Package: flowCore

Version: 1.17.2

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch flowCore_1.17.2.tar.gz

StartedAt: 2011-03-17 16:12:58 -0700 (Thu, 17 Mar 2011)

EndedAt: 2011-03-17 16:15:47 -0700 (Thu, 17 Mar 2011)

EllapsedTime: 169.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: flowCore.Rcheck

Warnings: 1

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/flowCore.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-03-06 r54683)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'flowCore/DESCRIPTION' ... OK
* this is package 'flowCore' version '1.17.2'
* 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 ... OK
* checking installed package size ... NOTE
  installed size is 17.6Mb
  sub-directories of 1Mb or more:
    data      8.1Mb
    doc       7.2Mb
    extdata   1.1Mb
* 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 ... OK
* 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 ... WARNING
Assignments in \usage in documentation object 'fcReference-class':
  fcReference <- function(ID = paste("genericRef", guid(), sep = "_"), 
      env = new.env(parent = emptyenv())) fcTreeReference <- function(ID = paste("treeRef", 
      guid(), sep = "_"), env = new.env(parent = emptyenv())) fcAliasReference <- function(ID = paste("aliasRef", 
      guid(), sep = "_"), env = new.env(parent = emptyenv())) fcDataReference <- function(ID = paste("dataRef", 
      guid(), sep = "_"), env = new.env(parent = emptyenv())) fcActionReference <- function(ID = paste("actionRef", 
      guid(), sep = "_"), env = new.env(parent = emptyenv())) fcViewReference <- function(ID = paste("viewRef", 
      guid(), sep = "_"), env = new.env(parent = emptyenv())) fcFilterResultReference <- function(ID = paste("fresRef", 
      guid(), sep = "_"), env = new.env(parent = emptyenv())) fcFilterReference <- function(ID = paste("filterRef", 
      guid(), sep = "_"), env = new.env(parent = emptyenv())) fcCompensateReference <- function(ID = paste("compRef", 
      guid(), sep = "_"), env = new.env(parent = emptyenv())) fcNormalizeReference <- function(ID = paste("normRef", 
      guid(), sep = "_"), env = new.env(parent = emptyenv())) fcSubsettingReference <- function(ID = paste("subRef", 
      guid(), sep = "_"), env = new.env(parent = emptyenv())) fcTransformReference <- function(ID = paste("transRef", 
      guid(), sep = "_"), env = new.env(parent = emptyenv())) fcNullReference <- function(...) new("fcNullReference")

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* 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 examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  '/Users/biocbuild/bbs-2.8-bioc/meat/flowCore.Rcheck/00check.log'
for details

* installing *source* package 'flowCore' ...
** libs
*** arch - i386
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c FastLogicle.cpp -o FastLogicle.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c Logicle.cpp -o Logicle.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c biexponential.c -o biexponential.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c inPolygon.c -o inPolygon.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c inPolytope.c -o inPolytope.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c init.c -o init.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c logicleTransform.cpp -o logicleTransform.o
g++ -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o flowCore.so FastLogicle.o Logicle.o biexponential.o inPolygon.o inPolytope.o init.o logicleTransform.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.8-bioc/meat/flowCore.Rcheck/flowCore/libs/i386
** R
** data
** inst
** preparing package for lazy loading

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: robustbase
Loading required package: pcaPP
Loading required package: mvtnorm
Scalable Robust Estimators with High Breakdown Point (version 1.1-00)
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
Scalable Robust Estimators with High Breakdown Point (version 1.1-00)

* DONE (flowCore)

name	user	system	elapsed
EHtrans-class	0.169	0.005	0.173
Subset-methods	1.115	0.017	1.131
actionItem-class	0.001	0.000	0.002
arcsinhTransform	0.135	0.003	0.138
asinht-class	0.051	0.002	0.053
biexponentialTransform	8.805	1.227	10.033
boundaryFilter-class	0.256	0.030	0.286
characterOrTransformation-class	0.001	0.000	0.002
coerce	0.109	0.017	0.126
compensateActionItem-class	0.001	0.000	0.002
compensateView-class	0.001	0.000	0.001
compensatedParameter-class	0.287	0.050	0.337
compensation-class	0.652	0.119	0.771
curv1Filter-class	1.005	0.119	1.124
curv2Filter-class	4.254	0.242	4.496
dg1polynomial-class	0.053	0.006	0.058
each_col-methods	0.065	0.007	0.072
ellipsoidGate	0.127	0.023	0.150
exponential-class	0.052	0.006	0.058
expressionFilter-class	0.131	0.022	0.154
fcReference-class	0.001	0.001	0.001
filter-methods	1.540	0.047	1.586
filter-on-methods	0.237	0.013	0.250
filterList-class	0.013	0.000	0.013
filterResult-class	0.001	0.000	0.002
filterResultList-class	2.256	0.264	2.520
filterSet-class	0.075	0.000	0.076
filterSummary-class	0.642	0.061	0.703
filterSummaryList-class	2.026	0.206	2.232
flowFrame-class	4.872	0.203	5.077
flowSet-class	4.998	0.249	5.267
fsApply	0.315	0.045	0.360
gateActionItem-class	0.001	0.000	0.001
gateView-class	0.001	0.000	0.002
hyperlog-class	2.169	0.003	2.173
identifier-methods	0.045	0.002	0.047
inverseLogicleTransform	1.252	0.044	1.296
invsplitscale-class	0.054	0.003	0.057
keyword-methods	1.257	0.111	1.369
kmeansFilter	0.309	0.023	0.333
linearTransform	0.076	0.013	0.088
lnTransform	3.428	0.648	4.076
logTransform	0.154	0.031	0.184
logarithm-class	0.054	0.006	0.059
logicalFilterResult-class	0.001	0.000	0.001
logicleTransform	1.258	0.042	1.301
manyFilterResult-class	0.001	0.000	0.002
multipleFilterResult-class	0.001	0.000	0.001
norm2Filter-class	0.268	0.019	0.287
normalizeActionItem-class	0.001	0.001	0.001
normalizeView-class	0.004	0.005	0.010
parameters-methods	0.047	0.005	0.052
polygonGate	0.122	0.013	0.135
quadGate	0.351	0.033	0.385
quadratic-class	0.053	0.010	0.063
quadraticTransform	0.072	0.006	0.077
ratio-class	0.050	0.006	0.056
read.FCS	0.088	0.007	0.096
read.FCSheader	0.006	0.002	0.009
read.flowSet	0.196	0.039	0.235
rectangleGate	0.219	0.022	0.242
sampleFilter-class	0.096	0.013	0.109
scaleTransform	0.071	0.009	0.080
singleParameterTransform-class	0.002	0.000	0.001
sinht-class	0.058	0.022	0.081
split-methods	2.069	0.161	2.231
splitScaleTransform	3.199	0.711	3.910
splitscale-class	0.135	0.027	0.162
squareroot-class	0.055	0.006	0.060
subsettingActionItem-class	0.001	0.000	0.001
subsettingView-class	0.001	0.001	0.001
timeFilter-class	3.004	0.103	3.108
transform-class	0.003	0.001	0.003
transformActionItem-class	0.001	0.000	0.001
transformFilter-class	0.208	0.017	0.225
transformList-class	1.118	0.035	1.153
transformMap-class	0.000	0.000	0.002
transformView-class	0.001	0.001	0.001
truncateTransform	0.164	0.029	0.194
unitytransform-class	0.046	0.006	0.051
view-class	0.001	0.000	0.001
workFlow-class	0.001	0.001	0.001
write.FCS	0.082	0.014	0.184
write.flowSet	1.465	0.096	1.561