flowCore 1.25.10
M.Jiang
| Snapshot Date: 2013-01-15 17:01:14 -0800 (Tue, 15 Jan 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowCore | | Last Changed Rev: 72298 / Revision: 72575 | | Last Changed Date: 2013-01-04 13:18:09 -0800 (Fri, 04 Jan 2013) |
| george2 | Linux (Ubuntu 12.04.1 LTS) / x86_64 | OK | WARNINGS | |
| lamb2 | Linux (openSUSE 11.4) / x86_64 | OK | [ WARNINGS ] | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | WARNINGS | OK |
| petty | Mac OS X Leopard (10.5.8) / i386 | OK | WARNINGS | OK |
* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/flowCore.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowCore/DESCRIPTION’ ... OK
* this is package ‘flowCore’ version ‘1.25.10’
* 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 ‘flowCore’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 8.8Mb
sub-directories of 1Mb or more:
data 5.0Mb
doc 1.2Mb
extdata 1.1Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 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
[[<-,filterSet-character-ANY-formula : harvest: warning in exists(f,
env = x@env): partial argument match of 'env' to 'envir'
coerce,environment-flowSet: warning in ls(env = from): partial argument
match of 'env' to 'envir'
coerce,environment-flowSet : <anonymous>: warning in get(f, env =
from): partial argument match of 'env' to 'envir'
coerce,filterSet-list: warning in ls(env = from@env): partial argument
match of 'env' to 'envir'
identifier,filterReference: warning in exists(object@name, env =
object@env): partial argument match of 'env' to 'envir'
names,filterSet: warning in ls(env = x@env): partial argument match of
'env' to 'envir'
plot,workFlow-missing : <anonymous>: warning in edgeData(..., at =
"actionItem"): partial argument match of 'at' to 'attr'
show,filterReference: warning in exists(object@name, env = object@env):
partial argument match of 'env' to 'envir'
summary,transform: warning in ls(env = e): partial argument match of
'env' to 'envir'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'logicleTransform':
estimateLogicle
Code: function(x, channels, ...)
Docs: function(x, channels)
Argument names in code not in docs:
...
Codoc mismatches from documentation object 'normalization-class':
normalize
Code: function(data, x, ...)
Docs: function(data, x)
Argument names in code not in docs:
...
Codoc mismatches from documentation object 'read.flowSet':
read.flowSet
Code: function(files = NULL, path = ".", pattern = NULL, phenoData,
descriptions, name.keyword, alter.names = FALSE,
transformation = "linearize", which.lines = NULL,
column.pattern = NULL, decades = 0, sep = "\t", as.is
= TRUE, name, ncdf = FALSE, dataset = NULL, min.limit
= NULL, ...)
Docs: function(files = NULL, path = ".", pattern = NULL, phenoData,
descriptions, name.keyword, alter.names = FALSE,
transformation = "linearize", which.lines = NULL,
column.pattern = NULL, decades = 0, sep = "\t", as.is
= TRUE, name, ncdf = FALSE, dataset = NULL, ...)
Argument names in code not in docs:
min.limit
Mismatches in argument names:
Position: 17 Code: min.limit Docs: ...
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
biexponentialTransform 11.805 0.212 12.027
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK
WARNING: There was 1 warning.
NOTE: There were 2 notes.
See
‘/loc/home/biocbuild/bbs-2.12-bioc/meat/flowCore.Rcheck/00check.log’
for details.