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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD check --install=check:GWASTools.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings GWASTools_1.57.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/GWASTools.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GWASTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GWASTools’ version ‘1.57.0’
* checking package namespace information ... OK
* checking package dependencies ... 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 ... ERROR
Running examples in ‘GWASTools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: NcdfGenotypeReader
> ### Title: Class NcdfGenotypeReader
> ### Aliases: NcdfGenotypeReader-class NcdfGenotypeReader
> ###   getVariable,NcdfGenotypeReader-method
> ###   getSnpID,NcdfGenotypeReader-method
> ###   getChromosome,NcdfGenotypeReader-method
> ###   getPosition,NcdfGenotypeReader-method
> ###   getScanID,NcdfGenotypeReader-method
> ###   getGenotype,NcdfGenotypeReader-method nsnp,NcdfGenotypeReader-method
> ###   nscan,NcdfGenotypeReader-method
> ###   autosomeCode,NcdfGenotypeReader-method
> ###   XchromCode,NcdfGenotypeReader-method
> ###   XYchromCode,NcdfGenotypeReader-method
> ###   YchromCode,NcdfGenotypeReader-method
> ###   MchromCode,NcdfGenotypeReader-method
> ### Keywords: methods classes
> 
> ### ** Examples
> 
> file <- system.file("extdata", "illumina_geno.nc", package="GWASdata")
> nc <- NcdfGenotypeReader(file)
Loading required namespace: ncdf4
Failed with error:  ‘unable to load shared object '/home/biocbuild/R/R-devel_2025-02-19/site-library/ncdf4/libs/ncdf4.so':
  libnetcdf.so.19: cannot open shared object file: No such file or directory’
Error in NcdfReader(filename) : 
  please install ncdf4 to work with NetCDF files
Calls: NcdfGenotypeReader -> new -> initialize -> initialize -> NcdfReader
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.R’
 ERROR
Running the tests in ‘tests/test.R’ failed.
Last 13 lines of output:
      mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
      rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
      unsplit, which.max, which.min
  
  Welcome to Bioconductor
  
      Vignettes contain introductory material; view with
      'browseVignettes()'. To cite Bioconductor, see
      'citation("Biobase")', and for packages 'citation("pkgname")'.
  
  > library(ncdf4)
  Error: package or namespace load failed for 'ncdf4' in dyn.load(file, DLLpath = DLLpath, ...):
   unable to load shared object '/home/biocbuild/R/R-devel_2025-02-19/site-library/ncdf4/libs/ncdf4.so':
    libnetcdf.so.19: cannot open shared object file: No such file or directory
  Execution halted
* 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: 2 ERRORs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/GWASTools.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL GWASTools
###
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* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘GWASTools’ ...
** this is package ‘GWASTools’ version ‘1.57.0’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GWASTools)

R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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.

> library(GWASdata)
Loading required package: GWASTools
Loading required package: Biobase
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

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> library(ncdf4)
Error: package or namespace load failed for 'ncdf4' in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/home/biocbuild/R/R-devel_2025-02-19/site-library/ncdf4/libs/ncdf4.so':
  libnetcdf.so.19: cannot open shared object file: No such file or directory
Execution halted