############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CAGEr.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings CAGEr_1.34.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/CAGEr.Rcheck' * using R version 4.1.1 (2021-08-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'CAGEr/DESCRIPTION' ... OK * this is package 'CAGEr' version '1.34.0' * 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 whether package 'CAGEr' can be installed ... WARNING Found the following significant warnings: Rd warning: C:/Users/biocbuild/bbs-3.13-bioc/tmpdir/Rtmp6fr891/R.INSTALL244462ae4867/CAGEr/man/CustomConsensusClusters.Rd:42: missing link '.ConsensusClusters' Rd warning: C:/Users/biocbuild/bbs-3.13-bioc/tmpdir/Rtmp6fr891/R.INSTALL244462ae4867/CAGEr/man/clusterCTSS.Rd:89: missing link 'TagClusters' Rd warning: C:/Users/biocbuild/bbs-3.13-bioc/tmpdir/Rtmp6fr891/R.INSTALL244462ae4867/CAGEr/man/consensusClusters.Rd:52: missing link 'ConsensusClusters' Rd warning: C:/Users/biocbuild/bbs-3.13-bioc/tmpdir/Rtmp6fr891/R.INSTALL244462ae4867/CAGEr/man/tagClusters.Rd:58: missing link 'TagClusters' See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/CAGEr.Rcheck/00install.out' for details. * 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 * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 ... WARNING Missing link or links in documentation object 'CustomConsensusClusters.Rd': '.ConsensusClusters' Missing link or links in documentation object 'clusterCTSS.Rd': 'TagClusters' Missing link or links in documentation object 'consensusClusters.Rd': 'ConsensusClusters' Missing link or links in documentation object 'tagClusters.Rd': 'TagClusters' See section 'Cross-references' in the 'Writing R Extensions' manual. * checking for missing documentation entries ... WARNING Undocumented S4 methods: generic 'show' and siglist 'CTSS' All user-level objects in a package (including S4 classes and methods) should have documentation entries. See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual. * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... WARNING Undocumented arguments in documentation object 'CTSS-class' '.Object' '...' 'bsgenomeName' 'seqnames' 'pos' 'strand' 'seqinfo' 'seqlengths' 'from' 'to' 'strict' Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual. * 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 LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed importPublicData 29.64 1.30 37.51 cumulativeCTSSdistribution 21.64 4.31 25.96 scoreShift 24.78 0.05 24.83 quantilePositions 20.15 0.50 20.65 aggregateTagClusters 10.74 0.00 10.74 CAGEexp-class 5.77 1.08 7.34 distclu-functions 5.86 0.67 6.53 clusterCTSS 5.23 0.28 5.51 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed scoreShift 28.11 0.05 28.15 importPublicData 25.34 1.39 31.69 cumulativeCTSSdistribution 21.03 5.41 26.45 quantilePositions 19.43 0.53 19.95 aggregateTagClusters 11.53 0.00 11.53 clusterCTSS 6.16 0.49 6.64 distclu-functions 5.75 0.84 6.60 CAGEexp-class 5.10 0.96 6.04 * 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: 4 WARNINGs See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/CAGEr.Rcheck/00check.log' for details.