Package: COHCAP

Version: 1.24.0

Command: rm -rf COHCAP.buildbin-libdir COHCAP.Rcheck && mkdir COHCAP.buildbin-libdir COHCAP.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=COHCAP.buildbin-libdir COHCAP_1.24.0.tar.gz >COHCAP.Rcheck\00install.out 2>&1 && cp COHCAP.Rcheck\00install.out COHCAP-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=COHCAP.buildbin-libdir --install="check:COHCAP-install.out" --force-multiarch --no-vignettes --timings COHCAP_1.24.0.tar.gz

StartedAt: 2018-04-11 23:07:00 -0400 (Wed, 11 Apr 2018)

EndedAt: 2018-04-11 23:08:49 -0400 (Wed, 11 Apr 2018)

EllapsedTime: 109.2 seconds

RetCode: 0

Status:  OK

CheckDir: COHCAP.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf COHCAP.buildbin-libdir COHCAP.Rcheck && mkdir COHCAP.buildbin-libdir COHCAP.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=COHCAP.buildbin-libdir COHCAP_1.24.0.tar.gz >COHCAP.Rcheck\00install.out 2>&1 && cp COHCAP.Rcheck\00install.out COHCAP-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=COHCAP.buildbin-libdir --install="check:COHCAP-install.out" --force-multiarch --no-vignettes --timings COHCAP_1.24.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/COHCAP.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'COHCAP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'COHCAP' version '1.24.0'
* 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 'COHCAP' 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 ... NOTE
COHCAP.annotate: no visible binding for global variable
  'COHCAP.450k.UCSC'
COHCAP.annotate: no visible binding for global variable
  'COHCAP.450k.HMM'
COHCAP.annotate: no visible binding for global variable 'COHCAP.27k'
COHCAP.avg.by.site: no visible binding for global variable 'ref'
COHCAP.integrate.avg.by.island: no visible binding for global variable
  'na.rm'
cor.test.est: no visible binding for global variable 'na.rm'
cor.test.pvalue: no visible binding for global variable 'na.rm'
Undefined global functions or variables:
  COHCAP.27k COHCAP.450k.HMM COHCAP.450k.UCSC na.rm ref
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
COHCAP.avg.by.island           3.50   0.08    6.29
COHCAP.integrate.avg.by.island 2.11   0.08    6.62
COHCAP.integrate.avg.by.site   1.87   0.08    5.77
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
COHCAP.avg.by.island           3.23   0.06    6.22
COHCAP.integrate.avg.by.island 2.58   0.12    6.75
COHCAP.avg.by.site             2.38   0.05    9.79
COHCAP.integrate.avg.by.site   2.11   0.08    5.59
* 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 NOTE
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/COHCAP.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'COHCAP' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'COHCAP'
    finding HTML links ... done
    COHCAP.BSSeq.preprocess                 html  
    COHCAP.annotate                         html  
    COHCAP.avg.by.island                    html  
    COHCAP.avg.by.site                      html  
    COHCAP.denovo                           html  
    COHCAP.integrate.avg.by.island          html  
    COHCAP.integrate.avg.by.site            html  
    COHCAP.qc                               html  
    COHCAP.reformatFinalReport              html  
    COHCAP.site                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'COHCAP' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'COHCAP' as COHCAP_1.24.0.zip
* DONE (COHCAP)
In R CMD INSTALL
In R CMD INSTALL