[R-pkg-devel] ERROR DUE TO EXISTING BIOCONDUCTOR PACKAGES NOT WORKING ON R-DEVEL

[Duncan Murdoch]

If the Bioconductor packages are unconditional requirements, maybe you 
should submit your package to Bioconductor rather than CRAN.  Just from 
the name ("multiomicsR") it looks like it might be appropriate there.

Duncan Murdoch



On 19/09/2022 2:14 a.m., Das, Sarmistha wrote:
> Hello,
> I ran (1) R CMD check --as-cran mypackage.tar.gz without any error. But it gives an error while running the package on (2) current version-of-R-devel as my package uses Bioconductor package (that does not run on R version 4.3). Please help me with any idea how to fix this error. I have attached the check results below.
> 
> Thanks,
> Sarmistha
> **********************************************
> R CMD check results:
> **********************************************
> 
> (1)  * using log directory
>    ‘/.../multiomicsR.Rcheck’
> *
>    using R version 4.2.1 (2022-06-23)
> * using platform:
>    x86_64-apple-darwin17.0 (64-bit)
> * using session
>    charset: UTF-8
> * using option ‘--as-cran’
> *
>    checking for file ‘multiomicsR/DESCRIPTION’ ...
>    OK
> * this is package ‘multiomicsR’ version
>    ‘0.1’
> * package encoding: UTF-8
> * checking CRAN
>    incoming feasibility ... NOTE
> Maintainer:
>    ‘Sarmistha Das <sarmistha.das using stjude.org>’
> 
> New
>    submission
> * checking package namespace information
>    ... OK
> * checking package dependencies ... OK
> *
>    checking if this is a source package ... OK
> *
>    checking if there is a namespace ... OK
> * checking
>    for executable files ... OK
> * checking for hidden
>    files and directories ... OK
> * checking for portable
>    file names ... OK
> * checking for sufficient/correct
>    file permissions ... OK
> * checking whether package
>    ‘multiomicsR’ can be installed ... OK
> * checking
>    installed package size ... OK
> * checking package
>    directory ... OK
> * checking for future file
>    timestamps ... OK
> * checking DESCRIPTION
>    meta-information ... OK
> * checking top-level files
>    ... OK
> * checking for left-over files ... OK
> *
>    checking index information ... OK
> * checking package
>    subdirectories ... OK
> * checking R files for
>    non-ASCII characters ... OK
> * checking R files for
>    syntax errors ... OK
> * checking whether the package
>    can be loaded ... OK
> * checking whether the package
>    can be loaded with stated dependencies ... OK
> *
>    checking whether the package can be unloaded cleanly
>    ... OK
> * checking whether the namespace can be
>    loaded with stated dependencies ... OK
> * checking
>    whether the namespace can be unloaded cleanly ...
>    OK
> * checking use of S3 registration ... OK
> *
>    checking dependencies in R code ... OK
> * checking S3
>    generic/method consistency ... OK
> * checking
>    replacement functions ... OK
> * checking foreign
>    function calls ... OK
> * checking R code for possible
>    problems ... OK
> * checking Rd files ... OK
> *
>    checking Rd metadata ... OK
> * checking Rd line
>    widths ... OK
> * checking Rd cross-references ...
>    OK
> * checking for missing documentation entries ...
>    OK
> * checking for code/documentation mismatches ...
>    OK
> * checking Rd \usage sections ... OK
> * checking
>    Rd contents ... OK
> * checking for unstated
>    dependencies in examples ... OK
> * checking examples
>    ... NOTE
> Examples with CPU (user + system) or
>    elapsed time > 5s
>             user system
>    elapsed
> iosearchR 59.22  5.586 211.242
> * checking
>    PDF version of manual ... OK
> * checking for
>    non-standard things in the check directory ...
>    NOTE
> Found the following files/directories:
> 
>    ‘GDCdata’ ‘MANIFEST.txt’ ‘TCGAbiolinks’
>    ‘clinical_InfoFile.txt’
>    ‘omic1_Group1.txt’
>    ‘omic1_Group2.txt’ ‘omic2_Group1.txt’
> 
>    ‘omic2_Group2.txt’ ‘pathway_genes.csv’
>    ‘pathway_omic1.expr.csv’
> 
>    ‘pathway_omic2.expr.csv’
>    ‘samplesheet_file.txt’ ‘status.txt’
> 
>    ‘subid.all.0.txt’ ‘subid.all.1.txt’
> *
>    checking for detritus in the temp directory ... OK
> *
>    DONE
> Status: 3
>    NOTEs
> 
> ***********************************************
> ***********************************************
> 
> (2)
>    On windows-x86_64-devel (r-devel)
>    checking package
>    dependencies ... ERROR
>    Packages required but not
>    available:
>      'AnnotationDbi', 'KEGGREST',
>    'org.Hs.eg.db', 'TCGAbiolinks'
> 
>    See section
>    'The DESCRIPTION file' in the 'Writing R
>    Extensions'
>    manual.
> 
> 1 error ✖ | 0 warnings
>    ✔ | 0 notes ✔
> 
> *************************************************************************
> Sarmistha Das, PhD. (she/her)
> Postdoctoral Research Associate
> Department of Biostatistics, St. Jude Children's Research Hospital
> 262 Danny Thomas Place
> Room R6025A (Longinotti Building); Mail Stop 768
> Memphis, TN 38105
> Email: sarmistha.das using stjude.org
> Phone: 901-595-1160
> 
> ________________________________
> 
> Email Disclaimer: www.stjude.org/emaildisclaimer
> Consultation Disclaimer: www.stjude.org/consultationdisclaimer
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