############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:signeR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings signeR_2.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/signeR.Rcheck’ * using R version 4.4.2 (2024-10-31) * 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 ‘signeR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘signeR’ version ‘2.8.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘signeR’ can be installed ... OK * used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * checking C++ specification ... NOTE Specified C++11: please drop specification unless essential * 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 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 covariate: no visible binding for global variable ‘.’ explorepage: no visible binding for global variable ‘.’ genCountMatrixFromMAF: no visible binding for global variable ‘Variant_Type’ genCountMatrixFromMAF: no visible binding for global variable ‘Reference_Allele’ genCountMatrixFromMAF: no visible binding for global variable ‘Tumor_Seq_Allele2’ genCountMatrixFromMAF: no visible binding for global variable ‘Tumor_Seq_Allele1’ genCountMatrixFromVcf: no visible global function definition for ‘alt<-’ signeRFlow : server : loadSig: no visible binding for global variable ‘sig’ signeRFlow : server : loadSig: no visible binding for global variable ‘sig_test’ tcgaexplorer : get_similarities_tcga: no visible binding for global variable ‘project’ tcgaexplorer: no visible binding for global variable ‘.’ DiffExp,SignExp-character: no visible binding for global variable ‘fc’ ExposureBarplot,SignExp: no visible binding for global variable ‘Samples’ ExposureBarplot,SignExp: no visible binding for global variable ‘Signatures’ ExposureBoxplot,SignExp: no visible binding for global variable ‘Signatures’ ExposureBoxplot,SignExp: no visible binding for global variable ‘Samples’ ExposureClassify,ANY-character: no visible binding for global variable ‘Col’ ExposureClassify,ANY-character: no visible binding for global variable ‘Frequency’ ExposureClassify,ANY-character: no visible binding for global variable ‘Row’ ExposureClassifyCV,ANY-character: no visible binding for global variable ‘Col’ ExposureClassifyCV,ANY-character: no visible binding for global variable ‘Frequency’ ExposureClassifyCV,ANY-character: no visible binding for global variable ‘Row’ ExposureCorrelation,SignExp-numeric: no visible binding for global variable ‘Feature’ ExposureCorrelation,SignExp-numeric: no visible binding for global variable ‘exposure’ ExposureCorrelation,matrix-numeric: no visible binding for global variable ‘Feature’ ExposureCorrelation,matrix-numeric: no visible binding for global variable ‘exposure’ Undefined global functions or variables: . Col Feature Frequency Reference_Allele Row Samples Signatures Tumor_Seq_Allele1 Tumor_Seq_Allele2 Variant_Type alt<- exposure fc project sig sig_test * checking Rd files ... NOTE prepare_Rd: cosmic_data.Rd:91-93: Dropping empty section \details prepare_Rd: cosmic_data.Rd:98-100: Dropping empty section \references prepare_Rd: cosmic_data.Rd:101-102: Dropping empty section \examples prepare_Rd: tcga_similarities.Rd:96-98: Dropping empty section \details prepare_Rd: tcga_similarities.Rd:99-101: Dropping empty section \source prepare_Rd: tcga_similarities.Rd:102-104: Dropping empty section \references prepare_Rd: tcga_similarities.Rd:105-106: Dropping empty section \examples prepare_Rd: tcga_tumors.Rd:18-20: Dropping empty section \details prepare_Rd: tcga_tumors.Rd:21-23: Dropping empty section \source prepare_Rd: tcga_tumors.Rd:24-26: Dropping empty section \references prepare_Rd: tcga_tumors.Rd:27-28: Dropping empty section \examples * 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 ... OK * checking data for ASCII and uncompressed saves ... OK * checking R/sysdata.rda ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... 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 ExposureClassifyCV 12.714 0.088 13.123 ExposureFuzzyClustering 12.449 0.094 12.763 ExposureClassify 8.309 0.104 5.597 ExposureSurvModel 7.229 0.088 7.414 Diffexp 6.194 0.163 6.482 genMatrix 5.619 0.221 5.882 methods 4.988 0.019 5.188 * 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: 4 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/signeR.Rcheck/00check.log’ for details.