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### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD check --install=check:VariantAnnotation.install-out.txt --library=/home/rapidbuild/bbs-3.23-bioc-rapid/R/site-library --timings VariantAnnotation_1.57.0.tar.gz
###
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* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/VariantAnnotation.Rcheck’
* using R Under development (unstable) (2025-10-28 r88973)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘VariantAnnotation/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘VariantAnnotation’ version ‘1.57.0’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Bioconductor Package Maintainer <maintainer@bioconductor.org>’

Unknown, possibly misspelled, fields in DESCRIPTION:
  ‘Video’ ‘git_url’ ‘git_branch’ ‘git_last_commit’ ‘git_last_commit_date’
* checking package namespace information ... OK
* checking package dependencies ... INFO
Depends: includes the non-default packages:
  'BiocGenerics', 'MatrixGenerics', 'Seqinfo', '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 ... INFO
  installed size is  7.3Mb
  sub-directories of 1Mb or more:
    R         2.2Mb
    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 use of S3 registration ... OK
* checking dependencies in R code ... NOTE
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) 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ScanVcfParam-class.Rd: GRanges-class
  VCF-class.Rd: DataFrame, GRanges, FaFile
  VCFHeader-class.Rd: DataFrameList
  VcfFile-class.Rd: TabixFile-class, TabixFileList-class
  defunct.Rd: expand
  filterVcf-methods.Rd: TabixFile, bgzip, FilterRules
  indexVcf-method.Rd: bgzip
  predictCoding-methods.Rd: IntegerRanges, GRanges, FaFile
  readVcf-methods.Rd: TabixFile, indexTabix, scanTabix, scanBcf
  scanVcf-methods.Rd: TabixFile, TabixFile-class, BcfFile
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 ... INFO
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/rapidbuild/bbs-3.23-bioc-rapid/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)

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.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... NOTE
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
locateVariants-methods    32.051  0.726  32.784
predictCoding-methods     19.598  0.044  19.647
summarizeVariants-methods  5.323  0.002   5.328
PROVEANDb-class            3.455  1.022  32.171
* 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 WARNING, 6 NOTEs
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/VariantAnnotation.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD INSTALL VariantAnnotation
###
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* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library’
* installing *source* package ‘VariantAnnotation’ ...
** this is package ‘VariantAnnotation’ version ‘1.57.0’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/XVector/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/XVector/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/XVector/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c R_init_VariantAnnotation.c -o R_init_VariantAnnotation.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/XVector/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c XVector_stubs.c -o XVector_stubs.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/XVector/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c dna_hash.c -o dna_hash.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/XVector/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c rle.c -o rle.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/XVector/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c strhash.c -o strhash.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/XVector/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c utilities.c -o utilities.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/XVector/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c vcffile.c -o vcffile.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/XVector/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c vcftype.c -o vcftype.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/XVector/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c writevcf.c -o writevcf.o
gcc -std=gnu2x -shared -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/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz
installing to /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/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)

R Under development (unstable) (2025-10-28 r88973) -- "Unsuffered Consequences"
Copyright (C) 2025 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
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, 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: Seqinfo
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

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: 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/RtmpX8XBgQ/file21feeb3d45993
compressing and indexing '/tmp/RtmpX8XBgQ/file21feeb3d45993'
starting filter
filtering 10376 records
completed filtering
compressing and indexing '/tmp/RtmpX8XBgQ/file21feeb24797c11'
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
GRanges object with 4 ranges and 9 metadata columns:
      seqnames    ranges strand |   LOCATION  LOCSTART    LOCEND   QUERYID
         <Rle> <IRanges>  <Rle> |   <factor> <integer> <integer> <integer>
  [1]     chr1     65565      + | spliceSite      <NA>      <NA>         1
  [2]     chr1    367659      + | spliceSite      <NA>      <NA>         2
  [3]     chr1    859812      + | spliceSite      <NA>      <NA>         3
  [4]     chr1    859812      + | spliceSite      <NA>      <NA>         3
           TXID         CDSID      GENEID       PRECEDEID        FOLLOWID
      <integer> <IntegerList> <character> <CharacterList> <CharacterList>
  [1]      <NA>                      <NA>                                
  [2]      <NA>                      <NA>                                
  [3]      <NA>                      <NA>                                
  [4]      <NA>                      <NA>                                
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths
Loading required package: BSgenome
Loading required package: BiocIO
Loading required package: rtracklayer
'select()' returned many:1 mapping between keys and columns
[W::bcf_hdr_check_sanity] PL should be declared as Number=G


RUNIT TEST PROTOCOL -- Fri Oct 31 09:26:15 2025 
*********************************************** 
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 .set_group_names(grl, use.names, txdb, by) :
  some group names are NAs or duplicated
4: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 1 out-of-bound range located on sequence
  ENST00000641515.2_6. 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 DataFrame(..., check.names = FALSE) : NAs introduced by coercion
6: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 7 out-of-bound ranges located on sequence 346665.
  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.
7: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 6 out-of-bound ranges located on sequence 346665.
  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 
 84.875   1.851  90.264