Package: les

Version: 1.34.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:les.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings les_1.34.0.tar.gz

StartedAt: 2019-10-16 04:46:39 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 04:48:15 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 96.2 seconds

RetCode: 0

Status:  OK

CheckDir: les.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:les.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings les_1.34.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/les.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'les/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'les' version '1.34.0'
* 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 'les' 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 ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... NOTE
Package in Depends field not imported from: 'fdrtool'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': 'stats:::lm.wfit'
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'calcSingle' 'cdfDuplicates' 'checkState' 'diagSquare' 'fitGsri'
  'gsri' 'itLinReg' 'mcsapply' 'modGrenander' 'qrSlope' 'reg2log'
  'seSlopeWeight' 'setState' 'slopeWeight' 'wcdf2' 'wcdfGrenander'
  'xvalWeight'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
  .C("C_isomean", ..., PACKAGE = "fdrtool")
Call with DUP:
   .C("C_isomean", as.double(rawslope), as.double(dx), as.integer(n), 
       ghat = double(n), PACKAGE = "fdrtool", DUP = FALSE)
DUP is no longer supported and will be ignored.
* checking R code for possible problems ... OK
* 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
les-package 12.86   0.02   12.91
ci          10.34   0.01   10.36
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
les-package 14.59   0.02   14.61
ci          12.25   0.02   12.27
* 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/les.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/les_1.34.0.tar.gz && rm -rf les.buildbin-libdir && mkdir les.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=les.buildbin-libdir les_1.34.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL les_1.34.0.zip && rm les_1.34.0.tar.gz les_1.34.0.zip
###
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install for i386

* installing *source* package 'les' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'les'
    finding HTML links ... done
    Les-class                               html  
    Les                                     html  
    chi2                                    html  
    ci                                      html  
    estimate                                html  
    export                                  html  
    les-internal                            html  
    les-package                             html  
    plot                                    html  
    regions                                 html  
    spikeInData                             html  
    spikeInStat                             html  
    threshold                               html  
    weighting                               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 'les' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'les' as les_1.34.0.zip
* DONE (les)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'les' successfully unpacked and MD5 sums checked