flowQ 1.13.0
F. Hahne
| Snapshot Date: 2011-05-09 07:20:56 -0700 (Mon, 09 May 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowQ | | Last Changed Rev: 54802 / Revision: 55359 | | Last Changed Date: 2011-04-13 15:36:43 -0700 (Wed, 13 Apr 2011) |
| wilson2 | Linux (openSUSE 11.4) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | OK |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | OK | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | [ OK ] | OK |
* using log directory ‘/Users/biocbuild/bbs-2.9-bioc/meat/flowQ.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-24 r55634)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowQ/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowQ’ version ‘1.13.0’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘flowQ’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 12.1Mb
sub-directories of 1Mb or more:
data 2.1Mb
doc 9.7Mb
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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
evaluateProcess: multiple local function definitions for ‘efun’ with
different formal arguments
normalizeSets : <anonymous>: no visible global function definition for
‘warpSet’
qaProcess.2DStatsPlot: no visible binding for global variable ‘Aliquot’
qaProcess.DensityPlot: no visible binding for global variable ‘Aliquot’
qaProcess.ECDFPlot: no visible binding for global variable ‘Aliquot’
* checking Rd files ... NOTE
prepare_Rd: normalizeSets.Rd:44-51: Dropping empty section \examples
* 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 sizes of PDF files under ‘inst/doc’ ... NOTE
‘qpdf’ made some significant size reductions:
compacted ‘DataQualityAssessment.pdf’ from 8.9Mb to 1.4Mb
consider running tools::compactPDF() on these files
* checking examples ... OK
* checking for unstated dependencies in vignettes ... NOTE
‘library’ or ‘require’ call not declared from: ‘flowStats’
* 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
* installing *source* package ‘flowQ’ ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: flowCore
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation("pkgname")'.
Loading required package: rrcov
Loading required package: robustbase
Loading required package: pcaPP
Loading required package: mvtnorm
Scalable Robust Estimators with High Breakdown Point (version 1.3-00)
Attaching package: ‘flowCore’
The following object(s) are masked from ‘package:stats’:
alias, filter
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
Loading required package: compositions
Loading required package: rgl
Loading required package: tensorA
Attaching package: ‘tensorA’
The following object(s) are masked from ‘package:base’:
norm
Loading required package: energy
Loading required package: boot
Attaching package: ‘boot’
The following object(s) are masked from ‘package:robustbase’:
salinity
The following object(s) are masked from ‘package:lattice’:
melanoma
Loading required package: MASS
Welcome to compositions, a package for compositional data analysis.
Get help with "? compositions"
Version info: to ensure compatibility with R > 2.7.0.
".inv" in function names has globaly been replaced by "Inv"
similarly ".row" and ".col" respectively by "Row" and "Col".
WARNING
Please, take into account that this piece of software does complex
geometric operations in high-dimensional spaces, possibly using
different incompatible geometries. In particular, be advised that
arithmetic operations (+ and *) might have non-conventional meanings.
Double-check that you are doing reasonable things. The mere fact that
the package computes something does not imply that this is reasonable
Attaching package: ‘compositions’
The following object(s) are masked from ‘package:flowCore’:
normalize
The following object(s) are masked from ‘package:stats’:
cor, cov, dist, var
The following object(s) are masked from ‘package:base’:
%*%, scale, scale.default
Loading required package: robCompositions
Loading required package: car
Loading required package: nnet
Loading required package: survival
Loading required package: splines
Attaching package: ‘survival’
The following object(s) are masked from ‘package:boot’:
aml
The following object(s) are masked from ‘package:robustbase’:
heart
Attaching package: ‘car’
The following object(s) are masked from ‘package:boot’:
logit
--------
for references have a look at
citation('robCompositions')
--------
Attaching package: ‘robCompositions’
The following object(s) are masked from ‘package:compositions’:
alr, clr, ilr
Loading required package: KernSmooth
Loading required package: tools
Attaching package: ‘latticeExtra’
The following object(s) are masked from ‘package:flowViz’:
ecdfplot
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
‘DataQualityAssessment.Rnw’
‘Extending-flowQ.Rnw’
** testing if installed package can be loaded
Scalable Robust Estimators with High Breakdown Point (version 1.3-00)
Welcome to compositions, a package for compositional data analysis.
Get help with "? compositions"
Version info: to ensure compatibility with R > 2.7.0.
".inv" in function names has globaly been replaced by "Inv"
similarly ".row" and ".col" respectively by "Row" and "Col".
WARNING
Please, take into account that this piece of software does complex
geometric operations in high-dimensional spaces, possibly using
different incompatible geometries. In particular, be advised that
arithmetic operations (+ and *) might have non-conventional meanings.
Double-check that you are doing reasonable things. The mere fact that
the package computes something does not imply that this is reasonable
--------
for references have a look at
citation('robCompositions')
--------
Using ImageMagic library at /usr/local/lib/ImageMagick-6.3.3
(version 6.3.3)
* DONE (flowQ)