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BioC 3.5: CHECK report for msgbsR on tokay2

This page was generated on 2017-08-16 13:26:59 -0400 (Wed, 16 Aug 2017).

Package 856/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
msgbsR 1.0.0
Benjamin Mayne
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/msgbsR
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: msgbsR
Version: 1.0.0
Command: rm -rf msgbsR.buildbin-libdir msgbsR.Rcheck && mkdir msgbsR.buildbin-libdir msgbsR.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=msgbsR.buildbin-libdir msgbsR_1.0.0.tar.gz >msgbsR.Rcheck\00install.out 2>&1 && cp msgbsR.Rcheck\00install.out msgbsR-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=msgbsR.buildbin-libdir --install="check:msgbsR-install.out" --force-multiarch --no-vignettes --timings msgbsR_1.0.0.tar.gz
StartedAt: 2017-08-16 01:25:56 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 01:35:21 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 565.8 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: msgbsR.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf msgbsR.buildbin-libdir msgbsR.Rcheck && mkdir msgbsR.buildbin-libdir msgbsR.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=msgbsR.buildbin-libdir msgbsR_1.0.0.tar.gz >msgbsR.Rcheck\00install.out 2>&1 && cp msgbsR.Rcheck\00install.out msgbsR-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=msgbsR.buildbin-libdir --install="check:msgbsR-install.out" --force-multiarch --no-vignettes --timings msgbsR_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/msgbsR.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 'msgbsR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'msgbsR' version '1.0.0'
* 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 'msgbsR' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 16.1Mb
  sub-directories of 1Mb or more:
    extdata  15.2Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* 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 ... NOTE
Namespace in Imports field not imported from: 'utils'
  All declared Imports should be used.
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
               old_size new_size compress
  ratdata.rda     318Kb    125Kb       xz
  ratdata2.rda    287Kb    116Kb       xz
* 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
rawCounts 8.36   0.13    8.49
checkCuts 3.17   0.88   12.08
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
rawCounts 11.01   0.08   11.09
* 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, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/msgbsR.Rcheck/00check.log'
for details.


msgbsR.Rcheck/00install.out:


install for i386

* installing *source* package 'msgbsR' ...
** R
** data
** inst
** preparing package for lazy loading
No methods found in "RSQLite" for requests: dbGetQuery
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "RSQLite" for requests: dbGetQuery

install for x64

* installing *source* package 'msgbsR' ...
** testing if installed package can be loaded
No methods found in "RSQLite" for requests: dbGetQuery
* MD5 sums
packaged installation of 'msgbsR' as msgbsR_1.0.0.zip
* DONE (msgbsR)

msgbsR.Rcheck/examples_i386/msgbsR-Ex.timings:

nameusersystemelapsed
checkCuts 3.17 0.8812.08
diffMeth3.060.063.12
plotCircos2.360.122.48
plotCounts0.720.020.73
rawCounts8.360.138.49

msgbsR.Rcheck/examples_x64/msgbsR-Ex.timings:

nameusersystemelapsed
checkCuts3.690.464.16
diffMeth2.780.002.78
plotCircos2.670.052.71
plotCounts0.750.000.75
rawCounts11.01 0.0811.09