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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GWASTools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GWASTools_1.53.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/GWASTools.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GWASTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GWASTools’ version ‘1.53.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 OK
* 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 ‘GWASTools’ can be installed ... OK
* checking installed package size ... OK
* 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 object imported by a ':::' call: ‘S4Vectors:::make_zero_col_DataFrame’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) imputedDosageFile.Rd:95: Lost braces in \itemize; meant \describe ?
checkRd: (-1) imputedDosageFile.Rd:96: Lost braces in \itemize; meant \describe ?
checkRd: (-1) imputedDosageFile.Rd:97: 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:
  BAFfromClusterMeans.Rd: add.gdsn
  BAFfromGenotypes.Rd: add.gdsn
  GWASTools-package.Rd: AnnotatedDataFrame
  GdsReader-class.Rd: put.attr.gdsn, gdsfmt
  ScanAnnotationDataFrame-class.Rd: AnnotatedDataFrame
  SnpAnnotationDataFrame-class.Rd: AnnotatedDataFrame
  anomDetectBAF.Rd: smooth.CNA, DNAcopy, segment
  anomDetectLOH.Rd: smooth.CNA, DNAcopy, segment
  anomIdentifyLowQuality.Rd: DNAcopy
  assocCoxPH.Rd: Surv, coxph, survival
  assocRegression.Rd: logistf, vcovHC, lrtest
  convertNcdfGds.Rd: add.gdsn, gdsfmt
  createDataFile.Rd: add.gdsn, gdsfmt
  exactHWE.Rd: HWExact, GWASExactHW
  gdsSubset.Rd: add.gdsn, gdsfmt
  imputedDosageFile.Rd: add.gdsn
  setMissingGenotypes.Rd: add.gdsn
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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
vcfWrite 10.769  0.607   11.46
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/GWASTools.Rcheck/00check.log’
for details.