BioC 2.13: CHECK report for jmosaics on moscato1

Package: jmosaics

Version: 1.2.0

Command: rm -rf jmosaics.buildbin-libdir && mkdir jmosaics.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=jmosaics.buildbin-libdir jmosaics_1.2.0.tar.gz >jmosaics-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=jmosaics.buildbin-libdir --install="check:jmosaics-install.out" --force-multiarch --no-vignettes --timings jmosaics_1.2.0.tar.gz && mv jmosaics.buildbin-libdir/* jmosaics.Rcheck/ && rmdir jmosaics.buildbin-libdir

StartedAt: 2014-04-05 04:46:51 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 05:02:52 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 961.6 seconds

RetCode: 0

Status:  OK

CheckDir: jmosaics.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/jmosaics.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 'jmosaics/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'jmosaics' 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 'jmosaics' 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 ... NOTE
Unexported object imported by a ':::' call: 'mosaics:::.margDist_2S'
  See the note in ?`:::` about the use of this operator.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* 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 for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'jmosaics.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [402s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
jmosaicsPattern  195.08   7.64  202.79
jmosaics-package 182.26   9.24  191.51
** running examples for arch 'x64' ... [457s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
jmosaics-package 213.86  11.31  225.22
jmosaicsPattern  213.19   9.31  222.51
* 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 were 2 notes.
See
  'D:/biocbld/bbs-2.13-bioc/meat/jmosaics.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'jmosaics' ...
** 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 'jmosaics' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'jmosaics' as jmosaics_1.2.0.zip
* DONE (jmosaics)

name	user	system	elapsed
jmosaics-package	182.26	9.24	191.51
jmosaicsPattern	195.08	7.64	202.79
jmosaics_example_data	1.14	0.06	1.20
origin_bin	1.19	0.02	1.20
readBinsMultiple	2.23	0.27	2.50

name	user	system	elapsed
jmosaics-package	213.86	11.31	225.22
jmosaicsPattern	213.19	9.31	222.51
jmosaics_example_data	0.95	0.00	0.95
origin_bin	1.04	0.04	1.08
readBinsMultiple	2.97	0.25	3.21