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BioC 2.13: CHECK report for flowQB on perceval

This page was generated on 2014-04-05 09:52:52 -0700 (Sat, 05 Apr 2014).

Package 260/750HostnameOS / ArchBUILDCHECKBUILD BIN
flowQB 1.4.0
Faysal El Khettabi
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/flowQB
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: flowQB
Version: 1.4.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch flowQB_1.4.0.tar.gz
StartedAt: 2014-04-05 01:17:37 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 01:20:53 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 196.3 seconds
RetCode: 0
Status:  OK 
CheckDir: flowQB.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/flowQB.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowQB/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowQB’ version ‘1.4.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘flowQB’ can be installed ... [9s/9s] OK
* checking installed package size ... NOTE
  installed size is 10.0Mb
  sub-directories of 1Mb or more:
    extdata   9.1Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘MASS’ ‘flowCore’
A package should be listed in only one of these fields.
* 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
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘AdvancedflowQBNIH2.Rnw’, ‘AdvancedflowQBNIH3.Rnw’,
  ‘IntroductoryflowQBNIH.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [104s/106s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
DiscriminantExamination 14.864  0.124  15.335
KmeansMeanSD            14.084  0.166  14.626
MFI2MESF                13.912  0.156  14.356
lrMESF                  13.805  0.150  14.392
flowQB-package          13.761  0.153  14.669
qrWEIGHTEDMESF          13.632  0.127  13.809
qrMESF                  13.380  0.118  13.512
* 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
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/flowQB.Rcheck/00check.log’
for details.

flowQB.Rcheck/00install.out:

* installing *source* package ‘flowQB’ ...
** R
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : error in rgl_init
No methods found in "MASS" for requests: fitdistr
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : error in rgl_init
No methods found in "MASS" for requests: fitdistr
* DONE (flowQB)

flowQB.Rcheck/flowQB-Ex.timings:

nameusersystemelapsed
DiscriminantExamination14.864 0.12415.335
KmeansMeanSD14.084 0.16614.626
KmeansMedianrSD0.0060.0020.008
MFI2MESF13.912 0.15614.356
MultilevelgPS0.0060.0020.007
MultilevelrPS0.0050.0040.010
ReadDD0.4650.0410.523
flowQB-package13.761 0.15314.669
gPS0.0040.0010.016
lrMESF13.805 0.15014.392
qrMESF13.380 0.11813.512
qrWEIGHTEDMESF13.632 0.12713.809
rPS0.0050.0010.007