############################################################################## ############################################################################## ### ### Running command: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:rpx.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings rpx_2.3.2.tar.gz ### ############################################################################## ############################################################################## * using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/rpx.Rcheck' * using R Under development (unstable) (2021-11-21 r81221) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'rpx/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'rpx' version '2.3.2' * 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 hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'rpx' can be installed ... OK * 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 R 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 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 ... OK * checking Rd files ... OK * checking Rd metadata ... 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 files in 'vignettes' ... OK * checking examples ... ERROR Running examples in 'rpx-Ex.R' failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: cache > ### Title: Package cache > ### Aliases: cache rpxCache pxCachedProjects > > ### ** Examples > > > ## Default rpx cache > rpxCache() class: BiocFileCache bfccache: C:\Users\biocbuild\AppData\Local/R/cache/R/rpx bfccount: 5 For more information see: bfcinfo() or bfcquery() > > ## Set up your own cache by providing a file or a directory to > ## BiocFileCache::BiocFileCache() > my_cache <- BiocFileCache::BiocFileCache(tempfile()) > my_cache class: BiocFileCache bfccache: D:\biocbuild\bbs-3.15-bioc\tmpdir\Rtmp8SuXoS\file698c1db2469 bfccount: 0 For more information see: bfcinfo() or bfcquery() > px <- PXDataset("PXD000001", cache = my_cache) Querying ProteomeXchange for PXD000001. Warning in file(file, "rt") : URL 'ftp://ftp.pride.ebi.ac.uk/pride-archive/2012/03/PXD000001/README.txt': status was 'Failure when receiving data from the peer' Error in file(file, "rt") : cannot open the connection to 'ftp://ftp.pride.ebi.ac.uk/pride-archive/2012/03/PXD000001/README.txt' Calls: PXDataset -> read.delim -> read.table -> file Execution halted * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testthat.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 ERROR See 'D:/biocbuild/bbs-3.15-bioc/meat/rpx.Rcheck/00check.log' for details.