################################################################################################################################################################## Running command:###### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:oppar.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings oppar_1.38.0.tar.gz###############################################################################################################################################################* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/oppar.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 ‘oppar/DESCRIPTION’ ... OK* checking extension type ... Package* this is package ‘oppar’ version ‘1.38.0’* 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 ‘oppar’ can be installed ... WARNINGFound the following significant warnings: Warning: multiple methods tables found for ‘gsva’See ‘/home/biocbuild/bbs-3.22-bioc/meat/oppar.Rcheck/00install.out’ for details.* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’* checking installed package size ... INFO installed size is 5.5Mb sub-directories of 1Mb or more: data 5.0Mb* 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 ... NOTEProblems with news in ‘NEWS’: Cannot process chunk/lines: Initial release* 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 ... NOTEWarning: multiple methods tables found for ‘gsva’A namespace must be able to be loaded with just the base namespaceloaded: otherwise if the namespace gets loaded by a saved object, thesession will be unable to start.Probably some imports need to be declared in the NAMESPACE file.* 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 ... OK* checking S3 generic/method consistency ... OK* checking replacement functions ... OK* checking foreign function calls ... OK* checking R code for possible problems ... NOTEcompute.gene.density : <anonymous>: no visible global function definition for ‘ecdf’compute.geneset.es: no visible global function definition for ‘txtProgressBar’compute.geneset.es: no visible global function definition for ‘setTxtProgressBar’ks_test_m: no visible global function definition for ‘setTxtProgressBar’plage: no visible global function definition for ‘txtProgressBar’plage : <anonymous>: no visible global function definition for ‘sd’plage : <anonymous>: no visible global function definition for ‘setTxtProgressBar’plage: no visible global function definition for ‘setTxtProgressBar’ssgsea: no visible global function definition for ‘txtProgressBar’ssgsea : <anonymous>: no visible global function definition for ‘setTxtProgressBar’ssgsea: no visible global function definition for ‘setTxtProgressBar’zscore: no visible global function definition for ‘txtProgressBar’zscore : <anonymous>: no visible global function definition for ‘sd’zscore : <anonymous>: no visible global function definition for ‘setTxtProgressBar’zscore: no visible global function definition for ‘setTxtProgressBar’computeGeneSetsOverlap,list-ExpressionSet : <anonymous>: no visible global function definition for ‘na.omit’computeGeneSetsOverlap,list-character : <anonymous>: no visible global function definition for ‘na.omit’gsva,ExpressionSet-GeneSetCollection: no visible binding for global variable ‘sd’gsva,ExpressionSet-GeneSetCollection : <anonymous>: no visible global function definition for ‘na.omit’gsva,ExpressionSet-list: no visible binding for global variable ‘sd’gsva,ExpressionSet-list : <anonymous>: no visible global function definition for ‘na.omit’gsva,matrix-GeneSetCollection: no visible binding for global variable ‘sd’gsva,matrix-GeneSetCollection : <anonymous>: no visible global function definition for ‘na.omit’gsva,matrix-list: no visible binding for global variable ‘sd’gsva,matrix-list : <anonymous>: no visible global function definition for ‘na.omit’opa,matrix: no visible global function definition for ‘relevel’opa,matrix : <anonymous>: no visible global function definition for ‘mad’opa,matrix : <anonymous>: no visible global function definition for ‘median’opa,matrix : <anonymous>: no visible binding for global variable ‘quantile’opa,matrix : <anonymous>: no visible global function definition for ‘IQR’show,OPPARList: no visible global function definition for ‘head’Undefined global functions or variables: IQR ecdf head mad median na.omit quantile relevel sd setTxtProgressBar txtProgressBarConsider adding importFrom("stats", "IQR", "ecdf", "mad", "median", "na.omit", "quantile", "relevel", "sd") importFrom("utils", "head", "setTxtProgressBar", "txtProgressBar")to your NAMESPACE file.* 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 LazyData ... WARNING LazyData DB of 5.0 MB without LazyDataCompression set See §1.1.6 of 'Writing R Extensions'* 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 elapsedopa 26.365 0.428 33.236getSubtypeProbes 17.135 0.304 18.096getSampleOutlier 16.152 0.457 16.609* 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: 2 WARNINGs, 4 NOTEsSee ‘/home/biocbuild/bbs-3.22-bioc/meat/oppar.Rcheck/00check.log’for details.################################################################################################################################################################## Running command:###### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL oppar###############################################################################################################################################################* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’* installing *source* package ‘oppar’ ...** this is package ‘oppar’ version ‘1.38.0’** 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 R_init_oppar.c -o R_init_oppar.ogcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c kernel_estimation.c -o kernel_estimation.ogcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c ks_test.c -o ks_test.oks_test.c: In function ‘ks_sample’:ks_test.c:22:16: warning: unused variable ‘mx_value’ [-Wunused-variable] 22 | double mx_value = 0.0; | ^~~~~~~~gcc -std=gnu2x -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o oppar.so R_init_oppar.o kernel_estimation.o ks_test.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lRinstalling to /home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-oppar/00new/oppar/libs** R** data*** moving datasets to lazyload DB** inst** byte-compile and prepare package for lazy loadingCreating a new generic function for ‘gsva’ in package ‘oppar’** help*** installing help indices** building package indices** installing vignettes** testing if installed package can be loaded from temporary locationWarning: multiple methods tables found for ‘gsva’** checking absolute paths in shared objects and dynamic libraries** testing if installed package can be loaded from final locationWarning: multiple methods tables found for ‘gsva’** testing if installed package keeps a record of temporary installation path* DONE (oppar)
