Skip to content

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

2 messages · Das, Sarmistha, Duncan Murdoch

Original
Das, Sarmistha
# 
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 at 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 at stjude.org
Phone: 901-595-1160

________________________________

Email Disclaimer: www.stjude.org/emaildisclaimer
Consultation Disclaimer: www.stjude.org/consultationdisclaimer
1 day later
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: