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Question: cran check shows that genefilter is not available
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gravatar for jinkaixiu
27 days ago by
jinkaixiu10
jinkaixiu10 wrote:

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.

ADD COMMENTlink modified 24 days ago • written 27 days ago by jinkaixiu10

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

ADD REPLYlink modified 27 days ago • written 27 days ago by shepherl ♦♦ 510

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 REPLYlink written 24 days ago by jinkaixiu10

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 REPLYlink written 23 days ago by shepherl ♦♦ 510

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 REPLYlink written 23 days ago by jinkaixiu10
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