm.egCHR                            html  

    org.Mm.egCHRLENGTHS                     html  

    org.Mm.egCHRLOC                         html  

    org.Mm.egENSEMBL                        html  

    org.Mm.egENSEMBLPROT                    html  

    org.Mm.egENSEMBLTRANS                   html  

    org.Mm.egENZYME                         html  

    org.Mm.egGENENAME                       html  

    org.Mm.egGO                             html  

    org.Mm.egMAPCOUNTS                      html  

    org.Mm.egMGI                            html  

    org.Mm.egORGANISM                       html  

    org.Mm.egPATH                           html  

    org.Mm.egPFAM                           html  

    org.Mm.egPMID                           html  

    org.Mm.egPROSITE                        html  

    org.Mm.egREFSEQ                         html  

    org.Mm.egSYMBOL                         html  

    org.Mm.egUNIGENE                        html  

    org.Mm.egUNIPROT                        html  

    org.Mm.eg_dbconn                        html  

** building package indices

** testing if installed package can be loaded

* DONE (org.Mm.eg.db)

In R CMD INSTALL

ok,这下可以了。再回头看,发现最开始已经提示没有RSQLite包,哎,真是太菜了,还是要细心呀

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