############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:rgsepd.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings rgsepd_1.34.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/rgsepd.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘rgsepd/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘rgsepd’ version ‘1.34.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘rgsepd’ 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 ... NOTE Problems with news in ‘NEWS’: Cannot process chunk/lines: Rebuilt for R 3.2.2 * 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 loading without being on the library search path ... OK * checking startup messages can be suppressed ... NOTE 'select()' returned 1:1 mapping between keys and columns 'select()' returned 1:1 mapping between keys and columns It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage. * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘rgsepd-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: ExtractProjection > ### Title: ExtractProjection > ### Aliases: ExtractProjection > ### Keywords: plot > > ### ** Examples > > > data("IlluminaBodymap") > data("IlluminaBodymapMeta") > set.seed(1000) #fixed randomness > x <- Name_to_RefSeq(c("HIF1A","EGFR","MYH7","CD33","BRCA2")) > isoform_ids = intersect(x, rownames(IlluminaBodymap)) > rows_of_interest <- unique( c( isoform_ids , + sample(rownames(IlluminaBodymap), + size=2000,replace=FALSE))) > G <- GSEPD_INIT(Output_Folder="OUT", + finalCounts=round(IlluminaBodymap[rows_of_interest , ]), + sampleMeta=IlluminaBodymapMeta, + COLORS=c("green","black","red")) Keeping rows with counts (1821 of 2003) > > G <- GSEPD_ChangeConditions( G, c("A","B")) #set testing groups first! > G <- GSEPD_Process( G ) #have to have processed results to plot them converting counts to integer mode Generating OUT/DESEQ.counts.Ax4.Bx8.csv converting counts to integer mode estimating size factors estimating dispersions gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates fitting model and testing using 'normal' for LFC shrinkage, the Normal prior from Love et al (2014). Note that type='apeglm' and type='ashr' have shown to have less bias than type='normal'. See ?lfcShrink for more details on shrinkage type, and the DESeq2 vignette. Reference: https://doi.org/10.1093/bioinformatics/bty895 Generating OUT/DESEQ.Volcano.Ax4.Bx8.png Generating OUT/DESEQ.RES.Ax4.Bx8.csv dropping rows with raw PVAL>0.990 OR baseMean < 1 OR on excludes list deseq txid rows remaining: 868 Converting identifiers with local DB Generating OUT/DESEQ.RES.Ax4.Bx8.Annote.csv Generating OUT/HM.Ax4.Bx8.330.pdf Loading hg19 length data... Fetching GO annotations... Loading required package: AnnotationDbi Calculating the p-values... 'select()' returned 1:1 mapping between keys and columns Loading hg19 length data... Fetching GO annotations... Calculating the p-values... 'select()' returned 1:1 mapping between keys and columns Loading hg19 length data... Fetching GO annotations... Calculating the p-values... 'select()' returned 1:1 mapping between keys and columns 'select()' returned 1:1 mapping between keys and columns 'select()' returned 1:1 mapping between keys and columns Generating OUT/GOSEQ.RES.Ax4.Bx8.GO.csv Written GO categories, now reverse mapping * 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, 2 NOTEs See ‘/home/biocbuild/bbs-3.18-bioc/meat/rgsepd.Rcheck/00check.log’ for details.