BioC 3.5: CHECK report for TSRchitect on tokay2

Package: TSRchitect

Version: 1.2.0

Command: rm -rf TSRchitect.buildbin-libdir TSRchitect.Rcheck && mkdir TSRchitect.buildbin-libdir TSRchitect.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=TSRchitect.buildbin-libdir TSRchitect_1.2.0.tar.gz >TSRchitect.Rcheck\00install.out 2>&1 && cp TSRchitect.Rcheck\00install.out TSRchitect-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=TSRchitect.buildbin-libdir --install="check:TSRchitect-install.out" --force-multiarch --no-vignettes --timings TSRchitect_1.2.0.tar.gz

StartedAt: 2017-10-18 03:30:45 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 03:38:18 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 453.2 seconds

RetCode: 0

Status:  OK

CheckDir: TSRchitect.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf TSRchitect.buildbin-libdir TSRchitect.Rcheck && mkdir TSRchitect.buildbin-libdir TSRchitect.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=TSRchitect.buildbin-libdir TSRchitect_1.2.0.tar.gz >TSRchitect.Rcheck\00install.out 2>&1 && cp TSRchitect.Rcheck\00install.out TSRchitect-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=TSRchitect.buildbin-libdir --install="check:TSRchitect-install.out" --force-multiarch --no-vignettes --timings TSRchitect_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/TSRchitect.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* 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 '1.2.0'
* 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
loadTSSobj-methods 9.81   0.45   10.27
processTSS-methods 0.29   0.01   38.72
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
loadTSSobj-methods 9.59   0.12    9.73
processTSS-methods 0.29   0.07   48.30
* 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-3.5-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_1.2.0.zip
* DONE (TSRchitect)

name	user	system	elapsed
TSRchitectUsersGuide	0	0	0
addAnnotationToTSR-methods	1.05	0.11	1.15
addTagCountsToTSR-methods	0.07	0.00	0.08
cDNAtoBED-methods	0.02	0.00	0.80
createSummarizedExperiment-methods	0.59	0.01	0.61
determineTSR-methods	0.16	0.00	0.15
getBamData-methods	0.23	0.00	0.24
getFileNames-methods	0.10	0.02	0.11
getTSRdata-methods	0.09	0.00	0.09
getTSScountData-methods	0.06	0.03	0.09
getTSStagData-methods	0.22	0.00	0.22
getTitle-methods	0.08	0.01	0.10
importAnnotationExternal-methods	0.50	0.02	0.51
inputToTSS-methods	1.03	0.00	1.03
loadTSSobj-methods	9.81	0.45	10.27
makeGRangesFromTSR-methods	0.13	0.00	0.12
mergeSampleData-methods	0.52	0.10	0.61
processTSS-methods	0.29	0.01	38.72
tssObject	0	0	0
writeTSR-methods	0.11	0.00	0.11

name	user	system	elapsed
TSRchitectUsersGuide	0	0	0
addAnnotationToTSR-methods	1.23	0.00	1.24
addTagCountsToTSR-methods	0.06	0.00	0.06
cDNAtoBED-methods	0.0	0.0	0.3
createSummarizedExperiment-methods	0.56	0.00	0.56
determineTSR-methods	0.11	0.00	0.11
getBamData-methods	0.16	0.00	0.16
getFileNames-methods	0.05	0.00	0.05
getTSRdata-methods	0.04	0.00	0.04
getTSScountData-methods	0.05	0.00	0.05
getTSStagData-methods	0.12	0.00	0.13
getTitle-methods	0.05	0.00	0.04
importAnnotationExternal-methods	0.3	0.0	0.3
inputToTSS-methods	0.83	0.00	0.83
loadTSSobj-methods	9.59	0.12	9.73
makeGRangesFromTSR-methods	0.08	0.02	0.10
mergeSampleData-methods	0.44	0.01	0.45
processTSS-methods	0.29	0.07	48.30
tssObject	0.02	0.00	0.01
writeTSR-methods	0.14	0.01	0.16