Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:03 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 2236/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
VariantAnnotation 1.52.0 (landing page) Bioconductor Package Maintainer
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | ERROR | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the VariantAnnotation package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/VariantAnnotation.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: VariantAnnotation |
Version: 1.52.0 |
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 |
StartedAt: 2024-11-20 11:10:11 -0500 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 11:19:21 -0500 (Wed, 20 Nov 2024) |
EllapsedTime: 550.6 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: VariantAnnotation.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### 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 ‘/media/volume/teran2_disk/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 13.2.0-23ubuntu4) 13.2.0’ * 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 ‘/media/volume/teran2_disk/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 ... ERROR Running examples in ‘VariantAnnotation-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: vep_by_region > ### Title: Use the VEP region API on variant information in a VCF object as > ### defined in VariantAnnotation. > ### Aliases: vep_by_region > > ### ** Examples > > fl <- system.file("extdata", "chr22.vcf.gz", package="VariantAnnotation") > r22 = readVcf(fl) > dr = which(width(rowRanges(r22))!=1) > r22s = r22[-dr] > res = vep_by_region(r22[1:100], snv_only=FALSE, chk_max=FALSE) Error in post_Hs_region(chr = as.character(seqnames(rr)), pos = start(rr), : Service Unavailable (HTTP 503). Calls: vep_by_region -> post_Hs_region -> <Anonymous> Execution halted * 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: 1 ERROR, 2 WARNINGs, 5 NOTEs See ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/VariantAnnotation.Rcheck/00check.log’ for details.
VariantAnnotation.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL VariantAnnotation ### ############################################################################## ############################################################################## * installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘VariantAnnotation’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -c IRanges_stubs.c -o IRanges_stubs.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -c R_init_VariantAnnotation.c -o R_init_VariantAnnotation.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -c XVector_stubs.c -o XVector_stubs.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -c dna_hash.c -o dna_hash.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -c rle.c -o rle.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -c strhash.c -o strhash.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -c utilities.c -o utilities.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -c vcffile.c -o vcffile.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -c vcftype.c -o vcftype.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -c writevcf.c -o writevcf.o gcc -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o VariantAnnotation.so Biostrings_stubs.o IRanges_stubs.o R_init_VariantAnnotation.o XVector_stubs.o dna_hash.o rle.o strhash.o utilities.o vcffile.o vcftype.o writevcf.o /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR installing to /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-VariantAnnotation/00new/VariantAnnotation/libs ** R ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘tabulate’ in package ‘VariantAnnotation’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (VariantAnnotation)
VariantAnnotation.Rcheck/tests/VariantAnnotation_unit_tests.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > require("VariantAnnotation") || stop("unable to load VariantAnnotation package") Loading required package: VariantAnnotation Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'MatrixGenerics' The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: GenomeInfoDb Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Loading required package: GenomicRanges Loading required package: SummarizedExperiment Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians Loading required package: Rsamtools Loading required package: Biostrings Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Attaching package: 'VariantAnnotation' The following object is masked from 'package:base': tabulate [1] TRUE > VariantAnnotation:::.test() Loading required package: RSQLite [W::tbx_parse1] VCF INFO/END=2827680 is smaller than POS at 1:2827692 This tag will be ignored. Note: only one invalid END tag will be reported. [W::bcf_hdr_register_hrec] The definition of Flag "INFO/TS" is invalid, forcing Number=0 [W::bcf_hdr_register_hrec] The definition of Flag "INFO/TS" is invalid, forcing Number=0 starting prefilter prefiltering 10376 records prefiltered to /tmp/RtmphTuucE/file28df962b947c3 compressing and indexing '/tmp/RtmphTuucE/file28df962b947c3' starting filter filtering 10376 records completed filtering compressing and indexing '/tmp/RtmphTuucE/file28df9670f01d15' Loading required package: survival Loading required package: Matrix Attaching package: 'Matrix' The following object is masked from 'package:VariantAnnotation': expand The following object is masked from 'package:S4Vectors': expand [W::bcf_hdr_check_sanity] GL should be declared as Number=G non-single nucleotide variations are set to NA non-single nucleotide variations are set to NA non-single nucleotide variations are set to NA non-single nucleotide variations are set to NA non-single nucleotide variations are set to NA non-single nucleotide variations are set to NA Loading required package: GenomicFeatures Loading required package: AnnotationDbi 'select()' returned 1:1 mapping between keys and columns Loading required package: BSgenome Loading required package: BiocIO Loading required package: rtracklayer Attaching package: 'rtracklayer' The following object is masked from 'package:BiocIO': FileForFormat 'select()' returned many:1 mapping between keys and columns [W::bcf_hdr_check_sanity] PL should be declared as Number=G RUNIT TEST PROTOCOL -- Wed Nov 20 11:17:21 2024 *********************************************** Number of test functions: 99 Number of errors: 0 Number of failures: 0 1 Test Suite : VariantAnnotation RUnit Tests - 99 test functions, 0 errors, 0 failures Number of test functions: 99 Number of errors: 0 Number of failures: 0 Warning messages: 1: info fields with no header: noMatch 2: In .bcfHeaderAsSimpleList(header) : duplicate keys in header will be forced to unique rownames 3: In DataFrame(..., check.names = FALSE) : NAs introduced by coercion 4: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 7 out-of-bound ranges located on sequence 70477. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. 5: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 6 out-of-bound ranges located on sequence 70477. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. > > proc.time() user system elapsed 73.996 1.879 79.553
VariantAnnotation.Rcheck/VariantAnnotation-Ex.timings
name | user | system | elapsed | |
GLtoGP | 0.792 | 0.266 | 1.064 | |
PROVEANDb-class | 3.681 | 0.995 | 27.439 | |
PolyPhenDb-class | 0.550 | 0.107 | 3.959 | |
SIFTDb-class | 0 | 0 | 0 | |
ScanVcfParam-class | 1.738 | 0.007 | 1.753 | |
VCF-class | 0.997 | 0.070 | 1.068 | |
VCFHeader-class | 0.053 | 0.000 | 0.053 | |
VRanges-class | 0.294 | 0.000 | 0.294 | |
VRangesList-class | 0.283 | 0.000 | 0.284 | |
VariantType-class | 0.004 | 0.001 | 0.004 | |
VcfFile-class | 0.346 | 0.000 | 0.349 | |
filterVcf-methods | 1.557 | 0.052 | 3.982 | |
genotypeToSnpMatrix-methods | 0.768 | 0.131 | 0.899 | |
getTranscriptSeqs-methods | 0.000 | 0.000 | 0.001 | |
indexVcf-method | 0.006 | 0.000 | 0.009 | |
isSNV-methods | 0.634 | 0.000 | 0.635 | |
locateVariants-methods | 12.578 | 0.351 | 12.936 | |
post_Hs_region | 0.064 | 0.003 | 37.932 | |
predictCoding-methods | 11.219 | 0.049 | 11.286 | |
probabilityToSnpMatrix | 0.001 | 0.000 | 0.001 | |
readVcf-methods | 2.229 | 0.003 | 2.232 | |
scanVcf-methods | 0.178 | 0.001 | 0.178 | |
seqinfo-method | 0.045 | 0.000 | 0.044 | |
snpSummary | 0.190 | 0.001 | 0.191 | |
summarizeVariants-methods | 3.161 | 0.003 | 3.166 | |