Multiple platform build/check report for BioC 3.9 - CHECK report for TSRchitect on malbec2

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:TSRchitect.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings TSRchitect_1.9.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/TSRchitect.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TSRchitect/DESCRIPTION’ ... OK
* this is package ‘TSRchitect’ version ‘1.9.0’
* 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 for sufficient/correct file permissions ... 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
* 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 ... 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 ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
writeTSR-methods   40.906  1.384   0.087
loadTSSobj-methods  8.061  0.372   8.695
processTSS-methods  0.273  0.304  11.820
* 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/TSRchitect.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL TSRchitect
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘TSRchitect’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘TSRchitect.Rmd’ using ‘UTF-8’ 
   ‘TSRchitectUsersGuide.Rmd’ using ‘UTF-8’ 
Warning in res[i] <- withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),  :
  number of items to replace is not a multiple of replacement length
Warning in res[i] <- withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),  :
  number of items to replace is not a multiple of replacement length
Warning in res[i] <- withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),  :
  number of items to replace is not a multiple of replacement length
** 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
* DONE (TSRchitect)

Tests output

Example timings

name	user	system	elapsed
TSRchitectUsersGuide	0.001	0.000	0.001
addAnnotationToTSR-methods	0.283	0.004	0.299
addTagCountsToTSR-methods	0.056	0.000	0.055
cDNAtoBED-methods	0.199	0.039	0.308
createSummarizedExperiment-methods	0.138	0.004	0.142
determineTSR-methods	0.101	0.000	0.102
getBamData-methods	0.105	0.008	0.112
getFileNames-methods	0.076	0.000	0.076
getTSRdata-methods	0.078	0.004	0.083
getTSScountData-methods	0.085	0.004	0.088
getTSStagData-methods	0.101	0.000	0.102
getTitle-methods	0.079	0.000	0.078
importAnnotationExternal-methods	0.411	0.004	0.437
inputToTSS-methods	0.858	0.020	0.879
loadTSSobj-methods	8.061	0.372	8.695
makeGRangesFromTSR-methods	0.519	0.171	0.121
mergeSampleData-methods	0.390	0.032	0.422
processTSS-methods	0.273	0.304	11.820
tssObject	0.001	0.000	0.000
writeTSR-methods	40.906	1.384	0.087

CHECK report for TSRchitect on malbec2

Summary

Command output

Installation output

Tests output

Example timings