Package: flowStats

Version: 1.17.0

Command: rm -rf flowStats.buildbin-libdir && mkdir flowStats.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=flowStats.buildbin-libdir flowStats_1.17.0.tar.gz >flowStats-install.out 2>&1 && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD check --library=flowStats.buildbin-libdir --install="check:flowStats-install.out" --force-multiarch --no-vignettes --timings flowStats_1.17.0.tar.gz && mv flowStats.buildbin-libdir/* flowStats.Rcheck/ && rmdir flowStats.buildbin-libdir

StartedAt: 2013-01-02 01:30:07 -0800 (Wed, 02 Jan 2013)

EndedAt: 2013-01-02 01:37:56 -0800 (Wed, 02 Jan 2013)

EllapsedTime: 469.0 seconds

RetCode: 0

Status:  OK

CheckDir: flowStats.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/flowStats.Rcheck'
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'flowStats/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flowStats' version '1.17.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'ncdfFlow'
* 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 'flowStats' can be installed ... OK
* checking installed package size ... OK
* checking package 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 for unstated 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
%in%,flowFrame-lymphFilter: warning in lymphGate(x, channels =
  parameters(table), preselection = pre, scale = table@scale, bwFac =
  table@bwFac, filterId = table@filterId, eval = TRUE, plot = FALSE):
  partial argument match of 'eval' to 'evaluate'
.plotGPAprocess: no visible binding for global variable 'whichS'
.plotGPAprocess: no visible binding for global variable 'cluster'
.plotWorkFlow: no visible binding for global variable 'cluster'
.plotWorkFlow: no visible binding for global variable 'bogus'
.usingSVD: no visible binding for global variable 'params'
normQA: no visible binding for global variable 'group'
normQA: no visible binding for global variable 'hasPeak'
* checking Rd files ... NOTE
prepare_Rd: normalizeGatingSet.Rd:53-55: Dropping empty section \note
prepare_Rd: normalizeGatingSet.Rd:47-49: Dropping empty section \references
prepare_Rd: normalizeGatingSet.Rd:62-63: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: 'ncdfFlow'
* 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 examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
warpSet      39.50   0.64   40.16
gaussNorm    14.12   0.48   14.60
lymphGate    13.31   0.23   13.54
density1d     7.53   0.41    7.94
quadrantGate  7.52   0.28    7.80
gpaSet        6.99   0.11    7.10
rangeGate     6.26   0.29    6.55
autoGate      5.29   0.07    5.37
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
warpSet      41.02   0.59   41.64
lymphGate    13.96   0.12   14.09
gaussNorm    12.89   0.34   13.23
density1d     9.42   0.30    9.73
quadrantGate  8.07   0.25    8.39
gpaSet        7.88   0.16    8.03
rangeGate     5.85   0.16    6.02
autoGate      5.21   0.08    5.29
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 4 notes.
See
  'E:/biocbld/bbs-2.12-bioc/meat/flowStats.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'flowStats' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'GettingStartedWithFlowStats.Rnw' 
** testing if installed package can be loaded

install for x64

* installing *source* package 'flowStats' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowStats' as flowStats_1.17.0.zip

* DONE (flowStats)