##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:REMP.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings REMP_1.31.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/REMP.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'REMP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'REMP' version '1.31.0'
* package encoding: UTF-8
* 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 whether package 'REMP' 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
  'IlluminaHumanMethylation450kanno.ilmn12.hg19'
  'IlluminaHumanMethylationEPICanno.ilm10b2.hg19'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
initREMP: no visible binding for global variable
  'IlluminaHumanMethylation450kanno.ilmn12.hg19'
initREMP: no visible binding for global variable
  'IlluminaHumanMethylationEPICanno.ilm10b2.hg19'
remprofile: no visible binding for global variable
  'IlluminaHumanMethylation450kanno.ilmn12.hg19'
remprofile: no visible binding for global variable
  'IlluminaHumanMethylationEPICanno.ilm10b2.hg19'
Undefined global functions or variables:
  IlluminaHumanMethylation450kanno.ilmn12.hg19
  IlluminaHumanMethylationEPICanno.ilm10b2.hg19
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Alu.hg19.demo.Rd: GRanges
  Alu.hg38.demo.Rd: GRanges
  GRannot.Rd: GRanges, GRangesList
  REMProduct-class.Rd: BiocParallelParam, org.Hs.eg.db
  fetchRMSK.Rd: GRanges
  fetchRefSeqGene.Rd: GRangesList, GRanges
  findRECpG.Rd: GRanges, BiocParallel
  getBackend.Rd: BiocParallel
  getGM12878.Rd: GenomicRatioSet, RatioSet
  grooMethy.Rd: RatioSet, GenomicRatioSet, DataFrame, GRanges,
    impute.knn
  initREMP.Rd: GRanges, AnnotationHub, BiocParallelParam
  remp.Rd: RatioSet, GenomicRatioSet, DataFrame, GRanges,
    BiocParallelParam, ranger
  rempTemplate.Rd: RatioSet, GenomicRatioSet, DataFrame, GRanges
  remprofile.Rd: RatioSet, GenomicRatioSet, DataFrame, GRanges,
    AnnotationHub
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
fetchRMSK       18.54   2.06   29.03
remp            16.60   1.39   17.48
rempTemplate    11.76   1.34   13.02
remprofile      11.63   1.28   12.77
GRannot         10.56   1.16   16.73
initREMP         9.10   0.93   10.29
fetchRefSeqGene  5.29   0.69    6.11
* 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
  'E:/biocbuild/bbs-3.21-bioc/meat/REMP.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL REMP
###
##############################################################################
##############################################################################


* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'REMP' ...
** 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 (REMP)