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

[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 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

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