############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:oppar.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings oppar_1.34.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/oppar.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘oppar/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘oppar’ version ‘1.34.0’ * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 ... WARNING Found the following significant warnings: Warning: multiple methods tables found for ‘gsva’ See ‘/Users/biocbuild/bbs-3.20-bioc/meat/oppar.Rcheck/00install.out’ for details. * used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * checking installed package size ... NOTE installed size is 5.6Mb sub-directories of 1Mb or more: data 5.1Mb * 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 ... NOTE Problems 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 ... NOTE Warning: multiple methods tables found for ‘gsva’ A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session 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 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 ... NOTE compute.gene.density : : 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 : : no visible global function definition for ‘sd’ plage : : no visible global function definition for ‘setTxtProgressBar’ plage: no visible global function definition for ‘setTxtProgressBar’ ssgsea: no visible global function definition for ‘txtProgressBar’ ssgsea : : no visible global function definition for ‘setTxtProgressBar’ ssgsea: no visible global function definition for ‘setTxtProgressBar’ zscore: no visible global function definition for ‘txtProgressBar’ zscore : : no visible global function definition for ‘sd’ zscore : : no visible global function definition for ‘setTxtProgressBar’ zscore: no visible global function definition for ‘setTxtProgressBar’ computeGeneSetsOverlap,list-ExpressionSet : : no visible global function definition for ‘na.omit’ computeGeneSetsOverlap,list-character : : no visible global function definition for ‘na.omit’ gsva,ExpressionSet-GeneSetCollection: no visible binding for global variable ‘sd’ gsva,ExpressionSet-GeneSetCollection : : no visible global function definition for ‘na.omit’ gsva,ExpressionSet-list: no visible binding for global variable ‘sd’ gsva,ExpressionSet-list : : no visible global function definition for ‘na.omit’ gsva,matrix-GeneSetCollection: no visible binding for global variable ‘sd’ gsva,matrix-GeneSetCollection : : no visible global function definition for ‘na.omit’ gsva,matrix-list: no visible binding for global variable ‘sd’ gsva,matrix-list : : no visible global function definition for ‘na.omit’ opa,matrix: no visible global function definition for ‘relevel’ opa,matrix : : no visible global function definition for ‘mad’ opa,matrix : : no visible global function definition for ‘median’ opa,matrix : : no visible binding for global variable ‘quantile’ opa,matrix : : 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 txtProgressBar Consider 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 5.1 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 ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed getSampleOutlier 17.737 1.294 21.752 opa 13.874 0.341 14.280 getSubtypeProbes 12.469 0.172 12.660 * 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: 2 WARNINGs, 5 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/oppar.Rcheck/00check.log’ for details.