flowCore 1.5.7
Nolwenn Le Meur
| Snapshot Date: 2007-12-11 00:09:07 -0800 (Tue, 11 Dec 2007) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowCore | | Last Changed Rev: 29112 / Revision: 29143 | | Last Changed Date: 2007-12-08 23:02:01 -0800 (Sat, 08 Dec 2007) |
| lamb1 | Linux (SUSE 10.1) / x86_64 | OK | WARNINGS | |
| wilson2 | Linux (openSUSE 10.3) / x86_64 | OK | WARNINGS | |
| wellington | Linux (openSUSE 10.3) / i686 | OK | WARNINGS | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | WARNINGS | OK |
| lemming | Windows Server 2003 (32-bit) / x64 | OK | [ WARNINGS ] | OK |
* checking for working latex ... OK
* using log directory 'D:/biocbld/bbs-2.2-bioc/meat/flowCore.Rcheck'
* using R version 2.7.0 Under development (unstable) (2007-12-06 r43609)
* checking for file 'flowCore/DESCRIPTION' ... OK
* this is package 'flowCore' version '1.5.7'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'flowCore' can be installed ... WARNING
Found the following significant warnings:
Warning: argument in method definition changed from (e1) to (x)
See 'D:/biocbld/bbs-2.2-bioc/meat/flowCore.Rcheck/00install.out' for details.
* checking package directory ... OK
* checking for portable file names ... 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 name space can be loaded with stated dependencies ... 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
read.FCS: no visible binding for global variable 'filname'
* checking Rd files ... WARNING
Rd files without 'description':
setOperationFilter-class.Rd
These entries are required in an Rd file.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
curv1Filter curv2Filter
Undocumented S4 classes:
curv1Filter curv2Filter
Undocumented S4 methods:
generic '%in%' and siglist 'flowFrame,curv1Filter'
generic '%in%' and siglist 'flowFrame,curv2Filter'
generic 'sampleNames<-' and siglist 'flowSet,ANY'
generic 'show' and siglist 'curv1Filter'
generic 'show' and siglist 'curv2Filter'
generic 'split' and siglist 'flowSet,list,ANY'
generic 'split' and siglist 'flowSet,factor,ANY'
generic 'split' and siglist 'flowSet,numeric,ANY'
generic 'split' and siglist 'flowSet,character,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking data for non-ASCII characters ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating flowCore-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating flowCore-manual.tex ... OK
* checking flowCore-manual.tex ... OK
WARNING: There were 3 warnings, see
D:/biocbld/bbs-2.2-bioc/meat/flowCore.Rcheck/00check.log
for details
installing R.css in D:/biocbld/bbs-2.2-bioc/meat/flowCore.Rcheck
---------- Making package flowCore ------------
adding build stamp to DESCRIPTION
installing NAMESPACE file and metadata
making DLL ...
making biexponential.d from biexponential.c
making inPolygon.d from inPolygon.c
gcc -std=gnu99 -Id:/biocbld/bbs-2.2-bioc/R/include -O3 -Wall -c biexponential.c -o biexponential.o
gcc -std=gnu99 -Id:/biocbld/bbs-2.2-bioc/R/include -O3 -Wall -c inPolygon.c -o inPolygon.o
windres --preprocessor="gcc -E -xc -DRC_INVOKED" -I d:/biocbld/bbs-2.2-bioc/R/include -i flowCore_res.rc -o flowCore_res.o
gcc -std=gnu99 -shared -s -o flowCore.dll flowCore.def biexponential.o inPolygon.o flowCore_res.o -Ld:/biocbld/bbs-2.2-bioc/R/bin -lR
... DLL made
installing DLL
installing R files
installing inst files
installing data files
preparing package flowCore for lazy loading
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
Loading required package: rrcov
Loading required package: robustbase
Loading required package: feature
Loading required package: KernSmooth
KernSmooth 2.22 installed
Copyright M. P. Wand 1997
Loading required package: misc3d
Loading required package: rgl
Warning: argument in method definition changed from (e1) to (x)
Creating a new generic function for "colnames" in "flowCore"
Creating a new generic function for "colnames<-" in "flowCore"
Creating a new generic function for "nrow" in "flowCore"
Creating a new generic function for "ncol" in "flowCore"
installing man source files
installing indices
not zipping data
installing help
Note: removing empty section \details
Note: removing empty section \details
Note: removing empty section \examples
Note: removing empty section \examples
Note: removing empty section \examples
Note: removing empty section \examples
Note: removing empty section \description
Note: removing empty section \description
>>> Building/Updating help pages for package 'flowCore'
Formats: text html latex example chm
GvHD text html latex chm
KmeansFilter text html latex example chm
Subset-methods text html latex example chm
arcsinhTransform text html latex example chm
biexponentialTransform text html latex example chm
coerce text html latex example chm
compensate text html latex example chm
concreteFilter-class text html latex chm
each_col text html latex example chm
ellipsoidGate text html latex example chm
expressionFilter-class text html latex chm
filter-and-methods text html latex chm
filter-class text html latex chm
filter-in-methods text html latex chm
filter-on-methods text html latex example chm
filter text html latex example chm
filterDetails-methods text html latex chm
filterReference-class text html latex chm
filterResult-class text html latex example chm
filterSet-class text html latex example chm
flowFrame-class text html latex chm
flowSet-class text html latex example chm
flowSet text html latex chm
fsApply text html latex example chm
identifier text html latex example chm
keyword-methods text html latex example chm
linearTransform text html latex example chm
lnTransform text html latex example chm
logTransform text html latex example chm
logicalFilterResult-class text html latex example chm
logicleTransform text html latex example chm
manyFilterResult-class text html latex example chm
multipleFilterResult-class text html latex example chm
norm2Filter-class text html latex example chm
parameterFilter-class text html latex chm
parameters text html latex example chm
print.filterSummary text html latex example chm
quadraticTransform text html latex example chm
randomFilterResult-class text html latex chm
read.FCS text html latex example chm
read.FCSheader text html latex example chm
read.flowSet text html latex example chm
rectangleGate text html latex example chm
sampleFilter-class text html latex example chm
sampleFilter text html latex example chm
scaleTransform text html latex example chm
setOperationFilter-class text html latex chm
spillover-flowSet text html latex chm
splitScaleTransform text html latex example chm
transform-class text html latex example chm
transformFilter-class text html latex example chm
transformList-class text html latex example chm
transformMap-class text html latex example chm
truncateTransform text html latex example chm
Microsoft HTML Help Compiler 4.74.8702
Compiling d:\biocbld\bbs-2.2-bioc\meat\flowCore.Rcheck\00_pkg_src\flowCore\chm\flowCore.chm
Compile time: 0 minutes, 0 seconds
55 Topics
535 Local links
2 Internet links
1 Graphic
Created d:\biocbld\bbs-2.2-bioc\meat\flowCore.Rcheck\00_pkg_src\flowCore\chm\flowCore.chm, 87,235 bytes
Compression decreased file by 185,831 bytes.
adding MD5 sums
* DONE (flowCore)