############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:GCSscore.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings GCSscore_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/GCSscore.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 * running under: Ubuntu 22.04.3 LTS * using session charset: UTF-8 * checking for file ‘GCSscore/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘GCSscore’ version ‘1.14.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘GCSscore’ can be installed ... OK * checking installed package size ... NOTE installed size is 7.2Mb sub-directories of 1Mb or more: extdata 6.8Mb * 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 loading without being on the library search path ... 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 ... OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘GCSscore.Rnw’ using ‘UTF-8’... failed ERROR Errors in running code in vignettes: when running code in ‘GCSscore.Rnw’ ... *This package will only be generated once for each chip-type* *Or if probeFile version for the chip-type needs to be updated* writing intermediary .probe_tab file to temporary directory Importing the data. Warning in packageDescription(thispkg) : no package 'AnnotationForge' was found When sourcing ‘GCSscore.R’: Error: $ operator is invalid for atomic vectors Execution halted * checking re-building of vignette outputs ... NOTE Error(s) in re-building vignettes: --- re-building ‘GCSscore.Rnw’ using Sweave GCSscore supports the selected chip-type: Clariom_S_Mouse Bioconductor platform design (.pd) package already installed for: Clariom_S_Mouse GCS-score analysis initiated for chip-type: Clariom_S_Mouse GCS-score 'probeFile' package needs to be installed for chip-type: Clariom_S_Mouse typeFilter set to (0) by default for best .CEL file scaling and normalization statistics all probe_id types (including control probe_ids and bgp probe_ids) will be for GCS-score calculation. it is generally recommended to leave the typeFilter option set to (0) ** Checking if Bioconductor annotation (.db) packages are installed chip-type: Clariom_S_Mouse ** Annotation package (clariomsmousetranscriptcluster.db) already installed for chip-type: Clariom_S_Mouse ** Generating probeFile package for chip-type: Clariom_S_Mouse ** *This package will only be generated once for each chip-type* *Or if probeFile version for the chip-type needs to be updated* writing intermediary .probe_tab file to temporary directory Warning in packageDescription(thispkg) : no package 'AnnotationForge' was found Error: processing vignette 'GCSscore.Rnw' failed with diagnostics: chunk 2 Error in desc$Package : $ operator is invalid for atomic vectors --- failed re-building ‘GCSscore.Rnw’ SUMMARY: processing the following file failed: ‘GCSscore.Rnw’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 2 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/GCSscore.Rcheck/00check.log’ for details.