Question: error installing org.Rn.eg.db
1
gravatar for E.M. Lodder
14 months ago by
E.M. Lodder40
E.M. Lodder40 wrote:

Hi,

I hope hope someone has a solution for me. I am trying to install the rat annotation package, but it keeps giving errors. I have now re-installed R and tried in the clean new install as the many dependencies were giving me a headache. Unfortunately this has not brought a solution. Below is  my code and the following output of R.

Thanks for your help!

Elisabeth Lodder

> source("https://bioconductor.org/biocLite.R")
Warning in install.packages("BiocInstaller", repos = a["BioCsoft", "URL"]) :
  'lib = "C:/Program Files/R/R-3.5.1/library"' is not writable
trying URL 'https://bioconductor.org/packages/3.7/bioc/bin/windows/contrib/3.5/BiocInstaller_1.30.0.zip'
Content type 'application/zip' length 102191 bytes (99 KB)
downloaded 99 KB

package ‘BiocInstaller’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\EMLodder\AppData\Local\Temp\Rtmpagj7os\downloaded_packages
Bioconductor version 3.7 (BiocInstaller 1.30.0), ?biocLite for help
> biocLite("org.Rn.eg.db", dependencies=TRUE)
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.5.1 (2018-07-02).
Installing package(s) ‘org.Rn.eg.db’
also installing the dependencies ‘magrittr’, ‘assertthat’, ‘bit’, ‘prettyunits’, ‘digest’, ‘bit64’, ‘blob’, ‘memoise’, ‘pkgconfig’, ‘Rcpp’, ‘BH’, ‘plogr’, ‘bitops’, ‘BiocGenerics’, ‘Biobase’, ‘IRanges’, ‘RSQLite’, ‘S4Vectors’, ‘XML’, ‘xtable’, ‘RCurl’, ‘AnnotationDbi’, ‘DBI’, ‘annotate’, ‘RUnit’

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/magrittr_1.5.zip'
Content type 'application/zip' length 155766 bytes (152 KB)
downloaded 152 KB


### I removed the text for the downloads of the other dependencies to remain in the space restraints


package ‘magrittr’ successfully unpacked and MD5 sums checked

package ‘assertthat’ successfully unpacked and MD5 sums checked
package ‘bit’ successfully unpacked and MD5 sums checked
package ‘prettyunits’ successfully unpacked and MD5 sums checked
package ‘digest’ successfully unpacked and MD5 sums checked
package ‘bit64’ successfully unpacked and MD5 sums checked
package ‘blob’ successfully unpacked and MD5 sums checked
package ‘memoise’ successfully unpacked and MD5 sums checked
package ‘pkgconfig’ successfully unpacked and MD5 sums checked
package ‘Rcpp’ successfully unpacked and MD5 sums checked
package ‘BH’ successfully unpacked and MD5 sums checked
package ‘plogr’ successfully unpacked and MD5 sums checked
package ‘bitops’ successfully unpacked and MD5 sums checked
package ‘BiocGenerics’ successfully unpacked and MD5 sums checked
package ‘Biobase’ successfully unpacked and MD5 sums checked
package ‘IRanges’ successfully unpacked and MD5 sums checked
package ‘RSQLite’ successfully unpacked and MD5 sums checked
package ‘S4Vectors’ successfully unpacked and MD5 sums checked
package ‘XML’ successfully unpacked and MD5 sums checked
package ‘xtable’ successfully unpacked and MD5 sums checked
package ‘RCurl’ successfully unpacked and MD5 sums checked
package ‘AnnotationDbi’ successfully unpacked and MD5 sums checked
package ‘DBI’ successfully unpacked and MD5 sums checked
package ‘annotate’ successfully unpacked and MD5 sums checked
package ‘RUnit’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\EMLodder\AppData\Local\Temp\Rtmpagj7os\downloaded_packages
installing the source package ‘org.Rn.eg.db’

trying URL 'https://bioconductor.org/packages/3.7/data/annotation/src/contrib/org.Rn.eg.db_3.6.0.tar.gz'
Content type 'application/x-gzip' length 55437052 bytes (52.9 MB)
downloaded 52.9 MB

'\\amc.intra\users\E\emlodder\home'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
* installing *source* package 'org.Rn.eg.db' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'org.Rn.eg.db'
    finding HTML links ... done
    org.Rn.egACCNUM                         html  
    org.Rn.egALIAS2EG                       html  
    org.Rn.egBASE                           html  
    org.Rn.egCHR                            html  
    org.Rn.egCHRLENGTHS                     html  
    org.Rn.egCHRLOC                         html  
    org.Rn.egENSEMBL                        html  
    org.Rn.egENSEMBLPROT                    html  
    org.Rn.egENSEMBLTRANS                   html  
    org.Rn.egENZYME                         html  
    org.Rn.egGENENAME                       html  
    org.Rn.egGO                             html  
    org.Rn.egMAPCOUNTS                      html  
    org.Rn.egORGANISM                       html  
    org.Rn.egPATH                           html  
    org.Rn.egPFAM                           html  
    org.Rn.egPMID                           html  
    org.Rn.egPROSITE                        html  
    org.Rn.egREFSEQ                         html  
    org.Rn.egSYMBOL                         html  
    org.Rn.egUNIGENE                        html  
    org.Rn.egUNIPROT                        html  
    org.Rn.eg_dbconn                        html  
** building package indices
** testing if installed package can be loaded
*** arch - i386


#### The error message starts here


Error: package or namespace load failed for 'org.Rn.eg.db':
 .onLoad failed in loadNamespace() for 'org.Rn.eg.db', details:
  call: dbFileConnect(dbfile)
  error: DB file '' not found
Error: loading failed
Execution halted
*** arch - x64
Error: package or namespace load failed for 'org.Rn.eg.db':
 .onLoad failed in loadNamespace() for 'org.Rn.eg.db', details:
  call: dbFileConnect(dbfile)
  error: DB file '' not found
Error: loading failed
Execution halted
ERROR: loading failed for 'i386', 'x64'
* removing '\\amc.intra/users/E/emlodder/home/R/win-library/3.5/org.Rn.eg.db'
In R CMD INSTALL

The downloaded source packages are in
        ‘C:\Users\EMLodder\AppData\Local\Temp\Rtmpagj7os\downloaded_packages’
installation path not writeable, unable to update packages: foreign, survival
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘org.Rn.eg.db’ had non-zero exit status
> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: i386-w64-mingw32/i386 (32-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale:
[1] LC_COLLATE=Dutch_Netherlands.1252  LC_CTYPE=Dutch_Netherlands.1252    LC_MONETARY=Dutch_Netherlands.1252 LC_NUMERIC=C                       LC_TIME=Dutch_Netherlands.1252    

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

other attached packages:
[1] BiocInstaller_1.30.0

loaded via a namespace (and not attached):
[1] compiler_3.5.1 tools_3.5.1

ADD COMMENTlink modified 14 months ago by James W. MacDonald51k • written 14 months ago by E.M. Lodder40
Answer: error installing org.Rn.eg.db
0
gravatar for James W. MacDonald
14 months ago by
United States
James W. MacDonald51k wrote:

This isn't really a Bioconductor issue, nor even an R issue, but has to do with how Windows interacts with network drives. I think this advice Unable to install GO.db is workable; map the network drive to a letter (e.g., W:) and then start R (or setwd to) that mapped drive and install.

ADD COMMENTlink written 14 months ago by James W. MacDonald51k

Thanks for your help, but unfortunately this doesn't solve the problem. The problem does not occur when I try installing other packages from Bioconductor (I tried aCGH as an example). But seems specific for org.Rn.eg.db and the rat rat2302.db. Could it be because these packages do not have a windows binary available?

> setwd("H:\\R\\win-library\\3.5")
>  source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.7 (BiocInstaller 1.30.0), ?biocLite for help

> biocLite("rat2302.db")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.5.1 (2018-07-02).
Installing package(s) ‘rat2302.db’
also installing the dependency ‘org.Rn.eg.db’

installing the source packages ‘org.Rn.eg.db’, ‘rat2302.db’

...

** building package indices
** testing if installed package can be loaded
*** arch - i386
Error: package or namespace load failed for 'org.Rn.eg.db':
 .onLoad failed in loadNamespace() for 'org.Rn.eg.db', details:
  call: dbFileConnect(dbfile)
  error: DB file '' not found
Error: loading failed
Execution halted
*** arch - x64
Error: package or namespace load failed for 'org.Rn.eg.db':
 .onLoad failed in loadNamespace() for 'org.Rn.eg.db', details:
  call: dbFileConnect(dbfile)
  error: DB file '' not found
Error: loading failed
Execution halted
ERROR: loading failed for 'i386', 'x64'
* removing '\\amc.intra/users/E/emlodder/home/R/win-library/3.5/org.Rn.eg.db'
In R CMD INSTALL
ERROR: dependency 'org.Rn.eg.db' is not available for package 'rat2302.db'
* removing '\\amc.intra/users/E/emlodder/home/R/win-library/3.5/rat2302.db'
In R CMD INSTALL

The downloaded source packages are in
        ‘C:\Users\EMLodder\AppData\Local\Temp\RtmpMvKj8W\downloaded_packages’
installation path not writeable, unable to update packages: foreign, survival
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘org.Rn.eg.db’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘rat2302.db’ had non-zero exit status
> biocLite("aCGH")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.5.1 (2018-07-02).
Installing package(s) ‘aCGH’
also installing the dependency ‘multtest’

...

package ‘multtest’ successfully unpacked and MD5 sums checked
package ‘aCGH’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\EMLodder\AppData\Local\Temp\RtmpMvKj8W\downloaded_packages
installation path not writeable, unable to update packages: foreign, survival
> library(multtest)
Loading required package: BiocGenerics
Loading required package: parallel

...

ADD REPLYlink written 14 months ago by E.M. Lodder40

You can see from 

* removing '\\amc.intra/users/E/emlodder/home/R/win-library/3.5/rat2302.db'

that somewhere R thinks it's  using 'UNC' paths, maybe in the icon you click to start R.

ADD REPLYlink written 14 months ago by Martin Morgan ♦♦ 23k
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