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BioC 3.5: CHECK report for BEAT on tokay2

This page was generated on 2017-10-18 14:23:09 -0400 (Wed, 18 Oct 2017).

Package 99/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BEAT 1.14.0
Kemal Akman
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/BEAT
Branch: RELEASE_3_5
Last Commit: 586c216
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BEAT
Version: 1.14.0
Command: rm -rf BEAT.buildbin-libdir BEAT.Rcheck && mkdir BEAT.buildbin-libdir BEAT.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BEAT.buildbin-libdir BEAT_1.14.0.tar.gz >BEAT.Rcheck\00install.out 2>&1 && cp BEAT.Rcheck\00install.out BEAT-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=BEAT.buildbin-libdir --install="check:BEAT-install.out" --force-multiarch --no-vignettes --timings BEAT_1.14.0.tar.gz
StartedAt: 2017-10-17 22:13:44 -0400 (Tue, 17 Oct 2017)
EndedAt: 2017-10-17 22:21:39 -0400 (Tue, 17 Oct 2017)
EllapsedTime: 474.6 seconds
RetCode: 0
Status:  OK  
CheckDir: BEAT.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf BEAT.buildbin-libdir BEAT.Rcheck && mkdir BEAT.buildbin-libdir BEAT.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BEAT.buildbin-libdir BEAT_1.14.0.tar.gz >BEAT.Rcheck\00install.out 2>&1 && cp BEAT.Rcheck\00install.out BEAT-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=BEAT.buildbin-libdir --install="check:BEAT-install.out" --force-multiarch --no-vignettes --timings BEAT_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/BEAT.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 'BEAT/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BEAT' version '1.14.0'
* 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 'BEAT' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 11.8Mb
  sub-directories of 1Mb or more:
    extdata  10.4Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
koeff: no visible global function definition for 'dbinom'
positionsReadCSV: no visible global function definition for 'read.csv'
printEpimutStats: no visible global function definition for 'median'
priorr: no visible global function definition for 'dbeta'
Undefined global functions or variables:
  dbeta dbinom median read.csv
Consider adding
  importFrom("stats", "dbeta", "dbinom", "median")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
* 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 ... 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
epimutation_calls 43.49   0.53   44.01
generate_results  41.66   0.05   41.70
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
epimutation_calls 42.28   0.23   42.51
generate_results  41.29   0.05   41.36
* 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/BEAT.Rcheck/00check.log'
for details.


BEAT.Rcheck/00install.out:


install for i386

* installing *source* package 'BEAT' ...
** R
** data
** 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 'BEAT' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BEAT' as BEAT_1.14.0.zip
* DONE (BEAT)

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

nameusersystemelapsed
epimutation_calls43.49 0.5344.01
generate_results41.66 0.0541.70
makeParams4.650.034.68
positions_to_regions4.630.094.72

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

nameusersystemelapsed
epimutation_calls42.28 0.2342.51
generate_results41.29 0.0541.36
makeParams3.980.064.04
positions_to_regions3.740.033.77