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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:XCIR.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings XCIR_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/XCIR.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'XCIR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'XCIR' version '1.2.0'
* 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 whether package 'XCIR' 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 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' ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
mart_genes   14.32   0.08   21.04
getXCIstate  12.06   0.43   12.52
plotQC       12.40   0.02   12.44
betaBinomXI  11.22   0.16   12.05
addAnno      10.52   0.42   14.76
sample_clean 10.61   0.03   10.59
annotateX     9.14   0.50   12.98
readRNASNPs   9.38   0.09   12.58
getGenicDP    9.20   0.13   13.06
readVCF4      9.19   0.08   12.59
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
getXCIstate  10.17   0.08   10.21
mart_genes   10.02   0.09   15.89
sample_clean  9.42   0.01    9.47
plotQC        9.31   0.02    9.33
betaBinomXI   8.98   0.01    9.00
addAnno       7.93   0.14   11.79
readVCF4      7.30   0.01   10.55
annotateX     7.00   0.13   11.34
readRNASNPs   6.77   0.08   10.90
getGenicDP    6.70   0.08   10.12
* 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: OK

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/XCIR_1.2.0.tar.gz && rm -rf XCIR.buildbin-libdir && mkdir XCIR.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=XCIR.buildbin-libdir XCIR_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL XCIR_1.2.0.zip && rm XCIR_1.2.0.tar.gz XCIR_1.2.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

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100  465k  100  465k    0     0  6130k      0 --:--:-- --:--:-- --:--:-- 6745k

install for i386

* installing *source* package 'XCIR' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'XCIR'
    finding HTML links ... done
    BetaConversion                          html  
    XCIR-package                            html  
    addAnno                                 html  
    annotateX                               html  
    betaBinomXI                             html  
    consensusXCI                            html  
    getGenicDP                              html  
    getXCIstate                             html  
    mart_genes                              html  
    plotBBCellFrac                          html  
    plotQC                                  html  
    readRNASNPs                             html  
    readVCF4                                html  
    readXCI                                 html  
    sample_clean                            html  
** 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

install for x64

* installing *source* package 'XCIR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'XCIR' as XCIR_1.2.0.zip
* DONE (XCIR)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'XCIR' successfully unpacked and MD5 sums checked