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Question: can not able to install go.db
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gravatar for jarraya.amina.fst
12 months ago by
jarraya.amina.fst0 wrote:

Hello,

I tried to install go.db by entering the following commands :

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

But, i have the following erros :

> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help
> biocLite("GO.db")
BioC_mirror: https://bioc.ism.ac.jp
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.0 (2016-05-03).
Installing package(s) ‘GO.db’
installing the source package ‘GO.db’

essai de l'URL 'https://bioc.ism.ac.jp/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

'C:\Program' n'est pas reconnu en tant que commande interne
ou externe, un programme ex‚cutable ou un fichier de commandes.

The downloaded source packages are in
        ‘C:\Users\dell\AppData\Local\Temp\RtmpsTEDMf\downloaded_packages’
Old packages: 'GO.db'
Update all/some/none? [a/s/n]: a
installing the source package ‘GO.db’

essai de l'URL 'https://bioc.ism.ac.jp/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

'C:\Program' n'est pas reconnu en tant que commande interne
ou externe, un programme ex‚cutable ou un fichier de commandes.

The downloaded source packages are in
        ‘C:\Users\dell\AppData\Local\Temp\RtmpsTEDMf\downloaded_packages’
Warning messages:
1: l'exécution de la commande '"C:/Program Files/R/R-33~1.0/bin/x64/R" CMD INSTALL -l "C:\Program Files\R\R-3.3.0\library" C:\Users\dell\AppData\Local\Temp\RtmpsTEDMf/downloaded_packages/GO.db_3.4.0.tar.gz' renvoie un statut 1
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘GO.db’ had non-zero exit status
3: l'exécution de la commande '"C:/Program Files/R/R-33~1.0/bin/x64/R" CMD INSTALL -l "C:\Program Files\R\R-3.3.0\library" C:\Users\dell\AppData\Local\Temp\RtmpsTEDMf/downloaded_packages/GO.db_3.4.0.tar.gz' renvoie un statut 1
4: In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  installation of package ‘GO.db’ had non-zero exit status
>

Have you an idea about this problem ?

Thank you in advance

 

ADD COMMENTlink modified 12 months ago by Martin Morgan ♦♦ 21k • written 12 months ago by jarraya.amina.fst0

I also tried the following code to install WGCNA :

install.packages(c("matrixStats", "Hmisc", "splines", "foreach", "doParallel", "fastcluster", "dynamicTreeCut", "survival"))
source("http://bioconductor.org/biocLite.R")
biocLite(c("GO.db", "preprocessCore", "impute"))

but it's the same errors :

> install.packages(c("matrixStats", "Hmisc", "splines", "foreach", "doParallel", "fastcluster", "dynamicTreeCut", "survival"))
Warning: les packages ‘fastcluster’, ‘dynamicTreeCut’ sont en cours d'utilisation et ne seront pas installés
essai de l'URL 'https://cran.usthb.dz/bin/windows/contrib/3.3/matrixStats_0.51.0.zip'
Content type 'application/zip' length 1540663 bytes (1.5 MB)
downloaded 1.5 MB

essai de l'URL 'https://cran.usthb.dz/bin/windows/contrib/3.3/Hmisc_4.0-0.zip'
Content type 'application/zip' length 1770793 bytes (1.7 MB)
downloaded 1.7 MB

essai de l'URL 'https://cran.usthb.dz/bin/windows/contrib/3.3/foreach_1.4.3.zip'
Content type 'application/zip' length 389171 bytes (380 KB)
downloaded 380 KB

essai de l'URL 'https://cran.usthb.dz/bin/windows/contrib/3.3/doParallel_1.0.10.zip'
Content type 'application/zip' length 184513 bytes (180 KB)
downloaded 180 KB

essai de l'URL 'https://cran.usthb.dz/bin/windows/contrib/3.3/survival_2.40-1.zip'
Content type 'application/zip' length 5109471 bytes (4.9 MB)
downloaded 4.9 MB

le package ‘matrixStats’ a été décompressé et les sommes MD5 ont été vérifiées avec succés
le package ‘Hmisc’ a été décompressé et les sommes MD5 ont été vérifiées avec succés
le package ‘foreach’ a été décompressé et les sommes MD5 ont été vérifiées avec succés
le package ‘doParallel’ a été décompressé et les sommes MD5 ont été vérifiées avec succés
le package ‘survival’ a été décompressé et les sommes MD5 ont été vérifiées avec succés

Les packages binaires téléchargés sont dans
        C:\Users\dell\AppData\Local\Temp\RtmpWmzmk3\downloaded_packages
Warning messages:
1: package ‘splines’ is not available (for R version 3.3.0)
2: package ‘splines’ is a base package, and should not be updated
> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help
> biocLite(c("GO.db", "preprocessCore", "impute"))
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.0 (2016-05-03).
Installing package(s) ‘GO.db’, ‘preprocessCore’, ‘impute’
essai de l'URL 'https://bioconductor.org/packages/3.4/bioc/bin/windows/contrib/3.3/preprocessCore_1.36.0.zip'
Content type 'application/zip' length 435309 bytes (425 KB)
downloaded 425 KB

essai de l'URL 'https://bioconductor.org/packages/3.4/bioc/bin/windows/contrib/3.3/impute_1.48.0.zip'
Content type 'application/zip' length 1342260 bytes (1.3 MB)
downloaded 1.3 MB

package ‘preprocessCore’ successfully unpacked and MD5 sums checked
package ‘impute’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\dell\AppData\Local\Temp\RtmpWmzmk3\downloaded_packages
installing the source package ‘GO.db’

essai de l'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

'C:\Program' n'est pas reconnu en tant que commande interne
ou externe, un programme ex‚cutable ou un fichier de commandes.

The downloaded source packages are in
        ‘C:\Users\dell\AppData\Local\Temp\RtmpWmzmk3\downloaded_packages’
Warning messages:
1: l'exécution de la commande '"C:/Program Files/R/R-33~1.0/bin/x64/R" CMD INSTALL -l "C:\Program Files\R\R-3.3.0\library" C:\Users\dell\AppData\Local\Temp\RtmpWmzmk3/downloaded_packages/GO.db_3.4.0.tar.gz' renvoie un statut 1
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘GO.db’ had non-zero exit status

Any idea ?

 

ADD REPLYlink written 12 months ago by jarraya.amina.fst0

for information :

 

For information :

> .libPaths()
[1] "C:/Program Files/R/R-3.3.0/library"
> sessionInfo()
R version 3.3.0 (2016-05-03)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7600)

locale:
[1] LC_COLLATE=French_France.1252  LC_CTYPE=French_France.1252   
[3] LC_MONETARY=French_France.1252 LC_NUMERIC=C                  
[5] LC_TIME=French_France.1252    

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets
[8] methods   base     

other attached packages:
 [1] AnnotationDbi_1.36.0  IRanges_2.8.1         S4Vectors_0.12.0     
 [4] Biobase_2.34.0        BiocGenerics_0.20.0   RSQLite_1.0.0        
 [7] DBI_0.5-1             fastcluster_1.1.21    dynamicTreeCut_1.63-1
[10] BiocInstaller_1.24.0  fuzzyforest_1.0.2    

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.8         magrittr_1.5        munsell_0.4.3      
 [4] doParallel_1.0.10   colorspace_1.3-1    xtable_1.8-2       
 [7] doRNG_1.6           foreach_1.4.3       pkgmaker_0.22      
[10] stringr_1.1.0       plyr_1.8.4          rngtools_1.2.4     
[13] tools_3.3.0         grid_3.3.0          gtable_0.2.0       
[16] registry_0.3        modeltools_0.2-21   iterators_1.0.8    
[19] randomForest_4.6-12 lazyeval_0.2.0      digest_0.6.10      
[22] assertthat_0.1      tibble_1.2          ggplot2_2.2.0      
[25] codetools_0.2-15    stringi_1.1.2       scales_0.4.1       
>
ADD REPLYlink written 12 months ago by jarraya.amina.fst0

Please any help ?

I can't install GO.db.. I have to translate warning and error messages in english ?

ADD REPLYlink written 12 months ago by jarraya.amina.fst0
1
gravatar for Martin Morgan
12 months ago by
Martin Morgan ♦♦ 21k
United States
Martin Morgan ♦♦ 21k wrote:

The general problem is the space in the path to R, C:\Program Files\ ... I don't really know why R is not interpreting this correctly, but you would like this to be a 'short' path name without spaces, something like C:\Progra~1\... Likely you'd like this in both the R command (probably adjusting your PATH system enironment variable) and in the .libPaths() (probably inherited from PATH).

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

Thank you very much for your answer,

I moved the folder R inside C:\ directly and the installation of go.db works fine!

 

ADD REPLYlink written 12 months ago by jarraya.amina.fst0
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