Question: fail to install org.Hs.eg.db and hgu133plus2.db
0
gravatar for xiaoyutian212
2.9 years ago by
xiaoyutian2120 wrote:

Hi, 

I have recently tried to install hgu133plus2.db package in order to perform microarray analysis. However, I can't get this package and its dependency package org.Hs.eg.db installed properly. The following is the warning information.

> biocLite("hgu133plus2.db")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.3 (BiocInstaller 1.22.3), R
  3.3.1 (2016-06-21).
Installing package(s) hgu133plus2.db?also installing the dependency org.Hs.eg.db?
installing the source packages org.Hs.eg.db? hgu133plus2.db?
trying URL 'https://bioconductor.org/packages/3.3/data/annotation/src/contrib/org.Hs.eg.db_3.3.0.tar.gz'
Content type 'application/x-gzip' length 69122902 bytes (65.9 MB)
downloaded 65.9 MB

trying URL 'https://bioconductor.org/packages/3.3/data/annotation/src/contrib/hgu133plus2.db_3.2.3.tar.gz'
Content type 'application/x-gzip' length 2139642 bytes (2.0 MB)
downloaded 2.0 MB

'D:\Program' 不是内部或外部命令,也不是可运行的程序
或批处理文件。('D:\Program' is not internal or external command, not executable program or batch file.)。

'D:\Program' 不是内部或外部命令,也不是可运行的程序
或批处理文件。('D:\Program' is not internal or external command, not executable program or batch file.)

The downloaded source packages are in
    C:\Users\Bobby Xiao\AppData\Local\Temp\RtmpCykWuV\downloaded_packages?
Warning messages:
1: running command '"D:/Program Files/R/bin/x64/R" CMD INSTALL -l "D:\Program Files\R\library" C:\Users\BOBBYX~1\AppData\Local\Temp\RtmpCykWuV/downloaded_packages/org.Hs.eg.db_3.3.0.tar.gz' had status 1 
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package org.Hs.eg.db?had non-zero exit status
3: running command '"D:/Program Files/R/bin/x64/R" CMD INSTALL -l "D:\Program Files\R\library" C:\Users\BOBBYX~1\AppData\Local\Temp\RtmpCykWuV/downloaded_packages/hgu133plus2.db_3.2.3.tar.gz' had status 1 
4: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package hgu133plus2.db?had non-zero exit status

 

I tried to install org.Hs.eg.db independently, but also failed. Same warning message appeared.

I am using R v3.3.1 on windows 10.

> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils    
[5] datasets  methods   base     

other attached packages:
[1] BiocInstaller_1.22.3

loaded via a namespace (and not attached):
[1] tools_3.3.1

Can anyone kindly give me some help? 

ADD COMMENTlink written 2.9 years ago by xiaoyutian2120

I can't be too helpful, but the problem is likely related to (a) spaces in the file name and (b) use of '\' rather than '/' as path separator. Also, I suspect that this is not restricted to installing Bioconductor packages, but any R package? You could make sure that the PATH environment variable uses 'short' file names, and that R_LIBS or R_LIBS_USER environment variables use short names and '/' path separators.

ADD REPLYlink written 2.9 years ago by Martin Morgan ♦♦ 23k
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