############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:iGC.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings iGC_1.37.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/iGC.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘iGC/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘iGC’ version ‘1.37.0’ * 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 ‘iGC’ can be installed ... OK * 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 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 create_gene_cna: no visible global function definition for ‘data’ create_gene_cna: no visible binding for global variable ‘hg19DBNM’ create_gene_cna: no visible binding for global variable ‘Gene.Symbol’ create_gene_cna: no visible binding for global variable ‘GENE’ direct_gene_cna : : no visible binding for global variable ‘GENE’ direct_gene_cna : : no visible binding for global variable ‘gain_loss’ direct_gene_cna: no visible binding for global variable ‘GENE’ find_cna_driven_gene: no visible binding for global variable ‘GENE’ find_cna_driven_gene : exp_grouptest_driven_by_cna: no visible binding for global variable ‘Gain’ find_cna_driven_gene : exp_grouptest_driven_by_cna: no visible binding for global variable ‘GENE’ find_cna_driven_gene : exp_grouptest_driven_by_cna: no visible binding for global variable ‘Loss’ find_cna_driven_gene : exp_grouptest_driven_by_cna : : no visible global function definition for ‘na.omit’ find_cna_driven_gene : exp_grouptest_driven_by_cna : : no visible global function definition for ‘t.test’ find_cna_driven_gene : exp_grouptest_driven_by_cna: no visible global function definition for ‘p.adjust’ find_cna_driven_gene: no visible binding for global variable ‘p_value’ find_cna_driven_gene: no visible binding for global variable ‘fdr’ find_cna_driven_gene: no visible binding for global variable ‘vs_rest_exp_diff’ process_cna_per_sample: no visible binding for global variable ‘gain_loss’ process_cna_per_sample: no visible binding for global variable ‘Segment_Mean’ process_cna_per_sample: no visible binding for global variable ‘Chromosome’ process_cna_per_sample: no visible binding for global variable ‘Start’ process_cna_per_sample: no visible binding for global variable ‘End’ process_cna_per_sample: no visible binding for global variable ‘Gene.Symbol’ process_cna_per_sample: no visible binding for global variable ‘cur_sample’ process_cna_per_sample_direct: no visible binding for global variable ‘Segment_Mean’ process_cna_per_sample_direct: no visible binding for global variable ‘gain_loss’ process_cna_per_sample_direct: no visible binding for global variable ‘cna_val’ read_cna_geo: no visible binding for global variable ‘GENE’ read_cna_geo: no visible binding for global variable ‘Segment_Mean’ read_gene_exp: no visible global function definition for ‘read.table’ Undefined global functions or variables: Chromosome End GENE Gain Gene.Symbol Loss Segment_Mean Start cna_val cur_sample data fdr gain_loss hg19DBNM na.omit p.adjust p_value read.table t.test vs_rest_exp_diff Consider adding importFrom("stats", "na.omit", "p.adjust", "t.test") importFrom("utils", "data", "read.table") 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 ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.21-bioc/meat/iGC.Rcheck/00check.log’ for details.