Unable to install "org.Hs.eg.db"

Question

[dliu201304]

Hi, I tried to install the package org.Hs.eg.db from the bioconductor, but the Rstudio failed to install.

The returning warning message is as followed:

BioC_mirror: http://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.1), R 3.2.3 (2015-12-10).
Installing package(s) 'org.Hs.eg.db'
installing the source package 'org.Hs.eg.db'

trying URL 'http://bioconductor.org/packages/3.2/data/annotation/src/contrib/org.Hs.eg.db_3.2.3.tar.gz'
Content type 'application/x-gzip' length 68856557 bytes (65.7 MB)
downloaded 65.7 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.)

The downloaded source packages are in
 'C:\Users\Liu\AppData\Local\Temp\RtmpQ9yUYt\downloaded_packages'
Warning messages:
1: running command '"D:/Program Files/R/R-3.2.3/bin/x64/R" CMD INSTALL -l "D:\Program Files\R\R-3.2.3\library" C:\Users\Liu\AppData\Local\Temp\RtmpQ9yUYt/downloaded_packages/org.Hs.eg.db_3.2.3.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

And my SessionInfo() is as followed:

R version 3.2.3 (2015-12-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.936
[2] LC_CTYPE=Chinese (Simplified)_China.936 
[3] LC_MONETARY=Chinese (Simplified)_China.936
[4] LC_NUMERIC=C               
[5] LC_TIME=Chinese (Simplified)_China.936  

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

other attached packages:
[1] BiocInstaller_1.20.1

loaded via a namespace (and not attached):
[1] tools_3.2.3

My .LibPaths() is as followed:

"D:/Program Files/R/R-3.2.3/library"

Could anynone help to debug this, it has plagued me for half a month, I tried all sorts of means, still no good result. Thank you so much!

[GouthamAtla]

Did you try ?

source("https://bioconductor.org/biocLite.R")
biocLite("org.Hs.eg.db")

[dliu201304]

Yes, I did. It's the exact command I used.

[dliu201304]

I updated the warning message.

[GouthamAtla]

My understand is that, its trying to execute the command:

"D:/Program Files/R/R-3.2.3/bin/x64/R" CMD INSTALL -l "D:\Program Files\R\R-3.2.3\library C:\Users\Liu\AppData\Local\Temp\RtmpQ9yUYt/downloaded_packages/org.Hs.eg.db_3.2.3.tar.gz"

But there is a space in the path, and its failing with an error message:

('D:\Program' is not internal or external command, not executable program or batch file.)

So go to the directory D:/Program Files/R/R-3.2.3/bin/x64/ and then run:

./R CMD INSTALL -l "D:\Program Files\R\R-3.2.3\library C:\Users\Liu\AppData\Local\Temp\RtmpQ9yUYt/downloaded_packages/org.Hs.eg.db_3.2.3.tar.gz"

Answer 1

[Sukhi Singh]

Try running R using,

D:/Program Files/R/R-3.2.3/bin/x64/R

The command prompt is not being able to run R from this location. Check where is R installed, and then you can run, which will install the package. There might be multiple R versions installed on your machine and thus the error.

locationofR/x64/R CMD INSTALL -l "D:\Program Files\R\R-3.2.3\library" C:\Users\Liu\AppData\Local\Temp\RtmpQ9yUYt/downloaded_packages/org.Hs.eg.db_3.2.3.tar.gz'