BioC 2.13: CHECK report for SNPchip on moscato1

Package: SNPchip

Version: 2.8.0

Command: rm -rf SNPchip.buildbin-libdir && mkdir SNPchip.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SNPchip.buildbin-libdir SNPchip_2.8.0.tar.gz >SNPchip-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=SNPchip.buildbin-libdir --install="check:SNPchip-install.out" --force-multiarch --no-vignettes --timings SNPchip_2.8.0.tar.gz && mv SNPchip.buildbin-libdir/* SNPchip.Rcheck/ && rmdir SNPchip.buildbin-libdir

StartedAt: 2014-04-05 06:50:57 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 06:55:59 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 302.4 seconds

RetCode: 0

Status:  OK

CheckDir: SNPchip.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/SNPchip.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 'SNPchip/DESCRIPTION' ... OK
* this is package 'SNPchip' version '2.8.0'
* 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 'SNPchip' 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: 'graphics'
  All declared Imports should be used.
':::' call which should be '::': 'lattice:::xyplot'
  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 ... NOTE
dataFrameSummarizedExperiment: no visible binding for global variable
  'j'
* checking Rd files ... NOTE
prepare_Rd: arrangeFigs.Rd:35-36: Dropping empty section \examples
prepare_Rd: dataFrame.Rd:43-44: Dropping empty section \examples
prepare_Rd: latticeFigs.Rd:27-29: Dropping empty section \details
prepare_Rd: latticeFigs.Rd:37-38: Dropping empty section \seealso
prepare_Rd: latticeFigs.Rd:39-40: Dropping empty section \examples
* 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' ... [34s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
xyplotLrrBaf 12.79   0.14   12.95
xyplot       11.27   0.11   11.61
** running examples for arch 'x64' ... [40s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
xyplotLrrBaf 17.36   0.16   17.54
xyplot       12.93   0.08   13.02
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
  Running 'doRUnit.R' [15s]
 [15s] OK
** running tests for arch 'x64'
  Running 'doRUnit.R' [22s]
 [23s] 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 3 notes.
See
  'D:/biocbld/bbs-2.13-bioc/meat/SNPchip.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'SNPchip' ...
** 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 'SNPchip' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SNPchip' as SNPchip_2.8.0.zip
* DONE (SNPchip)

name	user	system	elapsed
centromere	0.38	0.02	0.41
getCytoband	0.05	0.00	0.05
plotIdiogram	1.12	0.15	1.28
xypanel	0	0	0
xyplot	11.27	0.11	11.61
xyplotLrrBaf	12.79	0.14	12.95

name	user	system	elapsed
centromere	0.53	0.00	0.53
getCytoband	0.04	0.02	0.06
plotIdiogram	0.89	0.15	1.04
xypanel	0.22	0.00	0.22
xyplot	12.93	0.08	13.02
xyplotLrrBaf	17.36	0.16	17.54