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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:VariantAnnotation.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings VariantAnnotation_1.55.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/VariantAnnotation.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘VariantAnnotation/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘VariantAnnotation’ version ‘1.55.2’
* 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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.1.sdk’
* checking installed package size ... INFO
  installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R         3.0Mb
    extdata   1.2Mb
    libs      1.1Mb
* 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 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 ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/VariantAnnotation/libs/VariantAnnotation.so’:
  Found ‘___assert_rtn’, possibly from ‘assert’ (C)
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
  Found ‘_abort’, possibly from ‘abort’ (C)
  Found ‘_exit’, possibly from ‘exit’ (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,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
locateVariants-methods    59.392  1.964  61.776
predictCoding-methods     34.471  1.476  36.183
summarizeVariants-methods  9.656  0.173   9.867
PROVEANDb-class            4.983  2.078   9.663
vep_by_region              2.853  0.128   6.126
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/VariantAnnotation.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL VariantAnnotation
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘VariantAnnotation’ ...
** this is package ‘VariantAnnotation’ version ‘1.55.2’
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.1.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c Biostrings_stubs.c -o Biostrings_stubs.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c IRanges_stubs.c -o IRanges_stubs.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c R_init_VariantAnnotation.c -o R_init_VariantAnnotation.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c XVector_stubs.c -o XVector_stubs.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c dna_hash.c -o dna_hash.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c rle.c -o rle.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c strhash.c -o strhash.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c utilities.c -o utilities.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c vcffile.c -o vcffile.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c vcftype.c -o vcftype.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c writevcf.c -o writevcf.o
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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 version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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/RtmpC1Zlwc/file1667f4d94b65
compressing and indexing '/tmp/RtmpC1Zlwc/file1667f4d94b65'
starting filter
filtering 10376 records
completed filtering
compressing and indexing '/tmp/RtmpC1Zlwc/file1667f55e4d65f'
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 24 01:06:19 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 
146.474   4.807 152.387