* using log directory 'd:/RCompile/CRANincoming/R-devel/refseqR.Rcheck' * using R Under development (unstable) (2024-10-28 r87274 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'refseqR/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'refseqR' version '1.1.5' * package encoding: UTF-8 * checking CRAN incoming feasibility ... NOTE Maintainer: 'Jose V. Die ' Found the following (possibly) invalid URLs: URL: http://ncbi.nlm.nih.gov/refseq/ (moved to https://www.ncbi.nlm.nih.gov/refseq/) From: DESCRIPTION Status: 301 Message: Moved Permanently For content that is 'Moved Permanently', please change http to https, add trailing slashes, or replace the old by the new URL. * 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 hidden files and directories ... OK * checking for portable file names ... OK * checking serialization versions ... OK * checking whether package 'refseqR' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... 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 ... OK * checking loading without being on the library search path ... 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 ... [11s] 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 ... ERROR Running examples in 'refseqR-Ex.R' failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### 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 NCBI/eutils201 - WWW Error 500 Diagnostic

Server Error

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:

pubmed@nlm.nih.gov - for problems with PubMed
webadmin@ncbi.nlm.nih.gov - for problems with other services

Thank you for your assistance. We will try to fix the problem as soon as possible.

Diagnostic Information:

Error: 500

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 ... ERROR Error(s) in re-building vignettes: --- re-building 'refseqR.Rmd' using rmarkdown Quitting from lines 76-78 [unnamed-chunk-5] (refseqR.Rmd) Error: processing vignette 'refseqR.Rmd' failed with diagnostics: HTTP failure: 500 NCBI/eutils101 - WWW Error 500 Diagnostic

Server Error

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:

pubmed@nlm.nih.gov - for problems with PubMed
webadmin@ncbi.nlm.nih.gov - for problems with other services

Thank you for your assistance. We will try to fix the problem as soon as possible.

Diagnostic Information:

Error: 500

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 = g p & 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

Client: 130.14.18.165

Server: eutils101

Time: Tue Oct 29 19:12:39 EDT 2024

NOTE: The above is an internal URL which may differ from the one you used to address the page.

Rev. 01/04/08

--- 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 ... [13s] OK * checking HTML version of manual ... OK * DONE Status: 2 ERRORs, 1 NOTE