BioC 3.3: CHECK report for BEAT on windows2.bioconductor.org

Package: BEAT

Version: 1.9.0

Command: rm -rf BEAT.buildbin-libdir BEAT.Rcheck && mkdir BEAT.buildbin-libdir BEAT.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BEAT.buildbin-libdir BEAT_1.9.0.tar.gz >BEAT.Rcheck\00install.out 2>&1 && cp BEAT.Rcheck\00install.out BEAT-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=BEAT.buildbin-libdir --install="check:BEAT-install.out" --force-multiarch --no-vignettes --timings BEAT_1.9.0.tar.gz

StartedAt: 2015-10-27 00:47:38 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 00:54:23 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 405.0 seconds

RetCode: 0

Status:  OK

CheckDir: BEAT.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf BEAT.buildbin-libdir BEAT.Rcheck && mkdir BEAT.buildbin-libdir BEAT.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BEAT.buildbin-libdir BEAT_1.9.0.tar.gz >BEAT.Rcheck\00install.out 2>&1 && cp BEAT.Rcheck\00install.out BEAT-install.out  && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=BEAT.buildbin-libdir --install="check:BEAT-install.out" --force-multiarch --no-vignettes --timings BEAT_1.9.0.tar.gz
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* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/BEAT.Rcheck'
* using R Under development (unstable) (2015-09-22 r69418)
* 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 '1.9.0'
* 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 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 ... 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 ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [113s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
epimutation_calls 52.10   0.25   52.35
generate_results  47.22   0.03   47.25
** running examples for arch 'x64' ... [117s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
epimutation_calls 51.39   0.24   51.63
generate_results  49.91   0.04   49.96
* 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 NOTEs
See
  'c:/biocbld/bbs-3.3-bioc/meat/BEAT.Rcheck/00check.log'
for details.

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_1.9.0.zip
* DONE (BEAT)

name	user	system	elapsed
epimutation_calls	52.10	0.25	52.35
generate_results	47.22	0.03	47.25
makeParams	3.98	0.03	4.01
positions_to_regions	4.25	0.05	4.30

name	user	system	elapsed
epimutation_calls	51.39	0.24	51.63
generate_results	49.91	0.04	49.96
makeParams	4.28	0.00	4.28
positions_to_regions	4.68	0.00	4.69