############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:AMARETTO.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings AMARETTO_1.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/AMARETTO.Rcheck’ * using R version 4.4.1 (2024-06-14) * 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 ‘AMARETTO/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘AMARETTO’ version ‘1.22.0’ * 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 ‘AMARETTO’ can be installed ... OK * checking installed package size ... NOTE installed size is 6.1Mb sub-directories of 1Mb or more: data 1.5Mb extdata 3.8Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License components with restrictions not permitted: Apache License (== 2.0) + file LICENSE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘knitr’ A package should be listed in only one of these fields. 'LinkingTo' field is unused: package has no 'src' directory * 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 AMARETTO_HTMLreport: no visible binding for global variable ‘ModuleNr’ AMARETTO_HTMLreport: no visible binding for global variable ‘Weights’ AMARETTO_HTMLreport: no visible binding for global variable ‘RegulatorIDs’ AMARETTO_HTMLreport: no visible binding for global variable ‘TargetIDs’ AMARETTO_HTMLreport: no visible binding for global variable ‘moduleNr’ AMARETTO_HTMLreport: no visible binding for global variable ‘Testset’ AMARETTO_HTMLreport: no visible binding for global variable ‘padj’ AMARETTO_HTMLreport: no visible binding for global variable ‘n_Overlapping’ AMARETTO_HTMLreport: no visible binding for global variable ‘NumberGenes’ AMARETTO_HTMLreport: no visible binding for global variable ‘overlap_perc’ AMARETTO_HTMLreport: no visible binding for global variable ‘Geneset’ AMARETTO_HTMLreport: no visible binding for global variable ‘Description’ AMARETTO_HTMLreport: no visible binding for global variable ‘Geneset_length’ AMARETTO_HTMLreport: no visible binding for global variable ‘Overlapping_genes’ AMARETTO_HTMLreport: no visible binding for global variable ‘p_value’ AMARETTO_HTMLreport: no visible binding for global variable ‘p.value’ AMARETTO_HTMLreport: no visible binding for global variable ‘q.value’ AMARETTO_HTMLreport: no visible binding for global variable ‘Genes’ AMARETTO_HTMLreport: no visible binding for global variable ‘value’ AMARETTO_HTMLreport: no visible binding for global variable ‘Type’ AMARETTO_HTMLreport: no visible binding for global variable ‘Color’ AMARETTO_HTMLreport: no visible binding for global variable ‘Modules’ AMARETTO_HTMLreport: no visible binding for global variable ‘dt_gensesetsall’ GeneSetDescription: no visible binding for global variable ‘MsigdbMapping’ GeneSetDescription : : no visible binding for global variable ‘MsigdbMapping’ GmtFromModules: no visible binding for global variable ‘value’ GmtFromModules: no visible binding for global variable ‘variable’ GmtFromModules: no visible binding for global variable ‘GeneNames’ HyperGTestGeneEnrichment: no visible binding for global variable ‘i’ HyperGTestGeneEnrichment: no visible binding for global variable ‘j’ read_gct: no visible binding for global variable ‘Description’ Undefined global functions or variables: Color Description GeneNames Genes Geneset Geneset_length ModuleNr Modules MsigdbMapping NumberGenes Overlapping_genes RegulatorIDs TargetIDs Testset Type Weights dt_gensesetsall i j moduleNr n_Overlapping overlap_perc p.value p_value padj q.value value variable * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... WARNING Codoc mismatches from Rd file 'get_firehoseData.Rd': get_firehoseData Code: function(TargetDirectory = "./", TCGA_acronym_uppercase = "LUAD", dataType = "stddata", dataFileTag = "mRNAseq_Preprocess.Level_3", FFPE = FALSE, fileType = "tar.gz", gdacURL = "https://gdac.broadinstitute.org/runs/", untarUngzip = TRUE, printDisease_abbr = FALSE) Docs: function(TargetDirectory = "./", TCGA_acronym_uppercase = "LUAD", dataType = "stddata", dataFileTag = "mRNAseq_Preprocess.Level_3", FFPE = FALSE, fileType = "tar.gz", gdacURL = "http://gdac.broadinstitute.org/runs/", untarUngzip = TRUE, printDisease_abbr = FALSE) Mismatches in argument default values: Name: 'gdacURL' Code: "https://gdac.broadinstitute.org/runs/" Docs: "http://gdac.broadinstitute.org/runs/" * 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 ... NOTE Note: found 152 marked UTF-8 strings * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed AMARETTO_Download 8.042 0.843 10.711 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ 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 WARNING, 4 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/AMARETTO.Rcheck/00check.log’ for details.