iFlow 2.13.0
Kyongryun Lee
| Snapshot Date: 2013-10-07 17:00:06 -0700 (Mon, 07 Oct 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/iFlow | | Last Changed Rev: 75270 / Revision: 81259 | | Last Changed Date: 2013-04-03 15:06:11 -0700 (Wed, 03 Apr 2013) |
| zin2 | Linux (Ubuntu 12.04.2 LTS) / x86_64 | OK | [ WARNINGS ] | |
* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/iFlow.Rcheck’
* using R Under development (unstable) (2013-10-02 r64018)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘iFlow/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘iFlow’ version ‘2.13.0’
* 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 ... 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 ‘iFlow’ can be installed ... [15s/21s] OK
* checking installed package size ... NOTE
installed size is 6.2Mb
sub-directories of 1Mb or more:
doc 5.9Mb
* 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’ ‘flowStats’ ‘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
Unexported objects imported by ‘:::’ calls:
‘flowCore:::findTimeChannel’ ‘flowCore:::nameIdMapping’
See the note in ?`:::` about the use of this operator.
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
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
cleanupEnv: warning in ls(guiEnv(), all = TRUE): partial argument match
of 'all' to 'all.names'
gpaset.func: warning in normalization(normFun = function(x, parameters,
...) gpaSet(x, parameters, ...), parameters = channels[inds],
arguments = list(bgChannels = channels[bg], register =
"backgating")): partial argument match of 'normFun' to 'normFunction'
normal.menu: warning in normalization(normFun = function(x, parameters,
...) warpSet(x, parameters, ...), parameters = channels[inds],
arguments = list(grouping = NULL)): partial argument match of
'normFun' to 'normFunction'
normal.menu: warning in normalization(normFun = function(x, parameters,
...) gaussNorm(x, parameters, ...), parameters = channels[inds],
arguments = list(grouping = NULL)): partial argument match of
'normFun' to 'normFunction'
ask.dialog: no visible binding for global variable ‘selected.channels’
ask.graphics.details: no visible binding for global variable
‘selected.channels’
ask2.dialog: no visible binding for global variable ‘los’
help.menu: no visible global function definition for ‘openVignette’
manual.menu: no visible global function definition for ‘openVignette’
openGraphics: no visible binding for global variable ‘value.y’
openGraphics: no visible binding for global variable ‘value.x’
* 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 installed files from ‘inst/doc’ ... OK
* checking examples ... [8s/11s] WARNING
Found the following significant warnings:
Warning: ‘method’ is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
* 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
WARNING: There was 1 warning.
NOTE: There were 5 notes.
See
‘/home/biocbuild/bbs-2.14-bioc/meat/iFlow.Rcheck/00check.log’
for details.
* installing *source* package ‘iFlow’ ...
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import by ‘graphics::plot’ when loading ‘compositions’
Xlib: extension "RANDR" missing on display ":25004.0".
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import by ‘graphics::plot’ when loading ‘compositions’
Xlib: extension "RANDR" missing on display ":25004.0".
* DONE (iFlow)