Question: GO.db failure to install
0
gravatar for matt.a.bennett25890
21 months ago by
matt.a.bennett258900 wrote:

Hi all,

Having trouble installing GO.db, seems to be a similar error to other problems reported on here in the past but I still can't see where the issue is. Everything required is up to date and installed as far as I can see. Here's the error:

 

> biocLite("GO.db")

BioC_mirror: https://bioconductor.org

Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.3 (2017-11-30).

Installing package(s) ‘GO.db’

installing the source package ‘GO.db’


trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/GO.db_3.5.0.tar.gz'

Content type 'application/x-gzip' length 31663705 bytes (30.2 MB)

downloaded 30.2 MB


'\\cmvm.datastore.ed.ac.uk\cmvm\scs\users\s1795508'

CMD.EXE was started with the above path as the current directory.

UNC paths are not supported.  Defaulting to Windows directory.

* installing *source* package 'GO.db' ...

** R

** inst

** preparing package for lazy loading

** help

*** installing help indices

  converting help for package 'GO.db'

    finding HTML links ... done

    GOBASE                                  html  

    GOBPANCESTOR                            html  

    GOBPCHILDREN                            html  

    GOBPOFFSPRING                           html  

    GOBPPARENTS                             html  

    GOCCANCESTOR                            html  

    GOCCCHILDREN                            html  

    GOCCOFFSPRING                           html  

    GOCCPARENTS                             html  

    GOMAPCOUNTS                             html  

    GOMFANCESTOR                            html  

    GOMFCHILDREN                            html  

    GOMFOFFSPRING                           html  

    GOMFPARENTS                             html  

    GOOBSOLETE                              html  

    GOSYNONYM                               html  

    GOTERM                                  html  

    GO_dbconn                               html  

** building package indices

** testing if installed package can be loaded

*** arch - i386

Error: package or namespace load failed for 'GO.db':

 .onLoad failed in loadNamespace() for 'GO.db', details:

  call: dbFileConnect(dbfile)

  error: DB file '' not found

Error: loading failed

Execution halted

*** arch - x64

Error: package or namespace load failed for 'GO.db':

 .onLoad failed in loadNamespace() for 'GO.db', details:

  call: dbFileConnect(dbfile)

  error: DB file '' not found

Error: loading failed

Execution halted

ERROR: loading failed for 'i386', 'x64'

* removing '\\cmvm.datastore.ed.ac.uk/cmvm/scs/users/s1795508/R/win-library/3.4/GO.db'

In R CMD INSTALL


The downloaded source packages are in

‘C:\Users\s1795508\AppData\Local\Temp\Rtmpas4U9p\downloaded_packages’

Warning messages:

1: running command '"C:/PROGRA~1/R/R-34~1.3/bin/x64/R" CMD INSTALL -l "\\cmvm.datastore.ed.ac.uk\cmvm\scs\users\s1795508\R\win-library\3.4" C:\Users\s1795508\AppData\Local\Temp\Rtmpas4U9p/downloaded_packages/GO.db_3.5.0.tar.gz' had status 1 

2: In install.packages(pkgs = doing, lib = lib, ...) :

  installation of package ‘GO.db’ had non-zero exit status

 

And here's the session info:

 

> sessionInfo()
R version 3.4.3 (2017-11-30)
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=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252   
[3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C                           
[5] LC_TIME=English_United Kingdom.1252    

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

other attached packages:
 [1] RMySQL_0.10.13         DBI_0.7                RSQLite_2.0            geneLenDataBase_1.14.0 BiasedUrn_1.07        
 [6] bit64_0.9-7            bit_1.1-12             graph_1.56.0           AnnotationDbi_1.40.0   IRanges_2.12.0        
[11] S4Vectors_0.16.0       Biobase_2.38.0         BiocInstaller_1.28.0   AnnotationHub_2.10.1   BiocGenerics_0.24.0   

loaded via a namespace (and not attached):
Error in x[["Version"]] : subscript out of bounds
In addition: Warning message:
In FUN(X[[i]], ...) :
  DESCRIPTION file of package 'GenomicRanges' is missing or broken
> library("GenomicRanges", lib.loc="\\\\cmvm.datastore.ed.ac.uk/cmvm/scs/users/s1795508/R/win-library/3.4")

 

Thanks for reading,

 

Matt

 

software error go.db • 967 views
ADD COMMENTlink written 21 months ago by matt.a.bennett258900

It seems that this issue is related to your environment and not GO.db or R.  I'm not able to reproduce this error since it involves your computing environemnt, but as per this article: https://support.rstudio.com/hc/en-us/articles/203775903-Fixing-startup-error-where-manipulate-and-rstudio-packages-will-not-install-with-networked-drives , it appears that the library you are trying to install to is on a networked drive.  The library you are trying to install to appears to be located on a UNF path, and R does not support these file paths.  The referenced article may be able to help you, or further searches regarding the error :

CMD.EXE was started with the above path as the current directory.

UNC paths are not supported.  Defaulting to Windows directory.

May help you solve this issue.

ADD REPLYlink modified 21 months ago • written 21 months ago by daniel.vantwisk50
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