- using R Under development (unstable) (2025-07-25 r88448)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
clang version 20.1.8
flang version 20.1.8
- running under: Fedora Linux 42 (Workstation Edition)
- using session charset: UTF-8
- using option ‘--no-stop-on-test-error’
- checking for file ‘refseqR/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘refseqR’ version ‘1.1.5’
- package encoding: UTF-8
- 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 ‘refseqR’ can be installed ... [24s/32s] OK
See the install log for details.
- checking installed package size ... OK
- checking package directory ... OK
- checking ‘build’ directory ... 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 code 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 ... [7s/11s] OK
- checking loading without being on the library search path ... [7s/10s] 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 ... [32s/43s] 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 installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... [8s/12s] 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
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [10s/14s] 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: 130.14.19.52</div>
<div class="diags">Server: eutils101</div>
<div class="diags">Time: Sun Jul 27 11:10:13 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: 130.14.19.52</div>
<div class="diags">Server: eutils101</div>
<div class="diags">Time: Sun Jul 27 11:10:13 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
- checking PDF version of manual ... OK
- checking HTML version of manual ... OK
- checking for non-standard things in the check directory ... OK
- checking for detritus in the temp directory ... OK
- DONE
Status: 2 ERRORs