############################################################################## ############################################################################## ### ### Running command: ### ### chmod a+r annotate -R && F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data annotate ### ############################################################################## ############################################################################## * checking for file 'annotate/DESCRIPTION' ... OK * preparing 'annotate': * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building 'chromLOC.Rmd' using rmarkdown --- finished re-building 'chromLOC.Rmd' --- re-building 'useDataPkgs.Rmd' using rmarkdown --- finished re-building 'useDataPkgs.Rmd' --- re-building 'GOusage.Rnw' using Sweave Attaching package: 'graph' The following object is masked from 'package:XML': addNode Attaching package: 'Rgraphviz' The following object is masked from 'package:annotate': toFile The following objects are masked from 'package:IRanges': from, to The following objects are masked from 'package:S4Vectors': from, to --- finished re-building 'GOusage.Rnw' --- re-building 'annotate.Rnw' using Sweave --- finished re-building 'annotate.Rnw' --- re-building 'prettyOutput.Rnw' using Sweave --- finished re-building 'prettyOutput.Rnw' --- re-building 'query.Rnw' using Sweave Read 4 items Error: processing vignette 'query.Rnw' failed with diagnostics: chunk 6 Error in file(file, "r") : cannot open the connection to 'https://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?tool=bioconductor&rettype=xml&retmode=text&db=gene&id=1939271%2c2449431%2c7729427%2c7835343%2c7836461%2c7933101%2c8121496%2c8680883%2c8764009%2c8764062' --- failed re-building 'query.Rnw' --- re-building 'useProbeInfo.Rnw' using Sweave Loading required package: org.Rn.eg.db Loading required package: XVector Loading required package: GenomeInfoDb Attaching package: 'Biostrings' The following object is masked from 'package:grid': pattern The following object is masked from 'package:graph': complement The following object is masked from 'package:base': strsplit --- finished re-building 'useProbeInfo.Rnw' SUMMARY: processing the following file failed: 'query.Rnw' Error: Vignette re-building failed. In addition: Warning message: In file(file, "r") : cannot open URL 'https://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?tool=bioconductor&rettype=xml&retmode=text&db=gene&id=1939271%2c2449431%2c7729427%2c7835343%2c7836461%2c7933101%2c8121496%2c8680883%2c8764009%2c8764062': HTTP status was '400 Bad Request' Execution halted