## Hello everyone!
## I've been trying to install annaffy for a while and it doesn't work. It's the only one from 'affy' package that doesn't work. It says it is due to an error on installing 'Go.db' and 'KEGG.db'. I've tried to install those packages before and after annaffy, but it keeps on going on error. Thank you. - A.
> biocLite("annaffy") BioC_mirror: https://bioconductor.org Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2 (2016-10-31). Installing package(s) ‘annaffy’ also installing the dependencies ‘GO.db’, ‘KEGG.db’ trying URL 'https://bioconductor.org/packages/3.4/bioc/bin/windows/contrib/3.3/annaffy_1.46.0.zip' Content type 'application/zip' length 783907 bytes (765 KB) downloaded 765 KB package ‘annaffy’ successfully unpacked and MD5 sums checked The downloaded binary packages are in C:\Users\AppData\Local\Temp\Rtmp2FQ3E8\downloaded_packages installing the source packages ‘GO.db’, ‘KEGG.db’ trying URL 'https://bioconductor.org/packages/3.4/data/annotation/src/contrib/GO.db_3.4.0.tar.gz' Content type 'application/x-gzip' length 31897756 bytes (30.4 MB) downloaded 30.4 MB trying URL 'https://bioconductor.org/packages/3.4/data/annotation/src/contrib/KEGG.db_3.2.3.tar.gz' Content type 'application/x-gzip' length 1976342 bytes (1.9 MB) downloaded 1.9 MB * installing *source* package 'GO.db' ... Warning in file(file, if (append) "a" else "w") : cannot open file 'C:/Users/Documents/R/win-library/3.3/GO.db/DESCRIPTION': No such file or directory Error in file(file, if (append) "a" else "w") : no se puede abrir la conexión ERROR: installing package DESCRIPTION failed for package 'GO.db' * removing 'C:/Users/Documents/R/win-library/3.3/GO.db' * installing *source* package 'KEGG.db' ... Warning in file(file, if (append) "a" else "w") : cannot open file 'C:/Users/Documents/R/win-library/3.3/KEGG.db/DESCRIPTION': No such file or directory Error in file(file, if (append) "a" else "w") : no se puede abrir la conexión ERROR: installing package DESCRIPTION failed for package 'KEGG.db' * removing 'C:/Users/Documents/R/win-library/3.3/KEGG.db' The downloaded source packages are in ‘C:\Users\AppData\Local\Temp\Rtmp2FQ3E8\downloaded_packages’ installation path not writeable, unable to update packages: cluster, lattice, Matrix, mgcv, nlme, survival Warning messages: 1: running command '"C:/PROGRA~1/R/R-33~1.2/bin/x64/R" CMD INSTALL -l "C:\Users\Documents\R\win-library\3.3" C:\Users\AppData\Local\Temp\Rtmp2FQ3E8/downloaded_packages/GO.db_3.4.0.tar.gz' had status 1 2: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘GO.db’ had non-zero exit status 3: running command '"C:/PROGRA~1/R/R-33~1.2/bin/x64/R" CMD INSTALL -l "C:\Users\Documents\R\win-library\3.3" C:\Users\AppData\Local\Temp\Rtmp2FQ3E8/downloaded_packages/KEGG.db_3.2.3.tar.gz' had status 1 4: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘KEGG.db’ had non-zero exit status > library("annaffy") Error: package ‘GO.db’ required by ‘annaffy’ could not be found
The unusual thing about the output above is that the path "C:\Users\Documents" does not contain a user name, for instance I have "c:\Users\mtmorgan\Documents", so I wonder if there is a basic mis-configuration in either the R installation or elsewhere?
Sorry for the misunderstood. I deleted that info when I copied it due to personal information.