Multiple platform build/check report for BioC 3.6 - CHECK report for TSRchitect on tokay1

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf TSRchitect.buildbin-libdir TSRchitect.Rcheck && mkdir TSRchitect.buildbin-libdir TSRchitect.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=TSRchitect.buildbin-libdir TSRchitect_1.4.0.tar.gz >TSRchitect.Rcheck\00install.out 2>&1 && cp TSRchitect.Rcheck\00install.out TSRchitect-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=TSRchitect.buildbin-libdir --install="check:TSRchitect-install.out" --force-multiarch --no-vignettes --timings TSRchitect_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/TSRchitect.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 'TSRchitect/DESCRIPTION' ... OK
* this is package 'TSRchitect' version '1.4.0'
* 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 'TSRchitect' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6Dor2M/R.INSTALL3c9067d91219/TSRchitect/man/importAnnotationExternal-methods.Rd:37: missing file link 'import.bed'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6Dor2M/R.INSTALL3c9067d91219/TSRchitect/man/importAnnotationExternal-methods.Rd:38: missing file link 'import.gff'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6Dor2M/R.INSTALL3c9067d91219/TSRchitect/man/importAnnotationExternal-methods.Rd:39: missing file link 'import.gff3'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6Dor2M/R.INSTALL3c9067d91219/TSRchitect/man/importAnnotationHub-methods.Rd:44: missing file link 'AnnotationHub'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/TSRchitect.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  inst/LICENSE
will install at top-level and 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
** 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 ... 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 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
loadTSSobj-methods 9.50   0.41    9.91
processTSS-methods 0.28   0.12   44.46
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
loadTSSobj-methods 13.41   0.11   13.52
processTSS-methods  0.52   0.03   52.39
* 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 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/TSRchitect.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'TSRchitect' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'TSRchitect'
    finding HTML links ... done
    TSRchitectUsersGuide                    html  
    addAnnotationToTSR-methods              html  
    finding level-2 HTML links ... done

    addTagCountsToTSR-methods               html  
    bedToTSS-methods                        html  
    cDNAtoBED-methods                       html  
    createSummarizedExperiment-methods      html  
    detTSR-methods                          html  
    determineTSR-methods                    html  
    getBamData-methods                      html  
    getFileNames-methods                    html  
    getTSRdata-methods                      html  
    getTSScountData-methods                 html  
    getTSStagData-methods                   html  
    getTitle-methods                        html  
    importAnnotationExternal-methods        html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6Dor2M/R.INSTALL3c9067d91219/TSRchitect/man/importAnnotationExternal-methods.Rd:37: missing file link 'import.bed'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6Dor2M/R.INSTALL3c9067d91219/TSRchitect/man/importAnnotationExternal-methods.Rd:38: missing file link 'import.gff'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6Dor2M/R.INSTALL3c9067d91219/TSRchitect/man/importAnnotationExternal-methods.Rd:39: missing file link 'import.gff3'
    importAnnotationHub-methods             html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6Dor2M/R.INSTALL3c9067d91219/TSRchitect/man/importAnnotationHub-methods.Rd:44: missing file link 'AnnotationHub'
    inputToTSS-methods                      html  
    loadTSSobj-methods                      html  
    makeGRangesFromTSR-methods              html  
    mergeSampleData-methods                 html  
    processTSS-methods                      html  
    tsrCluster                              html  
    tssObject                               html  
    writeTSR-methods                        html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'TSRchitect' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TSRchitect' as TSRchitect_1.4.0.zip
* DONE (TSRchitect)
In R CMD INSTALL
In R CMD INSTALL

CHECK report for TSRchitect on tokay1

Summary

Command output

Installation output

Tests output

Example timings