############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:girafe.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings girafe_1.58.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/girafe.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 ‘girafe/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘girafe’ version ‘1.58.0’ * 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' NOTE Depends: includes the non-default packages: 'BiocGenerics', 'S4Vectors', 'Rsamtools', 'intervals', 'ShortRead', 'genomeIntervals', 'grid' Adding so many packages to the search path is excessive and importing selectively is preferable. * 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 ‘girafe’ 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 installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Packages listed in more than one of Depends, Imports, Suggests, Enhances: ‘methods’ ‘genomeIntervals’ A package should be listed in only one of these fields. * 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 ... NOTE No methods found in package ‘IRanges’ for requests: ‘score’, ‘score<-’, ‘sort’ when loading ‘girafe’ It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage. * checking dependencies in R code ... NOTE 'library' or 'require' call to ‘MASS’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Package in Depends field not imported from: ‘Rsamtools’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. Unexported object imported by a ':::' call: ‘genomeIntervals:::intervalsForOverlap’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE agiFromBam: no visible binding for global variable ‘mclapply’ agiFromBam: no visible global function definition for ‘scanBamHeader’ agiFromBam: no visible global function definition for ‘ScanBamParam’ agiFromBam : : no visible global function definition for ‘scanBamFlag’ agiFromBam : : no visible global function definition for ‘scanBam’ countReadsAnnotated: no visible binding for global variable ‘mclapply’ countReadsAnnotated: no visible binding for global variable ‘fraction1’ fracOverlap: no visible binding for global variable ‘fraction1’ fracOverlap: no visible binding for global variable ‘fraction2’ getFeatureCounts: no visible binding for global variable ‘fraction1’ getFeatureCounts: no visible binding for global variable ‘Index1’ intPhred: no visible binding for global variable ‘mclapply’ oldAGIoverlap: no visible binding for global variable ‘mclapply’ plotReads: no visible binding for global variable ‘x.start’ plotReads: no visible binding for global variable ‘x.end’ plotReads: no visible binding for global variable ‘y’ reduceOne: no visible binding for global variable ‘fraction1’ reduceOne: no visible binding for global variable ‘fraction2’ windowCountAndGC: no visible binding for global variable ‘n.reads’ windowCountAndGC: no visible global function definition for ‘unmasked’ clusters,AlignedGenomeIntervals: no visible binding for global variable ‘mclapply’ clusters,Genome_intervals: no visible binding for global variable ‘mclapply’ coverage,AlignedGenomeIntervals: no visible binding for global variable ‘mclapply’ coverage,AlignedGenomeIntervals : : no visible binding for global variable ‘on.minus’ interval_included,AlignedGenomeIntervals-AlignedGenomeIntervals: no visible binding for global variable ‘mclapply’ reduce,AlignedGenomeIntervals: no visible binding for global variable ‘mclapply’ reduce,Genome_intervals: no visible binding for global variable ‘mclapply’ reduce,Genome_intervals: no visible binding for global variable ‘fraction1’ reduce,Genome_intervals: no visible binding for global variable ‘fraction2’ Undefined global functions or variables: Index1 ScanBamParam fraction1 fraction2 mclapply n.reads on.minus scanBam scanBamFlag scanBamHeader unmasked x.end x.start y * 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 line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking for GNU extensions in Makefiles ... OK * checking include directives in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed negbinomsig 5.944 0.127 6.085 perWindow 5.863 0.095 5.967 * 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: 6 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/girafe.Rcheck/00check.log’ for details.