CRAN Package Check Results for Package refseqR

Last updated on 2025-07-29 07:49:54 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.1.5 13.80 125.07 138.87 OK
r-devel-linux-x86_64-debian-gcc 1.1.5 10.43 91.65 102.08 OK
r-devel-linux-x86_64-fedora-clang 1.1.5 212.04 OK
r-devel-linux-x86_64-fedora-gcc 1.1.5 215.81 OK
r-devel-windows-x86_64 1.1.5 15.00 121.00 136.00 ERROR
r-patched-linux-x86_64 1.1.5 14.00 116.76 130.76 OK
r-release-linux-x86_64 1.1.5 12.41 116.48 128.89 ERROR
r-release-macos-arm64 1.1.5 106.00 OK
r-release-macos-x86_64 1.1.5 177.00 OK
r-release-windows-x86_64 1.1.5 15.00 148.00 163.00 OK
r-oldrel-macos-arm64 1.1.5 118.00 OK
r-oldrel-macos-x86_64 1.1.5 130.00 OK
r-oldrel-windows-x86_64 1.1.5 19.00 194.00 213.00 OK

Check Details

Version: 1.1.5
Check: examples
Result: ERROR Running examples in 'refseqR-Ex.R' failed The error most likely occurred in: > ### Name: refseq_AAmol_wt > ### Title: Extract the molecular weight from a protein accession > ### Aliases: refseq_AAmol_wt > > ### ** Examples > > # Get the molecular weight from a single protein accession > protein <- "XP_020244413" > refseq_AAmol_wt(protein) Error: HTTP failure: 500 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.1//EN" "http://www.w3.org/TR/xhtml11/DTD/xhtml11.dtd"> <html> <head> <title>NCBI/eutils102 - WWW Error 500 Diagnostic</title> <style type="text/css"> h1.error {color: red; font-size: 40pt} div.diags {text-indent: 0.5in } </style> </head> <body> <h1>Server Error</h1> <p>Your request could not be processed due to a problem on our Web server. This could be a transient problem, please try the query again. If it doesn't clear up within a reasonable period of time, e-mail a short description of your query and the diagnostic information shown below to:</p> <p> pubmed@nlm.nih.gov - for problems with PubMed<br/> webadmin@ncbi.nlm.nih.gov - for problems with other services<br/> </p> <p>Thank you for your assistance. We will try to fix the problem as soon as possible. </p> <hr/> <p> Diagnostic Information:</p> <div class="diags">Error: 500</div> <div class="diags">URL: h t t p : / / e x t - h t t p - e u t i l s . l Execution halted Flavor: r-devel-windows-x86_64

Version: 1.1.5
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: --- re-building 'refseqR.Rmd' using rmarkdown Quitting from refseqR.Rmd:102-107 [unnamed-chunk-9] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error: ! HTTP failure: 500 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.1//EN" "http://www.w3.org/TR/xhtml11/DTD/xhtml11.dtd"> <html> <head> <title>NCBI/eutils101 - WWW Error 500 Diagnostic</title> <style type="text/css"> h1.error {color: red; font-size: 40pt} div.diags {text-indent: 0.5in } </style> </head> <body> <h1>Server Error</h1> <p>Your request could not be processed due to a problem on our Web server. This could be a transient problem, please try the query again. If it doesn't clear up within a reasonable period of time, e-mail a short description of your query and the diagnostic information shown below to:</p> <p> pubmed@nlm.nih.gov - for problems with PubMed<br/> webadmin@ncbi.nlm.nih.gov - for problems with other services<br/> </p> <p>Thank you for your assistance. We will try to fix the problem as soon as possible. </p> <hr/> <p> Diagnostic Information:</p> <div class="diags">Error: 500</div> <div class="diags">URL: h t t p : / / e x t - h t t p - e u t i l s . l i n k e r d . n c b i . n l m . n i h . g o v / e n t r e z / e u t i l s / e f e t c h . f c g i ? d b = n u c c o r e & a m p ; r e t t y p e = f a s t a & a m p ; r e t m o d e = & a m p ; i d = X M _ 0 0 4 4 8 7 7 0 1 & a m p ; e m a i l = d a v i d . w i n t e r 4 0 g m a i l . c o m & a m p ; t o o l = r e n t r e z </div> <div class="diags">Client: 130.14.18.165</div> <div class="diags">Server: eutils101</div> <div class="diags">Time: Sun Jul 27 11:56:21 EDT 2025</div> <p> NOTE: The above is an internal URL which may differ from the one you used to address the page.</p> <hr/> <p>Rev. 01/04/08</p> </body> </html> --- Backtrace: ▆ 1. └─rentrez::entrez_fetch(db = "nuccore", id = transcript, rettype = "fasta") 2. ├─base::do.call(make_entrez_query, args) 3. └─rentrez (local) `<fn>`(...) 4. └─rentrez:::entrez_check(response) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'refseqR.Rmd' failed with diagnostics: HTTP failure: 500 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.1//EN" "http://www.w3.org/TR/xhtml11/DTD/xhtml11.dtd"> <html> <head> <title>NCBI/eutils101 - WWW Error 500 Diagnostic</title> <style type="text/css"> h1.error {color: red; font-size: 40pt} div.diags {text-indent: 0.5in } </style> </head> <body> <h1>Server Error</h1> <p>Your request could not be processed due to a problem on our Web server. This could be a transient problem, please try the query again. If it doesn't clear up within a reasonable period of time, e-mail a short description of your query and the diagnostic information shown below to:</p> <p> pubmed@nlm.nih.gov - for problems with PubMed<br/> webadmin@ncbi.nlm.nih.gov - for problems with other services<br/> </p> <p>Thank you for your assistance. We will try to fix the problem as soon as possible. </p> <hr/> <p> Diagnostic Information:</p> <div class="diags">Error: 500</div> <div class="diags">URL: h t t p : / / e x t - h t t p - e u t i l s . l i n k e r d . n c b i . n l m . n i h . g o v / e n t r e z / e u t i l s / e f e t c h . f c g i ? d b = n u c c o r e & a m p ; r e t t y p e = f a s t a & a m p ; r e t m o d e = & a m p ; i d = X M _ 0 0 4 4 8 7 7 0 1 & a m p ; e m a i l = d a v i d . w i n t e r 4 0 g m a i l . c o m & a m p ; t o o l = r e n t r e z </div> <div class="diags">Client: 130.14.18.165</div> <div class="diags">Server: eutils101</div> <div class="diags">Time: Sun Jul 27 11:56:21 EDT 2025</div> <p> NOTE: The above is an internal URL which may differ from the one you used to address the page.</p> <hr/> <p>Rev. 01/04/08</p> </body> </html> --- failed re-building 'refseqR.Rmd' SUMMARY: processing the following file failed: 'refseqR.Rmd' Error: Vignette re-building failed. Execution halted Flavor: r-devel-windows-x86_64

Version: 1.1.5
Check: examples
Result: ERROR Running examples in ‘refseqR-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: refseq_CDScoords > ### Title: Extract the coding sequences (CDS) coordinates from a transcript > ### accession > ### Aliases: refseq_CDScoords > > ### ** Examples > > transcript = c("XM_004487701") > refseq_CDScoords(transcript) Error in refseq_CDScoords(transcript) : Exactly one CDS per file is expected. Contact the maintainer Execution halted Flavor: r-release-linux-x86_64

Version: 1.1.5
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘refseqR.Rmd’ using rmarkdown Quitting from refseqR.Rmd:109-111 [unnamed-chunk-10] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `refseq_CDScoords()`: ! Exactly one CDS per file is expected. Contact the maintainer --- Backtrace: ▆ 1. ├─base::substr(toString(refseq_CDSseq(transcript)), 1, 60) 2. ├─base::toString(refseq_CDSseq(transcript)) 3. └─refseqR::refseq_CDSseq(transcript) 4. └─refseqR::refseq_CDScoords(transcript) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'refseqR.Rmd' failed with diagnostics: Exactly one CDS per file is expected. Contact the maintainer --- failed re-building ‘refseqR.Rmd’ SUMMARY: processing the following file failed: ‘refseqR.Rmd’ Error: Vignette re-building failed. Execution halted Flavor: r-release-linux-x86_64