flowViz 1.33.2
Mike Jiang
| Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowViz | | Last Changed Rev: 102951 / Revision: 107696 | | Last Changed Date: 2015-04-22 11:38:40 -0700 (Wed, 22 Apr 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ OK ] | |  |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings flowViz_1.33.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/flowViz.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowViz/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowViz’ version ‘1.33.2’
* 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 ‘flowViz’ can be installed ... [5s/5s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘flowCore’ ‘lattice’
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 ... NOTE
Unexported objects imported by ':::' calls:
‘flowCore:::findTimeChannel’ ‘flowCore:::prepareSet’
‘lattice:::hist.constructor’ ‘lattice:::updateList’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
flowPlot,flowFrame : .local: warning in log(xd, b = 10): partial
argument match of 'b' to 'base'
flowPlot,flowFrame : .local: warning in log(yd, b = 10): partial
argument match of 'b' to 'base'
.densityplot.flowSet.stack: no visible global function definition for
‘lattice.getOption’
.xyplot.flowSet: no visible global function definition for ‘bwplot’
addMargin: no visible global function definition for ‘panel.segments’
glpoly: no visible global function definition for ‘panel.polygon’
glrect: no visible global function definition for ‘panel.rect’
mbar: no visible global function definition for ‘panel.segments’
panel.densityplot.flowFrame: no visible global function definition for
‘panel.polygon’
panel.densityplot.flowFrame: no visible global function definition for
‘panel.rect’
panel.densityplot.flowset.stack: no visible global function definition
for ‘panel.polygon’
panel.densityplot.flowset.stack: no visible global function definition
for ‘panel.rect’
panel.densityplot.flowset.stack : <anonymous>: no visible global
function definition for ‘panel.polygon’
panel.densityplot.flowset.stack: no visible binding for global variable
‘rl’
panel.xyplot.flowframe: no visible global function definition for
‘lpoints’
panel.xyplot.flowframe.old: no visible global function definition for
‘lpoints’
glpoints,filter-flowFrame-missing : .local: no visible binding for
global variable ‘parms’
glpoints,filter-flowFrame-missing : .local: no visible binding for
global variable ‘strict’
gpoints,quadGate-flowFrame-character : .local: no visible binding for
global variable ‘filterResult’
gpolygon,ellipsoidGate-character : .local: no visible binding for
global variable ‘fd’
parallel,flowFrame-missing : .local: no visible global function
definition for ‘parallelplot’
* checking Rd files ... NOTE
prepare_Rd: glines-methods.Rd:149-151: Dropping empty section ‘Methods’
prepare_Rd: timeLinePlot.Rd:72-74: Dropping empty section ‘Methods’
* 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 ... [60s/61s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
xyplot 10.844 0.036 10.894
densityplot 10.709 0.120 10.853
splom 9.917 0.052 10.010
lattice-methods 9.381 0.060 9.485
ecdfplot 7.503 0.019 7.539
timeLinePlot 5.696 0.028 5.722
* 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
* DONE
Status: 4 NOTEs
See
‘/home/biocbuild/bbs-3.2-bioc/meat/flowViz.Rcheck/00check.log’
for details.
* installing *source* package ‘flowViz’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘histogram’ from package ‘lattice’ in package ‘flowViz’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (flowViz)