################################################################################################################################################################## Running command:###### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:SIM.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings SIM_1.80.0.tar.gz###############################################################################################################################################################* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/SIM.Rcheck’* using R version 4.5.2 (2025-10-31)* using platform: x86_64-pc-linux-gnu* R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0* running under: Ubuntu 24.04.3 LTS* using session charset: UTF-8* checking for file ‘SIM/DESCRIPTION’ ... OK* checking extension type ... Package* this is package ‘SIM’ version ‘1.80.0’* 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 ‘SIM’ can be installed ... OK* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’* 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 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 loading without being on the library search path ... OK* checking whether startup messages can be suppressed ... OK* checking dependencies in R code ... NOTE'library' or 'require' call to ‘biomaRt’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual.Package in Depends field not imported from: ‘quantreg’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached.* checking S3 generic/method consistency ... OK* checking replacement functions ... OK* checking foreign function calls ... OK* checking R code for possible problems ... NOTEFile ‘SIM/R/zzz.R’: .onAttach calls: library.dynam("SIM", pkg, lib)See section ‘Good practice’ in '?.onAttach'.dependent.heatmap: warning in get(as.character(adjust[[2]]), env = attr(adjust, ".Environment")): partial argument match of 'env' to 'envir'sim.plot.zoom.in: warning in eval(call, env = attr(call, "env")): partial argument match of 'env' to 'envir'sim.update.chrom.table: warning in factor(table$name, level = c(1:22, "X", "Y")): partial argument match of 'level' to 'levels'assemble.data: no visible binding for global variable ‘chrom.table’convertGenomicRegion: no visible binding for global variable ‘chrom.table’dependent.heatmap: no visible global function definition for ‘strwidth’getoverlappingregions: no visible global function definition for ‘useMart’getoverlappingregions: no visible global function definition for ‘getBM’independent.heatmap: no visible global function definition for ‘strwidth’link.metadata: no visible binding for global variable ‘expr.data’link.metadata: no visible binding for global variable ‘hgu133plus2CHR’link.metadata: no visible binding for global variable ‘hgu133plus2CHRLOC’link.metadata: no visible binding for global variable ‘hgu133plus2SYMBOL’plotCytobands: no visible binding for global variable ‘chrom.table’sim.plot.overlapping.indep.dep.features: no visible global function definition for ‘box’sim.plot.pvals.on.genome: no visible binding for global variable ‘chrom.table’sim.update.chrom.table: no visible global function definition for ‘dbConnect’sim.update.chrom.table: no visible global function definition for ‘MySQL’sim.update.chrom.table: no visible global function definition for ‘dbGetQuery’Undefined global functions or variables: MySQL box chrom.table dbConnect dbGetQuery expr.data getBM hgu133plus2CHR hgu133plus2CHRLOC hgu133plus2SYMBOL strwidth useMartConsider adding importFrom("graphics", "box", "strwidth")to your NAMESPACE file.* checking Rd files ... WARNINGcheckRd: (5) integrated.analysis.Rd:116: \item in \value must have non-empty label* 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 line endings in C/C++/Fortran sources/headers ... OK* checking compiled code ... NOTENote: information on .o files is not available* checking files in ‘vignettes’ ... OK* checking examples ... OKExamples with CPU (user + system) or elapsed time > 5s user system elapsedSIM-package 5.491 0.211 5.703* checking for unstated dependencies in vignettes ... OK* checking package vignettes ... OK* checking re-building of vignette outputs ... OK* checking PDF version of manual ... OK* DONEStatus: 1 WARNING, 3 NOTEsSee ‘/home/biocbuild/bbs-3.22-bioc/meat/SIM.Rcheck/00check.log’for details.################################################################################################################################################################## Running command:###### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL SIM###############################################################################################################################################################* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’* installing *source* package ‘SIM’ ...** this is package ‘SIM’ version ‘1.80.0’** using staged installation** libsusing C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c withinWindow.c -o withinWindow.ogcc -std=gnu2x -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o SIM.so withinWindow.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lRinstalling to /home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-SIM/00new/SIM/libs** R** data** inst** byte-compile and prepare package for lazy loading** help*** installing help indices** building package indices** installing vignettes** testing if installed package can be loaded from temporary location** checking absolute paths in shared objects and dynamic libraries** testing if installed package can be loaded from final location** testing if installed package keeps a record of temporary installation path* DONE (SIM)
