cran check shows that genefilter is not available
0
1
Entering edit mode
jinkaixiu ▴ 10
@jinkaixiu-14417
Last seen 6.3 years ago

Hi,

Thank you for your time, I have a problem here. Hope you can help me with it.

Recently I submitted a package boclust to CRAN and passed the examination of maintainer. But when it's transformed to other platform, there is something wrong about genefilter:

 Version: 0.1.0 
 Check: package dependencies 
 Result: ERROR 
   Package required but not available: ‘genefilter’
   See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
    manual.

In my package, there are two functions relevant to genefilter. Specifically, I use two functions from genefilter: coltests and colFtests. So there is a line in NAMESPACE:

import(genefilter)

Also, because genefilter is a package from R package, in DESCRIPTION file, I use those description to import genefilter and other packages:

biocViews: genefilter(>= 1.58.1)
Imports:
    reshape2 (>= 1.4.2),
    psych (>= 1.7.3.21),
    Rtsne (>= 0.13),
    d3heatmap (>= 0.6.1.1),
    venn (>= 1.2),
    DT (>= 0.2),
    shiny (>= 1.0.5),
    ggplot2 (>= 2.2.1),
    stats,
    genefilter (>= 1.58.1)

And I found two similar mistakes from another packages apmsWAPP & ssizeRNA with the check result(apmsWAPP) &  check result(ssizeRNA)

Version: 1.0 
Check: package dependencies 
Result: ERROR 
    Packages required but not available:
     ‘genefilter’ ‘edgeR’ ‘DESeq’ ‘aroma.light’

Version: 1.2.9 
Check: package dependencies 
Result: ERROR 
    Packages required but not available: ‘edgeR’ ‘qvalue’
    
    See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
    manual. 
Flavor: r-release-osx-x86_64


So, I don't know whether this error is because of the R package's new version or package genefilter's modification?

Thank you for your time, hope you can help me with it.

genefilter • 1.8k views
ADD COMMENT
0
Entering edit mode

could you please provide your sessionInfo() ; what os are you using?

ADD REPLY
0
Entering edit mode

Thank you for reminding me for this. Here is my session information:

R version 3.4.2 (2017-09-28)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] zh_CN.UTF-8/zh_CN.UTF-8/zh_CN.UTF-8/C/zh_CN.UTF-8/zh_CN.UTF-8

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

loaded via a namespace (and not attached):
[1] compiler_3.4.2 tools_3.4.2   
ADD REPLY
0
Entering edit mode

And you have installed those packages: 

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

biocLite(c("genefilter","edgeR","DESeq","aroma.light"))

Are there any other ERRORs produced when trying to run the above code? 

 

ADD REPLY
0
Entering edit mode

Everything is fine in my computer. As for the old version of R, thanks to Uwe Ligges, I find the error is caused by that for BioC versions associated with R-3.3.x genefilter (≥ 1.58.1) is not available (actually the latest version for the R-3.3.x series was genefilter 1.56.0).

However, for the release version, there is something wrong, which is unsure yet.

ADD REPLY

Login before adding your answer.

Traffic: 711 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6