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....@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....@stjude.org
Phone: 901-595-1160
________________________________
Email Disclaimer: www.stjude.org/emaildisclaimer
Consultation Disclaimer: www.stjude.org/consultationdisclaimer
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