BioC 2.13: CHECK report for plethy on moscato1

Package: plethy

Version: 1.0.0

Command: rm -rf plethy.buildbin-libdir && mkdir plethy.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=plethy.buildbin-libdir plethy_1.0.0.tar.gz >plethy-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=plethy.buildbin-libdir --install="check:plethy-install.out" --force-multiarch --no-vignettes --timings plethy_1.0.0.tar.gz && mv plethy.buildbin-libdir/* plethy.Rcheck/ && rmdir plethy.buildbin-libdir

StartedAt: 2014-04-05 05:52:31 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 05:58:58 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 386.3 seconds

RetCode: 0

Status:  OK

CheckDir: plethy.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/plethy.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 'plethy/DESCRIPTION' ... OK
* this is package 'plethy' 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 'plethy' 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
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'csv.to.table' 'find.break.ranges.integer' 'fix.time' 'multi.grep'
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 installed files from 'inst/doc' ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'plethy.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [21s] OK
Examples with CPU or elapsed time > 5s
          user system elapsed
utilities 7.25   0.08    7.41
** running examples for arch 'x64' ... [29s] OK
Examples with CPU or elapsed time > 5s
          user system elapsed
utilities 8.12   0.08    8.19
parsing   6.46   0.03    6.93
plethy    5.61   0.03    5.66
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
  Running 'runTests.R' [99s]
 [99s] OK
** running tests for arch 'x64'
  Running 'runTests.R' [122s]
 [123s] 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

NOTE: There were 2 notes.
See
  'D:/biocbld/bbs-2.13-bioc/meat/plethy.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'plethy' ...
** 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 'plethy' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'plethy' as plethy_1.0.0.zip
* DONE (plethy)

name	user	system	elapsed
BuxcoDB	1.05	0.03	1.08
add_query_funcs	0.44	0.02	0.47
dbImport	0.56	0.05	0.62
parsing	4.02	0.00	4.07
plethy	3.82	0.04	3.87
utilities	7.25	0.08	7.41

name	user	system	elapsed
BuxcoDB	1.45	0.05	1.75
add_query_funcs	0.61	0.00	0.75
dbImport	0.90	0.00	0.93
parsing	6.46	0.03	6.93
plethy	5.61	0.03	5.66
utilities	8.12	0.08	8.19