############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:VariantAnnotation.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings VariantAnnotation_1.52.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/VariantAnnotation.Rcheck’ * using R version 4.4.2 (2024-10-31) * 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 ‘VariantAnnotation/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘VariantAnnotation’ version ‘1.52.0’ * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'BiocGenerics', 'MatrixGenerics', 'GenomeInfoDb', 'GenomicRanges', 'SummarizedExperiment', '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 ‘VariantAnnotation’ can be installed ... OK * used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ * checking installed package size ... NOTE installed size is 7.2Mb sub-directories of 1Mb or more: R 2.1Mb extdata 1.2Mb libs 3.4Mb * 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 ... WARNING '::' or ':::' import not declared from: ‘curl’ Unexported objects imported by ':::' calls: ‘BiocGenerics:::replaceSlots’ ‘BiocGenerics:::testPackage’ ‘S4Vectors:::expandByColumnSet’ ‘S4Vectors:::labeledLine’ ‘S4Vectors:::recycleVector’ ‘S4Vectors:::selectSome’ ‘SummarizedExperiment:::.SummarizedExperiment.charbound’ ‘SummarizedExperiment:::.cbind.DataFrame’ ‘rtracklayer:::checkArgFormat’ 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 VRangesForMatching: no visible binding for global variable ‘REF’ VRangesForMatching: no visible binding for global variable ‘ALT’ Undefined global functions or variables: ALT REF * checking Rd files ... WARNING checkRd: (5) PROVEANDb-class.Rd:24-27: \item in \describe must have non-empty label checkRd: (5) PROVEANDb-class.Rd:28-32: \item in \describe must have non-empty label checkRd: (5) PROVEANDb-class.Rd:33-37: \item in \describe must have non-empty label checkRd: (5) PROVEANDb-class.Rd:38-42: \item in \describe must have non-empty label checkRd: (5) PROVEANDb-class.Rd:43-49: \item in \describe must have non-empty label checkRd: (5) PolyPhenDb-class.Rd:25-28: \item in \describe must have non-empty label checkRd: (5) PolyPhenDb-class.Rd:29-33: \item in \describe must have non-empty label checkRd: (5) PolyPhenDb-class.Rd:34-38: \item in \describe must have non-empty label checkRd: (5) PolyPhenDb-class.Rd:39-45: \item in \describe must have non-empty label checkRd: (5) PolyPhenDb-class.Rd:46-52: \item in \describe must have non-empty label checkRd: (5) SIFTDb-class.Rd:24-27: \item in \describe must have non-empty label checkRd: (5) SIFTDb-class.Rd:28-32: \item in \describe must have non-empty label checkRd: (5) SIFTDb-class.Rd:33-37: \item in \describe must have non-empty label checkRd: (5) SIFTDb-class.Rd:38-44: \item in \describe must have non-empty label checkRd: (5) VCF-class.Rd:107-109: \item in \describe must have non-empty label checkRd: (5) VCF-class.Rd:110-121: \item in \describe must have non-empty label checkRd: (5) VCF-class.Rd:129-170: \item in \describe must have non-empty label checkRd: (5) VCF-class.Rd:171-177: \item in \describe must have non-empty label checkRd: (5) VCF-class.Rd:178-183: \item in \describe must have non-empty label checkRd: (5) VCF-class.Rd:184-188: \item in \describe must have non-empty label checkRd: (5) VCF-class.Rd:189-197: \item in \describe must have non-empty label checkRd: (5) VCF-class.Rd:198-204: \item in \describe must have non-empty label checkRd: (5) VCF-class.Rd:205-211: \item in \describe must have non-empty label checkRd: (5) VCF-class.Rd:212-216: \item in \describe must have non-empty label checkRd: (5) VCF-class.Rd:217-221: \item in \describe must have non-empty label checkRd: (5) VCF-class.Rd:222-226: \item in \describe must have non-empty label checkRd: (5) VCF-class.Rd:227-240: \item in \describe must have non-empty label checkRd: (5) VCF-class.Rd:241-246: \item in \describe must have non-empty label checkRd: (5) VCF-class.Rd:254-258: \item in \describe must have non-empty label checkRd: (5) VCF-class.Rd:259-266: \item in \describe must have non-empty label checkRd: (5) VCF-class.Rd:267-284: \item in \describe must have non-empty label checkRd: (5) VCF-class.Rd:291-304: \item in \describe must have non-empty label checkRd: (5) VCFHeader-class.Rd:47-51: \item in \describe must have non-empty label checkRd: (5) VCFHeader-class.Rd:58-61: \item in \describe must have non-empty label checkRd: (5) VCFHeader-class.Rd:62-66: \item in \describe must have non-empty label checkRd: (5) VCFHeader-class.Rd:67-86: \item in \describe must have non-empty label checkRd: (5) VCFHeader-class.Rd:87-94: \item in \describe must have non-empty label checkRd: (5) VCFHeader-class.Rd:95-100: \item in \describe must have non-empty label checkRd: (5) VCFHeader-class.Rd:101-106: \item in \describe must have non-empty label checkRd: (5) VCFHeader-class.Rd:107-111: \item in \describe must have non-empty label checkRd: (5) VCFHeader-class.Rd:112-118: \item in \describe must have non-empty label checkRd: (5) VRanges-class.Rd:146-178: \item in \describe must have non-empty label checkRd: (5) VRanges-class.Rd:179-224: \item in \describe must have non-empty label checkRd: (5) VRanges-class.Rd:232-265: \item in \describe must have non-empty label checkRd: (5) VRanges-class.Rd:266-268: \item in \describe must have non-empty label checkRd: (5) VRanges-class.Rd:269-281: \item in \describe must have non-empty label checkRd: (5) VRanges-class.Rd:290-292: \item in \describe must have non-empty label checkRd: (5) VRanges-class.Rd:293-295: \item in \describe must have non-empty label checkRd: (5) VRanges-class.Rd:296-299: \item in \describe must have non-empty label checkRd: (5) VRanges-class.Rd:300-303: \item in \describe must have non-empty label checkRd: (5) VRanges-class.Rd:304-307: \item in \describe must have non-empty label checkRd: (5) VRanges-class.Rd:308-310: \item in \describe must have non-empty label checkRd: (5) VRanges-class.Rd:311-314: \item in \describe must have non-empty label checkRd: (5) VRanges-class.Rd:315-319: \item in \describe must have non-empty label checkRd: (5) VRanges-class.Rd:320-322: \item in \describe must have non-empty label checkRd: (5) VRanges-class.Rd:323-326: \item in \describe must have non-empty label checkRd: (5) VRanges-class.Rd:327-330: \item in \describe must have non-empty label checkRd: (5) VRanges-class.Rd:336-339: \item in \describe must have non-empty label checkRd: (5) VRanges-class.Rd:340-344: \item in \describe must have non-empty label checkRd: (5) VRanges-class.Rd:345-349: \item in \describe must have non-empty label checkRd: (5) VRanges-class.Rd:355-358: \item in \describe must have non-empty label checkRd: (5) VRanges-class.Rd:359-372: \item in \describe must have non-empty label checkRd: (5) VRangesList-class.Rd:35-38: \item in \describe must have non-empty label checkRd: (5) VRangesList-class.Rd:44-47: \item in \describe must have non-empty label checkRd: (5) VRangesList-class.Rd:48-52: \item in \describe must have non-empty label checkRd: (5) VRangesList-class.Rd:58-62: \item in \describe must have non-empty label checkRd: (5) VariantType-class.Rd:134-138: \item in \describe must have non-empty label checkRd: (5) VariantType-class.Rd:139-143: \item in \describe must have non-empty label checkRd: (5) VariantType-class.Rd:144-149: \item in \describe must have non-empty label checkRd: (5) VariantType-class.Rd:150-154: \item in \describe must have non-empty label checkRd: (5) VariantType-class.Rd:155-159: \item in \describe must have non-empty label checkRd: (5) VcfFile-class.Rd:31-34: \item in \describe must have non-empty label checkRd: (5) VcfFile-class.Rd:35-37: \item in \describe must have non-empty label checkRd: (5) VcfFile-class.Rd:42-43: \item in \describe must have non-empty label checkRd: (5) VcfFile-class.Rd:44-45: \item in \describe must have non-empty label checkRd: (5) VcfFile-class.Rd:46-47: \item in \describe must have non-empty label checkRd: (5) VcfFile-class.Rd:48-49: \item in \describe must have non-empty label checkRd: (5) VcfFile-class.Rd:50-51: \item in \describe must have non-empty label checkRd: (5) VcfFile-class.Rd:52-54: \item in \describe must have non-empty label checkRd: (5) VcfFile-class.Rd:59-60: \item in \describe must have non-empty label checkRd: (5) VcfFile-class.Rd:61-62: \item in \describe must have non-empty label checkRd: (5) VcfFile-class.Rd:67-69: \item in \describe must have non-empty label checkRd: (-1) VcfFile-class.Rd:75: Lost braces in \itemize; meant \describe ? checkRd: (-1) VcfFile-class.Rd:77-78: Lost braces in \itemize; meant \describe ? checkRd: (-1) VcfFile-class.Rd:80: Lost braces in \itemize; meant \describe ? checkRd: (-1) VcfFile-class.Rd:82-83: Lost braces in \itemize; meant \describe ? checkRd: (-1) VcfFile-class.Rd:85-87: Lost braces in \itemize; meant \describe ? checkRd: (-1) VcfFile-class.Rd:89: Lost braces in \itemize; meant \describe ? checkRd: (-1) isSNV-methods.Rd:100-102: Lost braces in \itemize; meant \describe ? checkRd: (-1) isSNV-methods.Rd:103-107: Lost braces in \itemize; meant \describe ? checkRd: (-1) isSNV-methods.Rd:108-112: Lost braces in \itemize; meant \describe ? checkRd: (-1) isSNV-methods.Rd:113-116: Lost braces in \itemize; meant \describe ? checkRd: (-1) isSNV-methods.Rd:117-120: Lost braces in \itemize; meant \describe ? checkRd: (-1) isSNV-methods.Rd:121-124: Lost braces in \itemize; meant \describe ? checkRd: (-1) isSNV-methods.Rd:125-129: Lost braces in \itemize; meant \describe ? checkRd: (-1) readVcf-methods.Rd:64-69: Lost braces in \itemize; meant \describe ? checkRd: (-1) readVcf-methods.Rd:70-78: Lost braces in \itemize; meant \describe ? checkRd: (-1) summarizeVariants-methods.Rd:75-95: Lost braces in \itemize; meant \describe ? checkRd: (-1) summarizeVariants-methods.Rd:97-103: Lost braces in \itemize; meant \describe ? * 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 compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements. * 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 File ‘/home/biocbuild/bbs-3.20-bioc/R/site-library/VariantAnnotation/libs/VariantAnnotation.so’: Found ‘abort’, possibly from ‘abort’ (C) Found ‘exit’, possibly from ‘exit’ (C) Found ‘stderr’, possibly from ‘stderr’ (C) Found ‘stdout’, possibly from ‘stdout’ (C) File ‘VariantAnnotation/libs/VariantAnnotation.so’: Found non-API calls to R: ‘R_GetConnection’, ‘R_WriteConnection’ Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. The detected symbols are linked into the code but might come from libraries and not actually be called. Compiled code should not call non-API entry points in R. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed locateVariants-methods 18.541 1.387 19.929 predictCoding-methods 15.977 1.298 17.277 summarizeVariants-methods 4.859 0.156 5.015 PROVEANDb-class 4.038 0.648 6.866 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘VariantAnnotation_unit_tests.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: 2 WARNINGs, 5 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/VariantAnnotation.Rcheck/00check.log’ for details.