Hi,

Right now, it seems that none of the AnnotationData packages have Window Binary or Mac versions available, only Source. Did I just happen to try it when they are being rebuilt or are they no longer available? Here's an example:

http://bioconductor.org/packages/release/data/annotation/html/org.Mm.eg.db.html 

Thanks,

Jenny

None of the annotation data packages have binaries, nor do they need them since there is no compilation required. If you install using biocLite, it will just get the source package and install as usual:

Edit: I should note that the output below is from a windows box

> biocLite("org.Mm.eg.db")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.1), R 3.2.2 (2015-08-14).
Installing package(s) 'org.Mm.eg.db'
installing the source package 'org.Mm.eg.db'

trying URL 'https://bioconductor.org/packages/3.2/data/annotation/src/contrib/org.Mm.eg.db_3.2.3.tar.gz'
Content type 'application/x-gzip' length 63617232 bytes (60.7 MB)
downloaded 60.7 MB

* installing *source* package 'org.Mm.eg.db' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
*** arch - i386
*** arch - x64
* DONE (org.Mm.eg.db)

OK, here are the error messages. It seems like the system is not able to handle the space in in the path to R? The IT guy for the computer lab has no idea why that would be happening. I can probably get around it by directly installing from the command line, but why is this happening on the computer lab system and not my own PC?

Thanks for any help,

Jenny

> source("https://bioconductor.org/biocLite.R")

Bioconductor version 3.2 (BiocInstaller 1.20.1), ?biocLite for help

> biocLite("org.Mm.eg.db")

BioC_mirror: https://bioconductor.org

Using Bioconductor 3.2 (BiocInstaller 1.20.1), R 3.2.3 (2015-12-10).

Installing package(s) ‘org.Mm.eg.db’

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


trying URL 'https://bioconductor.org/packages/3.2/data/annotation/src/contrib/org.Mm.eg.db_3.2.3.tar.gz'

Content type 'application/x-gzip' length 63617232 bytes (60.7 MB)

downloaded 60.7 MB


'C:\Program' is not recognized as an internal or external command,

operable program or batch file.


The downloaded source packages are in

        ‘C:\users\igb\appdata\local\Temp\Rtmp8S7p7X\downloaded_packages’

Warning messages:

1: running command '"C:/Program Files/R/R-3.2.3/bin/x64/R" CMD INSTALL -l "C:\users\igb\Documents\R\win-library\3.2" C:\Users\IGB\AppData\Local\Temp\Rtmp8S7p7X/downloaded_packages/org.Mm.eg.db_3.2.3.tar.gz' had status 1 

2: In install.packages(pkgs = doing, lib = lib, ...) :

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


> sessionInfo()

R version 3.2.3 (2015-12-10)

Platform: x86_64-w64-mingw32/x64 (64-bit)

Running under: Windows 7 x64 (build 7601) Service Pack 1


locale:

[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252

[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    


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