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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:GWASTools.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings GWASTools_1.53.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/GWASTools.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* 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 ‘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 loading without being on the library search path ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
vcfWrite 10.699  0.435  11.162
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/GWASTools.Rcheck/00check.log’
for details.