Issues with earlier submissions are still there, no new issues.
0 errors | 0 warnings | 1 note
checking for non-standard things in the check directory ... NOTE Found the following files/directories: ‘Transcription_factor_RegulonDB_Escherichia_coli_GeneSymbol.gmt’
This note emerged after we replaced \dontrun{} with \donttest{} as requested by the CRAN Team.
These URLs are reported by url_check() but they seem to work:
- https://doi.org/10.1073/pnas.0506580102
- https://regulondb.ccg.unam.mx/
- https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE55662
0 errors | 0 warnings | 1 note
- This is a new release.
Error: SSL certificate problem: unable to get local issuer certificate https://regulondb.ccg.unam.mx/
My understanding is that the website should update its certificate but I did not find any direct contact to the website maintainers where I could request this.
Error: 403: Forbidden https://doi.org/10.1073/pnas.0506580102
The other doi.org urls pass the checks. The url seems to work.
"Please always write package names, software names and API (application programming interface) names in single quotes in title and description. e.g: --> 'mulea', ... Please note that package names are case sensitive."
mulea has been replaced with 'mulea' within the description section.
"Please always explain all acronyms in the description text. -> FDR"
While "FDR" is mentioned without explanation in the title, it is then explained in the description section: "'mulea' employs an innovative empirical false discovery rate (eFDR) correction method". If possible, I would like to keep the abbreviation as is in the title. Other packages on CRAN follow similar approach e.g. 'fftw' (https://cran.r-project.org/web/packages/fftw/index.html).
"\dontrun{} should only be used if the example really cannot be executed (e.g. because of missing additional software, missing API keys, ...) by the user. That's why wrapping examples in \dontrun{} adds the comment ("# Not run:") as a warning for the user. Does not seem necessary. Please replace \dontrun with \donttest.
Please unwrap the examples if they are executable in < 5 sec, or replace dontrun{} with \donttest{}."
\dontrun{} has been replaced with \donttest{}. However, please note that this results in the following note when running R CMD Check:
checking for non-standard things in the check directory ... NOTE Found the following files/directories: ‘Transcription_factor_RegulonDB_Escherichia_coli_GeneSymbol.gmt’