############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:iSEEu.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings iSEEu_1.17.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/iSEEu.Rcheck' * using R version 4.4.0 RC (2024-04-16 r86468 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'iSEEu/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'iSEEu' version '1.17.0' * 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 'iSEEu' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code 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 ... NOTE Package in Depends field not imported from: 'iSEEhex' These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. ':::' calls which should be '::': 'iSEE:::.dataParamBoxOpen' 'iSEE:::.multiSelectHistory' 'iSEE:::.noSelection' 'iSEE:::.organizationHeight' 'iSEE:::.organizationWidth' See the note in ?`:::` about the use of this operator. * 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 ... WARNING Found the following significant warnings: Warning in .setOrganism("org.Mm.eg.db") : '.setOrganism' is deprecated. Warning in GeneSetTable(PanelId = 1L) : 'GeneSetTable' is deprecated. Warning in setPValuePattern(old) : 'setPValuePattern' is deprecated. Warning in .getIdentifierType() : '.getIdentifierType' is deprecated. Warning in .setOrganism("org.Mm.eg.db") : '.setOrganism' is deprecated. Warning in .getOrganism() : '.getOrganism' is deprecated. Warning in .getOrganism() : '.getOrganism' is deprecated. Warning in .getOrganism() : '.getOrganism' is deprecated. Warning in .getIdentifierType() : '.getIdentifierType' is deprecated. Warning in .getOrganism() : '.getOrganism' is deprecated. Warning in .getOrganism() : '.getOrganism' is deprecated. Deprecated functions may be defunct as soon as of the next release of R. See ?Deprecated. Examples with CPU (user + system) or elapsed time > 5s user system elapsed AggregatedDotPlot 15.46 4.67 20.42 modeReducedDim 13.37 0.78 14.45 DynamicMarkerTable-class 6.86 0.78 11.74 DynamicReducedDimensionPlot-class 5.30 0.64 6.02 modeGating 4.85 0.69 5.72 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testthat.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 2 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/iSEEu.Rcheck/00check.log' for details.