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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DMRcate.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings DMRcate_2.4.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/DMRcate.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DMRcate/DESCRIPTION' ... OK
* this is package 'DMRcate' version '2.4.1'
* 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 'DMRcate' can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'minfi::getMeth' by 'bsseq::getMeth' when loading 'DMRcate'
See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/DMRcate.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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... OK
* 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 ... OK
* 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 ...
** running examples for arch 'i386' ... ERROR
Running examples in 'DMRcate-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: DMR.plot
> ### Title: Plotting DMRs
> ### Aliases: DMR.plot plot
> 
> ### ** Examples
> 
> library(ExperimentHub)
Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr

Attaching package: 'AnnotationHub'

The following object is masked from 'package:Biobase':

    cache

> library(limma)

Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA

> eh <- ExperimentHub()
snapshotDate(): 2020-10-27
> FlowSorted.Blood.EPIC <- eh[["EH1136"]]
see ?FlowSorted.Blood.EPIC and browseVignettes('FlowSorted.Blood.EPIC') for documentation
loading from cache
> tcell <- FlowSorted.Blood.EPIC[,colData(FlowSorted.Blood.EPIC)$CD4T==100 |
+                                 colData(FlowSorted.Blood.EPIC)$CD8T==100]
> detP <- detectionP(tcell)
Loading required package: IlluminaHumanMethylationEPICmanifest
> remove <- apply(detP, 1, function (x) any(x > 0.01))
> tcell <- tcell[!remove,]
> tcell <- preprocessFunnorm(tcell)
[preprocessFunnorm] Background and dye bias correction with noob
Error: cannot allocate vector of size 85.7 Mb
Execution halted
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
DMR.plot            205.09  14.00  232.62
extractRanges       188.59  11.14  202.74
DMRcate-package     185.45  12.76  199.95
cpg.annotate        163.37  15.60  180.97
rmSNPandCH          167.48   9.05  179.10
dmrcate             149.22  11.83  162.49
changeFDR            64.07   6.29  113.59
sequencing.annotate  54.58   4.98   60.12
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/DMRcate.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/DMRcate_2.4.1.tar.gz && rm -rf DMRcate.buildbin-libdir && mkdir DMRcate.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DMRcate.buildbin-libdir DMRcate_2.4.1.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL DMRcate_2.4.1.zip && rm DMRcate_2.4.1.tar.gz DMRcate_2.4.1.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 63827  100 63827    0     0  2482k      0 --:--:-- --:--:-- --:--:-- 2597k

install for i386

* installing *source* package 'DMRcate' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'minfi::getMeth' by 'bsseq::getMeth' when loading 'DMRcate'
** help
*** installing help indices
  converting help for package 'DMRcate'
    finding HTML links ... done
    CpGannotated-class                      html  
    DMR.plot                                html  
    DMRcate-internal                        html  
    DMRcate-package                         html  
    DMResults-class                         html  
    changeFDR                               html  
    cpg.annotate                            html  
    dmrcate                                 html  
    extractRanges                           html  
    rmSNPandCH                              html  
    sequencing.annotate                     html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'minfi::getMeth' by 'bsseq::getMeth' when loading 'DMRcate'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'minfi::getMeth' by 'bsseq::getMeth' when loading 'DMRcate'
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'DMRcate' ...
** testing if installed package can be loaded
Warning: replacing previous import 'minfi::getMeth' by 'bsseq::getMeth' when loading 'DMRcate'
* MD5 sums
packaged installation of 'DMRcate' as DMRcate_2.4.1.zip
* DONE (DMRcate)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'DMRcate' successfully unpacked and MD5 sums checked