BioC 2.13: CHECK report for PANR on moscato1

Package: PANR

Version: 1.8.0

Command: rm -rf PANR.buildbin-libdir && mkdir PANR.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=PANR.buildbin-libdir PANR_1.8.0.tar.gz >PANR-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=PANR.buildbin-libdir --install="check:PANR-install.out" --force-multiarch --no-vignettes --timings PANR_1.8.0.tar.gz && mv PANR.buildbin-libdir/* PANR.Rcheck/ && rmdir PANR.buildbin-libdir

StartedAt: 2014-04-05 05:40:22 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 05:42:26 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 124.8 seconds

RetCode: 0

Status:  OK

CheckDir: PANR.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/PANR.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 'PANR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PANR' version '1.8.0'
* 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 'PANR' 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 ... 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':
  'PANR-Vignette.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [34s] OK
Examples with CPU or elapsed time > 5s
         user system elapsed
fitNULL 31.32    0.1   31.42
** running examples for arch 'x64' ... [39s] OK
Examples with CPU or elapsed time > 5s
          user system elapsed
fitNULL  30.72   0.05   30.76
buildPAN  0.81   0.02    5.69
* 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/PANR.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'PANR' ...
** 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 'PANR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PANR' as PANR_1.8.0.zip
* DONE (PANR)

name	user	system	elapsed
BetaMixture-class	0.02	0.00	0.02
PAN-class	0	0	0
SNR2p	0	0	0
assoScore	0.02	0.00	0.01
buildPAN	0.79	0.03	0.89
cosineSim	0.02	0.00	0.02
data-Bakal2007	0.03	0.00	0.03
exportPAN	0	0	0
fitBM	0	0	0
fitNULL	31.32	0.10	31.42
infer	0.56	0.00	0.56
p2SNR	0	0	0
permNULL	0.01	0.00	0.01
pvclustModule	0	0	0
sigModules	0.00	0.01	0.01
summarize	0.01	0.00	0.02
view	0.22	0.02	0.23
viewLegend	0	0	0
viewNestedModules	0	0	0
viewPAN	0	0	0

name	user	system	elapsed
BetaMixture-class	0	0	0
PAN-class	0	0	0
SNR2p	0	0	0
assoScore	0.02	0.00	0.02
buildPAN	0.81	0.02	5.69
cosineSim	0.02	0.00	0.01
data-Bakal2007	0.01	0.00	0.02
exportPAN	0	0	0
fitBM	0	0	0
fitNULL	30.72	0.05	30.76
infer	0.68	0.00	0.69
p2SNR	0	0	0
permNULL	0.02	0.00	0.01
pvclustModule	0	0	0
sigModules	0	0	0
summarize	0.03	0.00	0.03
view	0.25	0.02	0.27
viewLegend	0	0	0
viewNestedModules	0.02	0.00	0.01
viewPAN	0	0	0