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### Running command:
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###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:XCIR.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings XCIR_1.6.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/XCIR.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘XCIR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘XCIR’ version ‘1.6.0’
* 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 for sufficient/correct file permissions ... 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
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
betaBinomXI  6.548  0.328   6.807
sample_clean 6.335  0.388   6.649
plotQC       5.595  0.236   5.765
getXCIstate  5.510  0.269   5.710
annotateX    3.392  0.355   6.212
addAnno      3.274  0.264   7.323
mart_genes   2.528  0.117  24.074
getGenicDP   2.455  0.116   5.124
readVCF4     2.368  0.181   5.138
readRNASNPs  2.388  0.143   5.242
* 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:
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###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL XCIR
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* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘XCIR’ ...
** using staged installation
** R
** 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 (XCIR)