BioC 3.6: CHECK report for TSRchitect on tokay1

Package: TSRchitect

Version: 1.1.0

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_1.1.0.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_1.1.0.tar.gz

StartedAt: 2017-08-16 02:57:58 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 03:04:20 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 382.4 seconds

RetCode: 0

Status:  OK

CheckDir: TSRchitect.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### 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_1.1.0.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_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/TSRchitect.Rcheck'
* using R version 3.4.1 (2017-06-30)
* 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 '1.1.0'
* 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 ... 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
  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
processTSS-methods 0.22   0.05   38.19
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
processTSS-methods 0.34   0.03   47.85
* 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-3.6-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
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'TSRchitect' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TSRchitect' as TSRchitect_1.1.0.zip
* DONE (TSRchitect)

name	user	system	elapsed
TSRchitectUsersGuide	0	0	0
addAnnotationToTSR-methods	0.96	0.08	1.03
addTagCountsToTSR-methods	0.06	0.00	0.06
bamToTSS-methods	0.91	0.00	0.91
createSummarizedExperiment-methods	0.08	0.00	0.08
determineTSR-methods	0.06	0.00	0.06
getBamData-methods	0.14	0.00	0.14
getFileNames-methods	0.05	0.00	0.05
getTSRdata-methods	0.06	0.00	0.06
getTSScountData-methods	0.05	0.01	0.07
getTSStagData-methods	0.09	0.00	0.09
getTitle-methods	0.05	0.00	0.05
importAnnotationExternal-methods	0.23	0.02	0.25
loadTSSobj-methods	0.42	0.01	0.43
makeGRangesFromTSR-methods	0.07	0.00	0.07
mergeSampleData-methods	0.25	0.00	0.25
processTSS-methods	0.22	0.05	38.19
tssObject	0	0	0
writeTSR-methods	0.06	0.00	0.06

name	user	system	elapsed
TSRchitectUsersGuide	0.01	0.00	0.02
addAnnotationToTSR-methods	2.06	0.06	2.12
addTagCountsToTSR-methods	0.08	0.00	0.08
bamToTSS-methods	1.65	0.00	1.65
createSummarizedExperiment-methods	0.13	0.02	0.14
determineTSR-methods	0.11	0.00	0.11
getBamData-methods	0.20	0.00	0.21
getFileNames-methods	0.08	0.00	0.08
getTSRdata-methods	0.07	0.00	0.08
getTSScountData-methods	0.10	0.00	0.09
getTSStagData-methods	0.17	0.00	0.17
getTitle-methods	0.09	0.00	0.10
importAnnotationExternal-methods	0.47	0.00	0.47
loadTSSobj-methods	0.83	0.01	0.84
makeGRangesFromTSR-methods	0.12	0.00	0.13
mergeSampleData-methods	0.57	0.02	0.57
processTSS-methods	0.34	0.03	47.85
tssObject	0	0	0
writeTSR-methods	0.06	0.00	0.06