Package: frma

Version: 1.35.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:frma.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings frma_1.35.0.tar.gz

StartedAt: 2019-04-09 02:49:59 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 02:54:56 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 297.6 seconds

RetCode: 0

Status:  OK

CheckDir: frma.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:frma.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings frma_1.35.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/frma.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 'frma/DESCRIPTION' ... OK
* this is package 'frma' version '1.35.0'
* 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 'frma' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'Biobase'
A package should be listed in only one of these fields.
* 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
GNUSE: no visible binding for global variable 'median'
GNUSE: no visible binding for global variable 'quantile'
GNUSE: no visible global function definition for 'boxplot'
barcode: no visible global function definition for 'pnorm'
batchFit: no visible global function definition for 'median'
coerce<-,frmaExpressionSet-ExpressionSet: no visible global function
  definition for 'slot<-'
coerce<-,frmaExpressionSet-ExpressionSet: no visible global function
  definition for 'slot'
randomeffects<-,frmaExpressionSet: no visible global function
  definition for 'validObject'
residuals<-,frmaExpressionSet: no visible global function definition
  for 'validObject'
se.exprs<-,ExpressionSet: no visible global function definition for
  'validObject'
se.exprs<-,frmaExpressionSet: no visible global function definition for
  'validObject'
weights<-,frmaExpressionSet: no visible global function definition for
  'validObject'
Undefined global functions or variables:
  boxplot median pnorm quantile slot slot<- validObject
Consider adding
  importFrom("graphics", "boxplot")
  importFrom("methods", "slot", "slot<-", "validObject")
  importFrom("stats", "median", "pnorm", "quantile")
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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
         user system elapsed
GNUSE   13.80   1.64   16.65
barcode 11.56   0.22   12.66
frma     9.86   0.11    9.97
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
         user system elapsed
GNUSE   15.57   0.22   15.80
frma     9.87   0.73   10.61
barcode  9.06   0.56    9.62
* 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-3.9-bioc/meat/frma.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/frma_1.35.0.tar.gz && rm -rf frma.buildbin-libdir && mkdir frma.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=frma.buildbin-libdir frma_1.35.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL frma_1.35.0.zip && rm frma_1.35.0.tar.gz frma_1.35.0.zip
###
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install for i386

* installing *source* package 'frma' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'frma'
    finding HTML links ... done
    GNUSE                                   html  
    barcode                                 html  
    frma                                    html  
    frmaExpressionSet-class                 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 'frma' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'frma' as frma_1.35.0.zip
* DONE (frma)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'frma' successfully unpacked and MD5 sums checked