Hello,
I am trying to use the GProx software for proteomic data analysis and for this I need to install R and some corresponding bioconductor pakcages.
I tried several things and everything failed until now. I tried to change R version (for previous ones), I tried to manually install packages in R... Some of the bioconductor packages are well installed, but there's always a problem with the three packages GO.db, KEGG.db and pfam.db. Are these packages obsolete perhaps? If yes, do you know of any alternative?
Here are the commands that I get from the R console (with the previous version of R, I didn't have the error message at the end, but the package loading didn't work either):
> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.5 (BiocInstaller 1.26.1), ?biocLite for help
>
> biocLite("Mfuzz")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.1), R 3.4.1 (2017-06-30).
Installing package(s) ‘Mfuzz’
also installing the dependency ‘Biobase’
essai de l'URL 'https://bioconductor.org/packages/3.5/bioc/bin/windows/contrib/3.4/Biobase_2.36.2.zip'
Content type 'application/zip' length 4241291 bytes (4.0 MB)
downloaded 4.0 MB
essai de l'URL 'https://bioconductor.org/packages/3.5/bioc/bin/windows/contrib/3.4/Mfuzz_2.36.0.zip'
Content type 'application/zip' length 1399820 bytes (1.3 MB)
downloaded 1.3 MB
package ‘Biobase’ successfully unpacked and MD5 sums checked
package ‘Mfuzz’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\LASCANOM\AppData\Local\Temp\RtmpSE1Zpz\downloaded_packages
installation path not writeable, unable to update packages: boot, Matrix, mgcv
>
> biocLite("GO.db")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.1), R 3.4.1 (2017-06-30).
Installing package(s) ‘GO.db’
installing the source package ‘GO.db’
essai de l'URL 'https://bioconductor.org/packages/3.5/data/annotation/src/contrib/GO.db_3.4.1.tar.gz'
Content type 'application/x-gzip' length 32989255 bytes (31.5 MB)
downloaded 31.5 MB
* installing *source* package 'GO.db' ...
** R
** inst
** preparing package for lazy loading
Error: package or namespace load failed for 'AnnotationDbi' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
there is no package called 'Rcpp'
Error : package 'AnnotationDbi' could not be loaded
ERROR: lazy loading failed for package 'GO.db'
* removing 'C:/Users/LASCANOM/Documents/R/win-library/3.4/GO.db'
The downloaded source packages are in
‘C:\Users\LASCANOM\AppData\Local\Temp\RtmpSE1Zpz\downloaded_packages’
installation path not writeable, unable to update packages: boot, Matrix, mgcv
Warning messages:
1: l'exécution de la commande '"C:/PROGRA~1/R/R-34~1.1/bin/x64/R" CMD INSTALL -l "C:\Users\LASCANOM\Documents\R\win-library\3.4" C:\Users\LASCANOM\AppData\Local\Temp\RtmpSE1Zpz/downloaded_packages/GO.db_3.4.1.tar.gz' renvoie un statut 1
2: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘GO.db’ had non-zero exit status
>
> biocLite("PFAM.db")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.1), R 3.4.1 (2017-06-30).
Installing package(s) ‘PFAM.db’
installing the source package ‘PFAM.db’
essai de l'URL 'https://bioconductor.org/packages/3.5/data/annotation/src/contrib/PFAM.db_3.4.1.tar.gz'
Content type 'application/x-gzip' length 4134831 bytes (3.9 MB)
downloaded 3.9 MB
* installing *source* package 'PFAM.db' ...
** R
** inst
** preparing package for lazy loading
Error: package or namespace load failed for 'AnnotationDbi' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
there is no package called 'Rcpp'
Error : package 'AnnotationDbi' could not be loaded
ERROR: lazy loading failed for package 'PFAM.db'
* removing 'C:/Users/LASCANOM/Documents/R/win-library/3.4/PFAM.db'
The downloaded source packages are in
‘C:\Users\LASCANOM\AppData\Local\Temp\RtmpSE1Zpz\downloaded_packages’
installation path not writeable, unable to update packages: boot, Matrix, mgcv
Warning messages:
1: l'exécution de la commande '"C:/PROGRA~1/R/R-34~1.1/bin/x64/R" CMD INSTALL -l "C:\Users\LASCANOM\Documents\R\win-library\3.4" C:\Users\LASCANOM\AppData\Local\Temp\RtmpSE1Zpz/downloaded_packages/PFAM.db_3.4.1.tar.gz' renvoie un statut 1
2: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘PFAM.db’ had non-zero exit status
>
> biocLite("goTools")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.1), R 3.4.1 (2017-06-30).
Installing package(s) ‘goTools’
also installing the dependency ‘GO.db’
essai de l'URL 'https://bioconductor.org/packages/3.5/bioc/bin/windows/contrib/3.4/goTools_1.50.0.zip'
Content type 'application/zip' length 340753 bytes (332 KB)
downloaded 332 KB
package ‘goTools’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\LASCANOM\AppData\Local\Temp\RtmpSE1Zpz\downloaded_packages
installing the source package ‘GO.db’
essai de l'URL 'https://bioconductor.org/packages/3.5/data/annotation/src/contrib/GO.db_3.4.1.tar.gz'
Content type 'application/x-gzip' length 32989255 bytes (31.5 MB)
downloaded 31.5 MB
* installing *source* package 'GO.db' ...
** R
** inst
** preparing package for lazy loading
Error: package or namespace load failed for 'AnnotationDbi' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
there is no package called 'Rcpp'
Error : package 'AnnotationDbi' could not be loaded
ERROR: lazy loading failed for package 'GO.db'
* removing 'C:/Users/LASCANOM/Documents/R/win-library/3.4/GO.db'
The downloaded source packages are in
‘C:\Users\LASCANOM\AppData\Local\Temp\RtmpSE1Zpz\downloaded_packages’
installation path not writeable, unable to update packages: boot, Matrix, mgcv
Warning messages:
1: l'exécution de la commande '"C:/PROGRA~1/R/R-34~1.1/bin/x64/R" CMD INSTALL -l "C:\Users\LASCANOM\Documents\R\win-library\3.4" C:\Users\LASCANOM\AppData\Local\Temp\RtmpSE1Zpz/downloaded_packages/GO.db_3.4.1.tar.gz' renvoie un statut 1
2: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘GO.db’ had non-zero exit status
>
> biocLite("biomaRt")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.1), R 3.4.1 (2017-06-30).
Installing package(s) ‘biomaRt’
essai de l'URL 'https://bioconductor.org/packages/3.5/bioc/bin/windows/contrib/3.4/biomaRt_2.32.1.zip'
Content type 'application/zip' length 394339 bytes (385 KB)
downloaded 385 KB
package ‘biomaRt’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\LASCANOM\AppData\Local\Temp\RtmpSE1Zpz\downloaded_packages
installation path not writeable, unable to update packages: boot, Matrix, mgcv
>
> biocLite("SPIA")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.1), R 3.4.1 (2017-06-30).
Installing package(s) ‘SPIA’
essai de l'URL 'https://bioconductor.org/packages/3.5/bioc/bin/windows/contrib/3.4/SPIA_2.28.0.zip'
Content type 'application/zip' length 5116654 bytes (4.9 MB)
downloaded 4.9 MB
package ‘SPIA’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\LASCANOM\AppData\Local\Temp\RtmpSE1Zpz\downloaded_packages
installation path not writeable, unable to update packages: boot, Matrix, mgcv
>
> biocLite("KEGGgraph")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.1), R 3.4.1 (2017-06-30).
Installing package(s) ‘KEGGgraph’
essai de l'URL 'https://bioconductor.org/packages/3.5/bioc/bin/windows/contrib/3.4/KEGGgraph_1.38.1.zip'
Content type 'application/zip' length 3361494 bytes (3.2 MB)
downloaded 3.2 MB
package ‘KEGGgraph’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\LASCANOM\AppData\Local\Temp\RtmpSE1Zpz\downloaded_packages
installation path not writeable, unable to update packages: boot, Matrix, mgcv
>
> biocLite("KEGG.db")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.1), R 3.4.1 (2017-06-30).
Installing package(s) ‘KEGG.db’
installing the source package ‘KEGG.db’
essai de l'URL 'https://bioconductor.org/packages/3.5/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 'KEGG.db' ...
** R
** inst
** preparing package for lazy loading
Error: package or namespace load failed for 'AnnotationDbi' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
there is no package called 'Rcpp'
Error : package 'AnnotationDbi' could not be loaded
ERROR: lazy loading failed for package 'KEGG.db'
* removing 'C:/Users/LASCANOM/Documents/R/win-library/3.4/KEGG.db'
The downloaded source packages are in
‘C:\Users\LASCANOM\AppData\Local\Temp\RtmpSE1Zpz\downloaded_packages’
installation path not writeable, unable to update packages: boot, Matrix, mgcv
Warning messages:
1: l'exécution de la commande '"C:/PROGRA~1/R/R-34~1.1/bin/x64/R" CMD INSTALL -l "C:\Users\LASCANOM\Documents\R\win-library\3.4" C:\Users\LASCANOM\AppData\Local\Temp\RtmpSE1Zpz/downloaded_packages/KEGG.db_3.2.3.tar.gz' renvoie un statut 1
2: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘KEGG.db’ had non-zero exit status
> biocLite("marray")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.1), R 3.4.1 (2017-06-30).
Installing package(s) ‘marray’
essai de l'URL 'https://bioconductor.org/packages/3.5/bioc/bin/windows/contrib/3.4/marray_1.54.0.zip'
Content type 'application/zip' length 8870731 bytes (8.5 MB)
downloaded 8.5 MB
package ‘marray’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\LASCANOM\AppData\Local\Temp\RtmpSE1Zpz\downloaded_packages
installation path not writeable, unable to update packages: boot, Matrix, mgcv
>
> “Done”
Erreur : unexpected input in "“"
>
>
and
> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
Matrix products: default
locale:
[1] LC_COLLATE=French_Switzerland.1252 LC_CTYPE=French_Switzerland.1252
[3] LC_MONETARY=French_Switzerland.1252 LC_NUMERIC=C
[5] LC_TIME=French_Switzerland.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocInstaller_1.26.1
loaded via a namespace (and not attached):
[1] compiler_3.4.1 tools_3.4.1
Thanks in advance for your help.
Josefina
