figure out DB loading on Win10
egonw opened this issue · comments
See this debug info: https://gist.github.com/kozo2/b3b2effa6bd0d980e91b082ceb3a5974
cc @kozo2
@kozo2, can you give me an update on this (if still interested)? Is it fixed?
@egonw I forgot to reply. I'm sorry.
Now I checked the gist operation of BridgeDbR 1.22.0 with Windows10.
It is fixed. (worked well.) There was no error.
Thank you very much for your update.
> BiocManager::install("BridgeDbR")
Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.0 (2020-04-24)
Installing package(s) 'BridgeDbR'
also installing the dependency ‘rJava’
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/rJava_0.9-12.zip'
Content type 'application/zip' length 1501700 bytes (1.4 MB)
downloaded 1.4 MB
trying URL 'https://bioconductor.org/packages/3.11/bioc/bin/windows/contrib/4.0/BridgeDbR_1.22.0.zip'
Content type 'application/zip' length 2763590 bytes (2.6 MB)
downloaded 2.6 MB
package ‘rJava’ successfully unpacked and MD5 sums checked
package ‘BridgeDbR’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\kozon\AppData\Local\Temp\RtmpQXQQvh\downloaded_packages
Installation path not writeable, unable to update packages: boot, class, foreign, KernSmooth, MASS, nnet, spatial
> library(BridgeDbR)
Loading required package: rJava
> metdb = loadDatabase("metabolites_20191025.bridge")
> map(metdb, "C05625", source="Ck", target="Ce")
source identifier target mapping
1 Ck C05625 Ce CHEBI:28527
2 Ck C05625 Ce 28527
3 Ck C05625 Ce CHEBI:8923
>