Issue with annotation package mouse4302.db
1
0
Entering edit mode
surajit • 0
@1449e5ac
Last seen 6 months ago
United States

Hi All,

I am trying to install mouse4302.db annotation package. I get a syntax error (see below). I tried installing using the tar.gz package too, but had the same result. Can anyone provide me a workaround for this issue?


if (!requireNamespace("BiocManager", quietly = TRUE))
+     install.packages("BiocManager")
> 
> BiocManager::install("mouse4302.db")
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
    CRAN: https://cran.rstudio.com/

Bioconductor version 3.13 (BiocManager 1.30.16), R 4.1.0 (2021-05-18)
Installing package(s) 'mouse4302.db'
installing the source package 'mouse4302.db'

trying URL 'https://bioconductor.org/packages/3.13/data/annotation/src/contrib/mouse4302.db_3.13.0.tar.gz'
Content type 'application/x-gzip' length 1808369 bytes (1.7 MB)
downloaded 1.7 MB

* installing *source* package 'mouse4302.db' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'mouse4302.db'
    finding HTML links ... done
    mouse4302ACCNUM                         html  
    mouse4302ALIAS2PROBE                    html  
    mouse4302BASE                           html  
    mouse4302CHR                            html  
    mouse4302CHRLENGTHS                     html  
    mouse4302CHRLOC                         html  
    mouse4302ENSEMBL                        html  
    mouse4302ENTREZID                       html  
    mouse4302ENZYME                         html  
    mouse4302GENENAME                       html  
    mouse4302GO                             html  
    mouse4302MAPCOUNTS                      html  
    mouse4302MGI                            html  
    mouse4302ORGANISM                       html  
    mouse4302PATH                           html  
    mouse4302PFAM                           html  
    mouse4302PMID                           html  
    mouse4302PROSITE                        html  
    mouse4302REFSEQ                         html  
    mouse4302SYMBOL                         html  
    mouse4302UNIPROT                        html  
    mouse4302_dbconn                        html  
** building package indices
** testing if installed package can be loaded from temporary location
*** arch - i386
Error: package or namespace load failed for 'mouse4302.db':
 .onLoad failed in loadNamespace() for 'mouse4302.db', details:
  call: NULL
  error: near "s": syntax error
Error: loading failed
Execution halted
*** arch - x64
Error: package or namespace load failed for 'mouse4302.db':
 .onLoad failed in loadNamespace() for 'mouse4302.db', details:
  call: NULL
  error: near "s": syntax error
Error: loading failed
Execution halted
ERROR: loading failed for 'i386', 'x64'
* removing 'C:/Users/sbhattach2/OneDrive - Children's National Hospital/Documents/R/win-library/4.1/mouse4302.db'

Thanks again for all the help in advance.

Surajit

mouse4302.db annotation • 254 views
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Entering edit mode
@james-w-macdonald-5106
Last seen 1 hour ago
United States

R is not going to like installing a source package into a directory with an apostrophe in it. Plus I wouldn't personally put my R library dir in a OneDrive folder. I normally use the default windows dir of C:/Users/<username>/AppData/Roaming/R/win-library, which has no spaces nor other problematic punctuation.

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