Package: mBPCR

Version: 1.37.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:mBPCR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings mBPCR_1.37.0.tar.gz

StartedAt: 2019-04-09 04:00:42 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 04:05:24 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 281.5 seconds

RetCode: 0

Status:  OK

CheckDir: mBPCR.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:mBPCR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings mBPCR_1.37.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/mBPCR.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* 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 '1.37.0'
* 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
* 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 ... 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
plotEstProfile      14.39   0.06   14.47
writeEstProfile      7.00   0.02    7.03
estProfileWithMBPCR  6.26   0.02    6.28
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
plotEstProfile      13.36   0.02   13.40
estProfileWithMBPCR  7.09   0.07    7.17
writeEstProfile      5.78   0.00    5.78
* 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-3.9-bioc/meat/mBPCR.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/mBPCR_1.37.0.tar.gz && rm -rf mBPCR.buildbin-libdir && mkdir mBPCR.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=mBPCR.buildbin-libdir mBPCR_1.37.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL mBPCR_1.37.0.zip && rm mBPCR_1.37.0.tar.gz mBPCR_1.37.0.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  452k  100  452k    0     0  8323k      0 --:--:-- --:--:-- --:--:-- 9232k

install for i386

* installing *source* package 'mBPCR' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare 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 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 'mBPCR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'mBPCR' as mBPCR_1.37.0.zip
* DONE (mBPCR)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'mBPCR' successfully unpacked and MD5 sums checked