############################################################################## ############################################################################## ### ### 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 4.4.1 (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 ‘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 ...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 ‘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 * 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.