Question: Issue installing packages ATACseqQC and GO.db
0
gravatar for n.pantelireis16
16 months ago by
n.pantelireis160 wrote:

Hi,

I'm having a little trouble with a couple installations at the moment. I've tried to install ATACseqQC on R3.4.4 and R3.4.3 using biocLite:

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

This seems to download all the files fine, but when I try to load the package using library("ATACseqQC") I get an error message

Error: package or namespace load failed for ‘ATACseqQC’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called ‘GO.db’

I then tried to install GO.db seperately using biocLite("GO.db") which fails to download outputting a number of error messages. I've pasted the output below can anyone help? 

Thank you,

Nick

 

biocLite("GO.db")

BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15).
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

'\\icnas4.cc.ic.ac.uk\np1216'
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 '\\icnas4.cc.ic.ac.uk/np1216/R/win-library/3.4/GO.db'
In R CMD INSTALL

The downloaded source packages are in
        ‘C:\Users\NP1216\AppData\Local\Temp\RtmpOMgF5w\downloaded_packages’
Old packages: 'GenomicRanges'
Update all/some/none? [a/s/n]: n
Warning messages:
1: running command '"C:/PROGRA~1/R/R-34~1.4/bin/x64/R" CMD INSTALL -l "\\icnas4.cc.ic.ac.uk\np1216\R\win-library\3.4" C:\Users\NP1216\AppData\Local\Temp\RtmpOMgF5w/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
ADD COMMENTlink modified 15 months ago by Ou, Jianhong1.1k • written 16 months ago by n.pantelireis160
Answer: Issue installing packages ATACseqQC and GO.db
0
gravatar for Ou, Jianhong
15 months ago by
Ou, Jianhong1.1k
United States
Ou, Jianhong1.1k wrote:

Could you try this:

 

biocLite(c("AnnotationDbi", "GO.db"), type="source")

 

also, please refer this post: Error loading GO.db

ADD COMMENTlink written 15 months ago by Ou, Jianhong1.1k
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