R坑一：installation of package ‘org
2019-10-23 本文已影响0人
scdzzdw
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Bioconductor version '3.8' is out-of-date; the current release version '3.9' is available with R version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
