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Question: Error installing org.Hs.eg.db
0
gravatar for fernanda.stapenhorst
5 weeks ago by
fernanda.stapenhorst0 wrote:

Hello!

I'm having trouble installing the package org.Hs.eg.db, and I don't know what is wrong! It downloads the package, but since it can't install it the file is deleted.

Here is what I get

> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help
> biocLite("org.Hs.eg.db")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.3 (2017-03-06).
Installing package(s) ‘org.Hs.eg.db’
installing the source package ‘org.Hs.eg.db’

tentando a URL 'https://bioconductor.org/packages/3.4/data/annotation/src/contrib/org.Hs.eg.db_3.4.0.tar.gz'
Content type 'application/x-gzip' length 69557350 bytes (66.3 MB)
downloaded 66.3 MB

* installing *source* package 'org.Hs.eg.db' ...
Warning in file(file, if (append) "a" else "w") :
  cannot open file 'C:/Users/Farmacia/Documents/R/win-library/3.3/org.Hs.eg.db/DESCRIPTION': No such file or directory
Error in file(file, if (append) "a" else "w") : 
  não é possível abrir a conexão
ERROR: installing package DESCRIPTION failed for package 'org.Hs.eg.db'
* removing 'C:/Users/Farmácia/Documents/R/win-library/3.3/org.Hs.eg.db'

The downloaded source packages are in
        ‘C:\Users\Farmácia\AppData\Local\Temp\Rtmp0mX6LX\downloaded_packages’
Warning messages:
1: execução do comando '"C:/PROGRA~1/R/R-33~1.3/bin/i386/R" CMD INSTALL -l "C:\Users\Farmácia\Documents\R\win-library\3.3" C:\Users\FARMCI~1\AppData\Local\Temp\Rtmp0mX6LX/downloaded_packages/org.Hs.eg.db_3.4.0.tar.gz' teve status 1 
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘org.Hs.eg.db’ had non-zero exit status

> sessionInfo()

R version 3.3.3 (2017-03-06)

Platform: i386-w64-mingw32/i386 (32-bit)

Running under: Windows 8.1 x64 (build 9600)


locale:

[1] LC_COLLATE=Portuguese_Brazil.1252  LC_CTYPE=Portuguese_Brazil.1252   

[3] LC_MONETARY=Portuguese_Brazil.1252 LC_NUMERIC=C                      

[5] LC_TIME=Portuguese_Brazil.1252    


attached base packages:

[1] stats     graphics  grDevices utils     datasets  methods   base     


other attached packages:

[1] installr_0.18.0      BiocInstaller_1.24.0


loaded via a namespace (and not attached):

[1] magrittr_1.5  tools_3.3.3   stringi_1.1.5 stringr_1.2.0

There are some parts of it in portuguese, where it says it cannot open connection (não é possível abrir a conexão - it has this weird characters because of portuguese accentuation) and that the command execution had status 1 (execução do comando '"C:/PROGRA~1/R/R-33~1.3/bin/i386/R" CMD INSTALL -l "C:\Users\Farmácia\Documents\R\win-library\3.3" C:\Users\FARMCI~1\AppData\Local\Temp\Rtmp0mX6LX/downloaded_packages/org.Hs.eg.db_3.4.0.tar.gz' teve status 1 )

How can I fix this?

Thanks!

 

ADD COMMENTlink modified 5 weeks ago by James W. MacDonald43k • written 5 weeks ago by fernanda.stapenhorst0
0
gravatar for James W. MacDonald
5 weeks ago by
United States
James W. MacDonald43k wrote:

R doesn't like the á in your library path. I don't know if there is a way to make R OK with that - you might google around a bit if you care - so the easiest thing to do is to use .libPaths() to set a library path that has just the base ASCII character set.

ADD COMMENTlink written 5 weeks ago by James W. MacDonald43k
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