Package: ffpe

Version: 1.30.0

Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ffpe.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings ffpe_1.30.0.tar.gz

StartedAt: 2020-04-15 03:08:34 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 03:15:35 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 421.2 seconds

RetCode: 0

Status:  OK

CheckDir: ffpe.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ffpe.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings ffpe_1.30.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/ffpe.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ffpe/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ffpe' version '1.30.0'
* 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 'ffpe' 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 ... NOTE
CATplot: no visible global function definition for 'abline'
sampleQC,matrix : makeplots: no visible global function definition for
  'cor'
sampleQC,matrix : makeplots: no visible global function definition for
  'median'
sampleQC,matrix : makeplots: no visible binding for global variable
  'median'
sampleQC,matrix : makeplots: no visible global function definition for
  'na.omit'
sampleQC,matrix : makeplots: no visible global function definition for
  'loess'
sampleQC,matrix : makeplots: no visible global function definition for
  'predict'
sampleQC,matrix : makeplots: no visible global function definition for
  'IQR'
sampleQC,matrix : makeplots: no visible global function definition for
  'abline'
sampleQC,matrix : makeplots: no visible global function definition for
  'legend'
sampleQC,matrix : makeplots: no visible global function definition for
  'lines'
sampleQC,matrix: no visible binding for global variable 'IQR'
sampleQC,matrix: no visible global function definition for 'na.omit'
sortedIqrPlot,matrix: no visible binding for global variable 'quantile'
sortedIqrPlot,matrix: no visible global function definition for
  'segments'
sortedIqrPlot,matrix: no visible binding for global variable 'IQR'
Undefined global functions or variables:
  IQR abline cor legend lines loess median na.omit predict quantile
  segments
Consider adding
  importFrom("graphics", "abline", "legend", "lines", "segments")
  importFrom("stats", "IQR", "cor", "loess", "median", "na.omit",
             "predict", "quantile")
to your NAMESPACE file.
* 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 or elapsed time > 5s
             user system elapsed
CATplot      6.70   0.50    8.19
ffpe-package 4.52   0.63    5.14
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
        user system elapsed
CATplot 4.89    0.2     5.1
* 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-3.10-bioc/meat/ffpe.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/ffpe_1.30.0.tar.gz && rm -rf ffpe.buildbin-libdir && mkdir ffpe.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ffpe.buildbin-libdir ffpe_1.30.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL ffpe_1.30.0.zip && rm ffpe_1.30.0.tar.gz ffpe_1.30.0.zip
###
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install for i386

* installing *source* package 'ffpe' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'lumi'
** help
*** installing help indices
  converting help for package 'ffpe'
    finding HTML links ... done
    CATplot                                 html  
    ffpe-package                            html  
    sampleQC                                html  
    sortedIqrPlot                           html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'lumi'
** testing if installed package can be loaded from final location
No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'lumi'
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'ffpe' ...
** testing if installed package can be loaded
No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'lumi'
* MD5 sums
packaged installation of 'ffpe' as ffpe_1.30.0.zip
* DONE (ffpe)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'ffpe' successfully unpacked and MD5 sums checked