Package: mBPCR

Version: 1.32.0

Command: rm -rf mBPCR.buildbin-libdir mBPCR.Rcheck && mkdir mBPCR.buildbin-libdir mBPCR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=mBPCR.buildbin-libdir mBPCR_1.32.0.tar.gz >mBPCR.Rcheck\00install.out 2>&1 && cp mBPCR.Rcheck\00install.out mBPCR-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=mBPCR.buildbin-libdir --install="check:mBPCR-install.out" --force-multiarch --no-vignettes --timings mBPCR_1.32.0.tar.gz

StartedAt: 2018-04-12 01:10:21 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 01:14:55 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 274.0 seconds

RetCode: 0

Status:  OK

CheckDir: mBPCR.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf mBPCR.buildbin-libdir mBPCR.Rcheck && mkdir mBPCR.buildbin-libdir mBPCR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=mBPCR.buildbin-libdir mBPCR_1.32.0.tar.gz >mBPCR.Rcheck\00install.out 2>&1 && cp mBPCR.Rcheck\00install.out mBPCR-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=mBPCR.buildbin-libdir --install="check:mBPCR-install.out" --force-multiarch --no-vignettes --timings mBPCR_1.32.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/mBPCR.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 'mBPCR/DESCRIPTION' ... OK
* this is package 'mBPCR' version '1.32.0'
* 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 'mBPCR' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
estProfileWithMBPCRforOligoSnpSet: no visible global function
  definition for 'new'
estProfileWithMBPCRforOligoSnpSet: no visible global function
  definition for 'integerMatrix'
importCNData: no visible global function definition for 'read.table'
plotEstProfile: no visible global function definition for 'x11'
plotEstProfile: no visible global function definition for 'plot'
plotEstProfile: no visible global function definition for 'title'
plotEstProfile: no visible global function definition for 'legend'
plotEstProfile: no visible global function definition for 'points'
writeEstProfile: no visible global function definition for
  'write.table'
Undefined global functions or variables:
  integerMatrix legend new plot points read.table title write.table x11
Consider adding
  importFrom("grDevices", "x11")
  importFrom("graphics", "legend", "plot", "points", "title")
  importFrom("methods", "new")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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
plotEstProfile      14.33   0.00   14.33
writeEstProfile      7.74   0.00    7.74
estProfileWithMBPCR  6.94   0.09    7.03
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
plotEstProfile      12.94      0   12.94
estProfileWithMBPCR  6.88      0    6.88
writeEstProfile      6.62      0    6.62
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/mBPCR.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'mBPCR' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'mBPCR'
    finding HTML links ... done
    computeMBPCR                            html  
    estGlobParam                            html  
    estProfileWithMBPCR                     html  
    estProfileWithMBPCRforOligoSnpSet       html  
    importCNData                            html  
    jekoChr11Array250Knsp                   html  
    logAdd                                  html  
    mBPCR-internal                          html  
    plotEstProfile                          html  
    rec10k                                  html  
    writeEstProfile                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'mBPCR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'mBPCR' as mBPCR_1.32.0.zip
* DONE (mBPCR)
In R CMD INSTALL
In R CMD INSTALL