flowStats 3.20.12
Greg Finak and Mike Jiang
| 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/flowStats | | Last Changed Rev: 87318 / Revision: 88450 | | Last Changed Date: 2014-03-11 12:25:51 -0700 (Tue, 11 Mar 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | [ OK ] | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | N O T S U P P O R T E D |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK |
* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/flowStats.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowStats/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowStats’ version ‘3.20.12’
* 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 ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘flowStats’ can be installed ... [15s/15s] 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’ ‘fda’ ‘flowViz’
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
Package in Depends field not imported from: ‘cluster’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
Missing or unexported object: ‘flowWorkspace::getDimensions’
‘:::’ calls which should be ‘::’:
‘flowWorkspace:::flowData’ ‘flowWorkspace:::getNodes’
‘flowWorkspace:::isNcdf’ ‘flowWorkspace:::plotGate’
‘flowWorkspace:::sampleNames’ ‘graph:::nodeData’
‘ncdfFlow:::clone.ncdfFlowSet’ ‘ncdfFlow:::updateIndices’
See the note in ?`:::` about the use of this operator.
Missing object imported by a ‘:::’ call: ‘flowWorkspace:::.isBooleanGate.graphNEL’
Unexported objects imported by ‘:::’ calls:
‘flowCore:::checkClass’ ‘flowCore:::copyFlowSet’
‘flowCore:::findTimeChannel’ ‘flowViz:::plotType’
‘flowWorkspace:::.isBoolGate’
See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘backGating’ ‘curvPeaks’ ‘getPeakRegions’ ‘idFeaturesByBackgating’
‘landmarkMatrixWithoutFilterResult’
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
%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’
density1d_simple: no visible binding for global variable ‘y’
normQA: no visible binding for global variable ‘group’
normQA: no visible binding for global variable ‘hasPeak’
* 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 files in ‘vignettes’ ... OK
* checking examples ... [95s/95s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
warpSet 32.478 0.092 32.710
gaussNorm 11.421 0.036 11.510
lymphGate 10.309 0.040 10.530
density1d 6.649 0.096 6.974
gpaSet 6.024 0.020 6.054
rangeGate 5.432 0.092 5.534
* 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 4 notes.
See
‘/home/biocbuild/bbs-2.13-bioc/meat/flowStats.Rcheck/00check.log’
for details.