BioC 2.13: CHECK report for chipenrich on moscato1

Package: chipenrich

Version: 1.0.0

Command: rm -rf chipenrich.buildbin-libdir && mkdir chipenrich.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=chipenrich.buildbin-libdir chipenrich_1.0.0.tar.gz >chipenrich-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=chipenrich.buildbin-libdir --install="check:chipenrich-install.out" --force-multiarch --no-vignettes --timings chipenrich_1.0.0.tar.gz && mv chipenrich.buildbin-libdir/* chipenrich.Rcheck/ && rmdir chipenrich.buildbin-libdir

StartedAt: 2014-04-05 02:55:40 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 03:05:56 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 616.0 seconds

RetCode: 0

Status:  OK

CheckDir: chipenrich.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/chipenrich.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'chipenrich/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'chipenrich' 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 'chipenrich' 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
* 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 ... NOTE
chipenrich: no visible binding for global variable 'P.value'
load_peaks: no visible binding for global variable 'chrom'
read_bed: no visible binding for global variable 'chrom'
read_peaks: no visible binding for global variable 'chrom'
setup_ldef: no visible binding for global variable 'chrom'
test_binomial: no visible binding for global variable 'geneid'
test_fisher_exact: no visible binding for global variable 'geneid'
test_gam: no visible binding for global variable 'geneid'
* 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' ... [202s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
chipenrich          85.55   0.01   85.64
plot_expected_peaks 53.60   0.07   53.87
plot_spline_length  52.38   0.07   52.55
** running examples for arch 'x64' ... [211s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
chipenrich          90.22   0.05   90.30
plot_spline_length  56.10   0.10   56.21
plot_expected_peaks 53.07   0.03   53.12
* 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

NOTE: There was 1 note.
See
  'D:/biocbld/bbs-2.13-bioc/meat/chipenrich.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'chipenrich' ...
** R
** 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 'chipenrich' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'chipenrich' as chipenrich_1.0.0.zip
* DONE (chipenrich)

name	user	system	elapsed
chipenrich	85.55	0.01	85.64
plot_dist_to_tss	3.13	0.00	3.15
plot_expected_peaks	53.60	0.07	53.87
plot_spline_length	52.38	0.07	52.55
supported_genesets	0.01	0.00	0.03
supported_genomes	0.02	0.00	0.01
supported_locusdefs	0.01	0.00	0.02
supported_methods	0	0	0
supported_read_lengths	0	0	0

name	user	system	elapsed
chipenrich	90.22	0.05	90.30
plot_dist_to_tss	2.91	0.04	2.97
plot_expected_peaks	53.07	0.03	53.12
plot_spline_length	56.10	0.10	56.21
supported_genesets	0.01	0.00	0.01
supported_genomes	0.02	0.00	0.02
supported_locusdefs	0.02	0.00	0.02
supported_methods	0	0	0
supported_read_lengths	0.02	0.00	0.02