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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:XCIR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings XCIR_1.4.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/XCIR.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 'XCIR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'XCIR' version '1.4.0'
* 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   13.11   0.12   32.79
betaBinomXI  11.69   0.09   11.78
getXCIstate  11.25   0.50   11.75
addAnno      10.64   0.70   15.06
sample_clean 10.67   0.17   10.84
plotQC       10.40   0.19   10.60
annotateX     8.79   0.30   12.66
getGenicDP    8.07   0.26   11.89
readRNASNPs   7.85   0.08   12.14
readVCF4      7.87   0.01   11.28
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
betaBinomXI  10.65   0.00   10.66
plotQC       10.30   0.05   10.36
getXCIstate   9.73   0.01    9.75
sample_clean  9.36   0.10    9.45
mart_genes    8.72   0.05   21.28
addAnno       7.14   0.08   10.94
annotateX     5.61   0.09    9.33
readRNASNPs   5.64   0.03    9.55
getGenicDP    5.58   0.06    9.86
readVCF4      5.50   0.06    9.03
* 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 http://172.29.0.3/BBS/3.12/bioc/src/contrib/XCIR_1.4.0.tar.gz && rm -rf XCIR.buildbin-libdir && mkdir XCIR.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=XCIR.buildbin-libdir XCIR_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL XCIR_1.4.0.zip && rm XCIR_1.4.0.tar.gz XCIR_1.4.0.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  466k  100  466k    0     0  19.1M      0 --:--:-- --:--:-- --:--:-- 19.7M

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_1.4.0.zip
* DONE (XCIR)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'XCIR' successfully unpacked and MD5 sums checked