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Question: GO.db, pfma.db, KEGG.db
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gravatar for josefina.lascanomaillard
12 weeks ago by

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

ADD COMMENTlink modified 12 weeks ago by Martin Morgan ♦♦ 21k • written 12 weeks ago by josefina.lascanomaillard0
0
gravatar for Martin Morgan
12 weeks ago by
Martin Morgan ♦♦ 21k
United States
Martin Morgan ♦♦ 21k wrote:

Start from the first failure and work forward

>      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

The error is 

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'

So install Rcpp

    biocLite("Rcpp")

and try again to install GO.db

  biocLite("GO.db")

Usually this is not necessary (dependencies would be installed correctly) but somehow you've got things into a state where a previoulsy installed and loadable package (AnnotationDbi) can no longer be loaded (Rcpp, which itself must have previously been installed, is no longer installed).

 

ADD COMMENTlink written 12 weeks ago by Martin Morgan ♦♦ 21k
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