############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GenomicAlignments.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GenomicAlignments_1.36.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/GenomicAlignments.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.3 (clang-1403.0.22.14.1) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.6.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GenomicAlignments/DESCRIPTION’ ... OK * this is package ‘GenomicAlignments’ version ‘1.36.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'BiocGenerics', 'S4Vectors', 'IRanges', 'GenomeInfoDb', 'GenomicRanges', 'SummarizedExperiment', 'Biostrings', 'Rsamtools' 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 ‘GenomicAlignments’ can be installed ... OK * 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’ ‘BiocGenerics’ ‘S4Vectors’ ‘IRanges’ ‘GenomicRanges’ ‘Biostrings’ ‘Rsamtools’ 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 ... NOTE Problems with news in ‘NEWS’: Cannot process chunk/lines: No NEW FEATURES or SIGNIFICANT USER-VISIBLE CHANGES or BUG FIXES since Cannot process chunk/lines: version 1.18.0 Cannot process chunk/lines: No NEW FEATURES or SIGNIFICANT USER-VISIBLE CHANGES or BUG FIXES since Cannot process chunk/lines: version 1.16.0 Cannot process chunk/lines: The first version of GenomicAlignments was included in Bioconductor 2.14. Cannot process chunk/lines: The package was created from existing code in IRanges, ShortRead, Cannot process chunk/lines: Rsamtools and GenomicRanges. * checking R 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 dependencies in R code ... NOTE ':::' calls which should be '::': ‘S4Vectors:::makeClassinfoRowForCompactPrinting’ ‘S4Vectors:::makePrettyMatrixForCompactPrinting’ See the note in ?`:::` about the use of this operator. Unexported objects imported by ':::' calls: ‘Rsamtools:::.BamViews_delegate’ ‘Rsamtools:::.findMateWithinGroups’ ‘Rsamtools:::.load_bamcols_from_scanBam_res’ 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 ... OK * checking Rd files ... WARNING checkRd: (5) GAlignmentPairs-class.Rd:90-94: \item in \describe must have non-empty label checkRd: (5) GAlignmentPairs-class.Rd:102-133: \item in \describe must have non-empty label checkRd: (5) GAlignmentPairs-class.Rd:134-137: \item in \describe must have non-empty label checkRd: (5) GAlignmentPairs-class.Rd:138-143: \item in \describe must have non-empty label checkRd: (5) GAlignmentPairs-class.Rd:144-160: \item in \describe must have non-empty label checkRd: (5) GAlignmentPairs-class.Rd:161-172: \item in \describe must have non-empty label checkRd: (5) GAlignmentPairs-class.Rd:173-179: \item in \describe must have non-empty label checkRd: (5) GAlignmentPairs-class.Rd:180-183: \item in \describe must have non-empty label checkRd: (5) GAlignmentPairs-class.Rd:184-188: \item in \describe must have non-empty label checkRd: (5) GAlignmentPairs-class.Rd:189-193: \item in \describe must have non-empty label checkRd: (5) GAlignmentPairs-class.Rd:194-203: \item in \describe must have non-empty label checkRd: (5) GAlignmentPairs-class.Rd:204-210: \item in \describe must have non-empty label checkRd: (5) GAlignmentPairs-class.Rd:211-216: \item in \describe must have non-empty label checkRd: (5) GAlignmentPairs-class.Rd:217-222: \item in \describe must have non-empty label checkRd: (5) GAlignmentPairs-class.Rd:223-232: \item in \describe must have non-empty label checkRd: (5) GAlignmentPairs-class.Rd:240-244: \item in \describe must have non-empty label checkRd: (5) GAlignmentPairs-class.Rd:252-257: \item in \describe must have non-empty label checkRd: (5) GAlignmentPairs-class.Rd:258-264: \item in \describe must have non-empty label checkRd: (5) GAlignmentPairs-class.Rd:272-298: \item in \describe must have non-empty label checkRd: (5) GAlignmentPairs-class.Rd:299-328: \item in \describe must have non-empty label checkRd: (5) GAlignmentPairs-class.Rd:329-336: \item in \describe must have non-empty label checkRd: (5) GAlignmentPairs-class.Rd:337-340: \item in \describe must have non-empty label checkRd: (5) GAlignmentPairs-class.Rd:348-359: \item in \describe must have non-empty label checkRd: (5) GAlignments-class.Rd:148-154: \item in \describe must have non-empty label checkRd: (5) GAlignments-class.Rd:162-165: \item in \describe must have non-empty label checkRd: (5) GAlignments-class.Rd:166-171: \item in \describe must have non-empty label checkRd: (5) GAlignments-class.Rd:172-179: \item in \describe must have non-empty label checkRd: (5) GAlignments-class.Rd:180-183: \item in \describe must have non-empty label checkRd: (5) GAlignments-class.Rd:184-190: \item in \describe must have non-empty label checkRd: (5) GAlignments-class.Rd:191-195: \item in \describe must have non-empty label checkRd: (5) GAlignments-class.Rd:196-202: \item in \describe must have non-empty label checkRd: (5) GAlignments-class.Rd:203-213: \item in \describe must have non-empty label checkRd: (5) GAlignments-class.Rd:214-221: \item in \describe must have non-empty label checkRd: (5) GAlignments-class.Rd:222-227: \item in \describe must have non-empty label checkRd: (5) GAlignments-class.Rd:228-232: \item in \describe must have non-empty label checkRd: (5) GAlignments-class.Rd:233-241: \item in \describe must have non-empty label checkRd: (5) GAlignments-class.Rd:242-248: \item in \describe must have non-empty label checkRd: (5) GAlignments-class.Rd:249-254: \item in \describe must have non-empty label checkRd: (5) GAlignments-class.Rd:255-260: \item in \describe must have non-empty label checkRd: (5) GAlignments-class.Rd:261-270: \item in \describe must have non-empty label checkRd: (5) GAlignments-class.Rd:278-292: \item in \describe must have non-empty label checkRd: (5) GAlignments-class.Rd:293-335: \item in \describe must have non-empty label checkRd: (5) GAlignments-class.Rd:336-344: \item in \describe must have non-empty label checkRd: (5) GAlignments-class.Rd:351-357: \item in \describe must have non-empty label checkRd: (5) GAlignments-class.Rd:365-369: \item in \describe must have non-empty label checkRd: (5) GAlignments-class.Rd:375-381: \item in \describe must have non-empty label checkRd: (5) GAlignments-class.Rd:388-400: \item in \describe must have non-empty label checkRd: (5) GAlignmentsList-class.Rd:67-70: \item in \describe must have non-empty label checkRd: (5) GAlignmentsList-class.Rd:78-81: \item in \describe must have non-empty label checkRd: (5) GAlignmentsList-class.Rd:82-85: \item in \describe must have non-empty label checkRd: (5) GAlignmentsList-class.Rd:86-90: \item in \describe must have non-empty label checkRd: (5) GAlignmentsList-class.Rd:91-94: \item in \describe must have non-empty label checkRd: (5) GAlignmentsList-class.Rd:95-99: \item in \describe must have non-empty label checkRd: (5) GAlignmentsList-class.Rd:100-105: \item in \describe must have non-empty label checkRd: (5) GAlignmentsList-class.Rd:106-112: \item in \describe must have non-empty label checkRd: (5) GAlignmentsList-class.Rd:113-118: \item in \describe must have non-empty label checkRd: (5) GAlignmentsList-class.Rd:119-123: \item in \describe must have non-empty label checkRd: (5) GAlignmentsList-class.Rd:124-129: \item in \describe must have non-empty label checkRd: (5) GAlignmentsList-class.Rd:130-134: \item in \describe must have non-empty label checkRd: (5) GAlignmentsList-class.Rd:135-139: \item in \describe must have non-empty label checkRd: (5) GAlignmentsList-class.Rd:140-146: \item in \describe must have non-empty label checkRd: (5) GAlignmentsList-class.Rd:147-152: \item in \describe must have non-empty label checkRd: (5) GAlignmentsList-class.Rd:153-158: \item in \describe must have non-empty label checkRd: (5) GAlignmentsList-class.Rd:159-162: \item in \describe must have non-empty label checkRd: (5) GAlignmentsList-class.Rd:170-187: \item in \describe must have non-empty label checkRd: (5) GAlignmentsList-class.Rd:188-206: \item in \describe must have non-empty label checkRd: (5) GAlignmentsList-class.Rd:207-215: \item in \describe must have non-empty label checkRd: (5) GAlignmentsList-class.Rd:216-222: \item in \describe must have non-empty label checkRd: (5) GAlignmentsList-class.Rd:223-228: \item in \describe must have non-empty label checkRd: (5) GAlignmentsList-class.Rd:236-240: \item in \describe must have non-empty label checkRd: (5) GAlignmentsList-class.Rd:241-244: \item in \describe must have non-empty label checkRd: (5) GAlignmentsList-class.Rd:245-250: \item in \describe must have non-empty label checkRd: (5) GAlignmentsList-class.Rd:256-262: \item in \describe must have non-empty label checkRd: (5) GappedReads-class.Rd:40-44: \item in \describe must have non-empty label checkRd: (5) OverlapEncodings-class.Rd:133-137: \item in \describe must have non-empty label checkRd: (5) OverlapEncodings-class.Rd:138-155: \item in \describe must have non-empty label checkRd: (5) OverlapEncodings-class.Rd:156-182: \item in \describe must have non-empty label checkRd: (5) OverlapEncodings-class.Rd:183-185: \item in \describe must have non-empty label checkRd: (5) OverlapEncodings-class.Rd:186-192: \item in \describe must have non-empty label checkRd: (5) OverlapEncodings-class.Rd:200-204: \item in \describe must have non-empty label checkRd: (5) OverlapEncodings-class.Rd:213-227: \item in \describe must have non-empty label checkRd: (5) OverlapEncodings-class.Rd:228-235: \item in \describe must have non-empty label checkRd: (5) OverlapEncodings-class.Rd:236-245: \item in \describe must have non-empty label checkRd: (5) OverlapEncodings-class.Rd:246-261: \item in \describe must have non-empty label checkRd: (5) summarizeOverlaps-methods.Rd:226-246: \item in \describe must have non-empty label * 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 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 readGAlignments 24.522 5.152 37.799 junctions-methods 21.784 2.236 30.680 summarizeOverlaps-methods 14.384 4.054 22.829 coordinate-mapping-methods 13.716 0.450 17.730 sequenceLayer 11.075 2.290 17.982 findSpliceOverlaps-methods 9.201 0.274 11.979 stackStringsFromGAlignments 7.358 0.411 10.205 GAlignmentsList-class 4.623 0.139 6.070 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘run_unitTests.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 5 NOTEs See ‘/Users/biocbuild/bbs-3.17-bioc/meat/GenomicAlignments.Rcheck/00check.log’ for details.