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CHECK report for TSRchitect on tokay1

This page was generated on 2019-04-13 11:27:51 -0400 (Sat, 13 Apr 2019).

Package 1596/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TSRchitect 1.8.9
R. Taylor Raborn
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/TSRchitect
Branch: RELEASE_3_8
Last Commit: eea6a50
Last Changed Date: 2018-11-15 19:12:38 -0400 (Thu, 15 Nov 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  NA 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: TSRchitect
Version: 1.8.9
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TSRchitect.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings TSRchitect_1.8.9.tar.gz
StartedAt: 2019-04-13 06:04:15 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 06:09:30 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 314.8 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: TSRchitect.Rcheck
Warnings: 2

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TSRchitect.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings TSRchitect_1.8.9.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/TSRchitect.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.8.9'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ... WARNING
Empty or missing file 'demo/00Index'.
See sections 'The INDEX file' and 'Package subdirectories' in the
'Writing R Extensions' manual.
* checking package subdirectories ... WARNING
Subdirectory 'demo' contains no demos.
* 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 ... 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 7.61   0.54    9.06
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
loadTSSobj-methods 7.89   0.14    8.03
* 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: 2 WARNINGs, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/TSRchitect.Rcheck/00check.log'
for details.



Installation output

TSRchitect.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/TSRchitect_1.8.9.tar.gz && rm -rf TSRchitect.buildbin-libdir && mkdir TSRchitect.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TSRchitect.buildbin-libdir TSRchitect_1.8.9.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL TSRchitect_1.8.9.zip && rm TSRchitect_1.8.9.tar.gz TSRchitect_1.8.9.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 2029k  100 2029k    0     0  14.1M      0 --:--:-- --:--:-- --:--:-- 14.4M

install for i386

* installing *source* package 'TSRchitect' ...
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'TSRchitect'
    finding HTML links ... done
    TSRchitectUsersGuide                    html  
    TSRmshapeIndex                          html  
    TSRshapeIndex                           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  
    importAnnotationHub-methods             html  
    inputToTSS-methods                      html  
    loadTSSobj-methods                      html  
    makeGRangesFromTSR-methods              html  
    mergeSampleData-methods                 html  
    prcTSS                                  html  
    processTSS-methods                      html  
    tagCountTSS                             html  
    tsrCluster                              html  
    tssArrayProperties                      html  
    tssObject                               html  
    writeTSR-methods                        html  
** 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
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
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_1.8.9.zip
* DONE (TSRchitect)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'TSRchitect' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

TSRchitect.Rcheck/examples_i386/TSRchitect-Ex.timings

nameusersystemelapsed
TSRchitectUsersGuide000
addAnnotationToTSR-methods0.200.010.30
addTagCountsToTSR-methods0.060.000.06
cDNAtoBED-methods0.000.000.82
createSummarizedExperiment-methods0.120.000.12
determineTSR-methods0.080.000.08
getBamData-methods0.070.000.06
getFileNames-methods0.030.020.04
getTSRdata-methods0.060.000.07
getTSScountData-methods0.050.000.04
getTSStagData-methods0.080.000.08
getTitle-methods0.060.000.06
importAnnotationExternal-methods0.270.000.71
inputToTSS-methods1.060.041.11
loadTSSobj-methods7.610.549.06
makeGRangesFromTSR-methods0.060.010.08
mergeSampleData-methods0.360.050.40
processTSS-methods0.160.150.32
tssObject000
writeTSR-methods0.060.020.07

TSRchitect.Rcheck/examples_x64/TSRchitect-Ex.timings

nameusersystemelapsed
TSRchitectUsersGuide000
addAnnotationToTSR-methods1.30.01.3
addTagCountsToTSR-methods0.110.000.11
cDNAtoBED-methods0.000.000.38
createSummarizedExperiment-methods0.140.000.14
determineTSR-methods0.110.000.11
getBamData-methods0.110.020.12
getFileNames-methods0.050.000.05
getTSRdata-methods0.060.000.06
getTSScountData-methods0.080.010.10
getTSStagData-methods0.080.020.15
getTitle-methods0.030.030.06
importAnnotationExternal-methods0.260.010.28
inputToTSS-methods0.600.020.61
loadTSSobj-methods7.890.148.03
makeGRangesFromTSR-methods0.060.000.06
mergeSampleData-methods0.230.000.24
processTSS-methods0.300.010.31
tssObject000
writeTSR-methods0.030.020.05