BioC 3.0: CHECK report for DMRforPairs on moscato1

Package: DMRforPairs

Version: 1.2.0

Command: rm -rf DMRforPairs.buildbin-libdir DMRforPairs.Rcheck && mkdir DMRforPairs.buildbin-libdir DMRforPairs.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DMRforPairs.buildbin-libdir DMRforPairs_1.2.0.tar.gz >DMRforPairs.Rcheck\00install.out 2>&1 && cp DMRforPairs.Rcheck\00install.out DMRforPairs-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=DMRforPairs.buildbin-libdir --install="check:DMRforPairs-install.out" --force-multiarch --no-vignettes --timings DMRforPairs_1.2.0.tar.gz

StartedAt: 2015-04-10 00:36:00 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 00:44:31 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 510.6 seconds

RetCode: 0

Status:  OK

CheckDir: DMRforPairs.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf DMRforPairs.buildbin-libdir DMRforPairs.Rcheck && mkdir DMRforPairs.buildbin-libdir DMRforPairs.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DMRforPairs.buildbin-libdir DMRforPairs_1.2.0.tar.gz >DMRforPairs.Rcheck\00install.out 2>&1 && cp DMRforPairs.Rcheck\00install.out DMRforPairs-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=DMRforPairs.buildbin-libdir --install="check:DMRforPairs-install.out" --force-multiarch --no-vignettes --timings DMRforPairs_1.2.0.tar.gz
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* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/DMRforPairs.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DMRforPairs/DESCRIPTION' ... OK
* this is package 'DMRforPairs' version '1.2.0'
* 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 'DMRforPairs' 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 ... 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
plot_annotate_probes: no visible global function definition for
  'seqlevels<-'
plot_annotate_probes: no visible global function definition for 'Rle'
plot_annotate_probes: no visible global function definition for
  'IRanges'
* 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' ... [27s] OK
** running examples for arch 'x64' ... [32s] OK
* 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

NOTE: There was 1 note.
See
  'D:/biocbld/bbs-3.0-bioc/meat/DMRforPairs.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'DMRforPairs' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'DMRforPairs' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DMRforPairs' as DMRforPairs_1.2.0.zip
* DONE (DMRforPairs)

name	user	system	elapsed
DMRforPairs	3.29	0.05	3.34
calc_stats	0	0	0
export_data	2.02	0.04	2.61
merge_classes	0	0	0
plot_annotate_custom_region	1.34	0.00	1.34
plot_annotate_gene	1.25	0.00	1.25
plot_annotate_probes	0	0	0
plot_annotate_region	1.28	0.00	1.28
regionfinder	0	0	0
testregion	0.01	0.00	0.02
tune_parameters	1.83	0.00	1.82

name	user	system	elapsed
DMRforPairs	3.35	0.06	3.41
calc_stats	0	0	0
export_data	1.87	0.08	3.82
merge_classes	0	0	0
plot_annotate_custom_region	1.16	0.01	1.17
plot_annotate_gene	1.14	0.03	1.17
plot_annotate_probes	0	0	0
plot_annotate_region	1.06	0.04	1.10
regionfinder	0	0	0
testregion	0	0	0
tune_parameters	1.35	0.00	1.35