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###
### Running command:
###
###   E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GRaNIE.install-out.txt --library=E:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings GRaNIE_1.8.0.tar.gz
###
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* using log directory 'E:/biocbuild/bbs-3.19-bioc/meat/GRaNIE.Rcheck'
* using R version 4.4.1 (2024-06-14 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 'GRaNIE/DESCRIPTION' ... OK
* this is package 'GRaNIE' version '1.8.0'
* 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 'GRaNIE' can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'GenomicRanges::windows' by 'grDevices::windows' when loading 'GRaNIE'
See 'E:/biocbuild/bbs-3.19-bioc/meat/GRaNIE.Rcheck/00install.out' for details.
* 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 ... WARNING
Missing or unexported object: 'AnnotationHub::getAnnotationHub'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.getAnnotationHub: no visible global function definition for 'is'
.performIHW: no visible binding for global variable 'adj_pvalue'
.retrieveAnnotationData: no visible global function definition for 'is'
Undefined global functions or variables:
  adj_pvalue is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
checkRd: (-1) addData.Rd:36: Lost braces; missing escapes or markup?
    36 | The required format must be {chr}:{start}-{end}", with {chr} denoting the abbreviated chromosome name, and {start} and {end} the begin and end 
       |                             ^
checkRd: (-1) addData.Rd:36: Lost braces; missing escapes or markup?
    36 | The required format must be {chr}:{start}-{end}", with {chr} denoting the abbreviated chromosome name, and {start} and {end} the begin and end 
       |                                   ^
checkRd: (-1) addData.Rd:36: Lost braces; missing escapes or markup?
    36 | The required format must be {chr}:{start}-{end}", with {chr} denoting the abbreviated chromosome name, and {start} and {end} the begin and end 
       |                                           ^
checkRd: (-1) addData.Rd:36: Lost braces; missing escapes or markup?
    36 | The required format must be {chr}:{start}-{end}", with {chr} denoting the abbreviated chromosome name, and {start} and {end} the begin and end 
       |                                                        ^
checkRd: (-1) addData.Rd:36: Lost braces; missing escapes or markup?
    36 | The required format must be {chr}:{start}-{end}", with {chr} denoting the abbreviated chromosome name, and {start} and {end} the begin and end 
       |                                                                                                            ^
checkRd: (-1) addData.Rd:36: Lost braces; missing escapes or markup?
    36 | The required format must be {chr}:{start}-{end}", with {chr} denoting the abbreviated chromosome name, and {start} and {end} the begin and end 
       |                                                                                                                        ^
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* 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 files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                               user system elapsed
generateStatsSummary           9.69   0.29   10.66
addConnections_TF_peak         6.13   1.89   10.56
addSNPData                     6.70   0.39   20.01
plotDiagnosticPlots_peakGene   5.94   0.28    6.73
plotPCA_all                    4.54   0.23    5.24
plotDiagnosticPlots_TFPeaks    4.39   0.35    5.80
plotCommunitiesEnrichment      4.25   0.36    5.27
plotCorrelations               4.34   0.12    5.47
calculateCommunitiesEnrichment 4.28   0.15    5.05
* 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 WARNINGs, 2 NOTEs
See
  'E:/biocbuild/bbs-3.19-bioc/meat/GRaNIE.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL GRaNIE
###
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* installing to library 'E:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'GRaNIE' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'GenomicRanges::windows' by 'grDevices::windows' when loading 'GRaNIE'
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'GenomicRanges::windows' by 'grDevices::windows' when loading 'GRaNIE'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'GenomicRanges::windows' by 'grDevices::windows' when loading 'GRaNIE'
** testing if installed package keeps a record of temporary installation path
* DONE (GRaNIE)