Package: flowCore

Version: 1.26.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch flowCore_1.26.0.tar.gz

StartedAt: 2013-05-01 05:14:05 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 05:18:17 -0700 (Wed, 01 May 2013)

EllapsedTime: 252.4 seconds

RetCode: 0

Status:  OK

CheckDir: flowCore.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/flowCore.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'flowCore/DESCRIPTION' ... OK
* this is package 'flowCore' version '1.26.0'
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'flowCore' can be installed ... [19s/25s] OK
* checking installed package size ... NOTE
  installed size is  8.7Mb
  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 ... 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 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 ... [82s/85s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
biexponentialTransform 13.882  2.131  16.982
lnTransform             4.991  1.267   6.385
flowFrame-class         5.401  0.550   6.194
flowSet-class           5.047  0.602   5.763
* 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

NOTE: There were 2 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/flowCore.Rcheck/00check.log'
for details.

* installing *source* package 'flowCore' ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c FastLogicle.cpp -o FastLogicle.o
FastLogicle.cpp:55:48: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memcpy(p->lookup, logicle.p->lookup, (p->bins + 1) * sizeof (double));
                                              ˜˜˜˜˜˜˜˜^˜˜  ˜
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c Logicle.cpp -o Logicle.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c biexponential.c -o biexponential.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c inPolygon.c -o inPolygon.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c inPolytope.c -o inPolytope.o
inPolytope.c:33:26: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
    sigma[i+nRowA*k]=temp+b[i];
                    ˜˜˜˜˜^˜˜˜˜
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c init.c -o init.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c logicleTransform.cpp -o logicleTransform.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c zeroin.c -o zeroin.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o flowCore.so FastLogicle.o Logicle.o biexponential.o inPolygon.o inPolytope.o init.o logicleTransform.o zeroin.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/flowCore.Rcheck/flowCore/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for 'filter' in package 'flowCore'
Creating a new generic function for 'ls' in package 'flowCore'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (flowCore)

name	user	system	elapsed
EHtrans-class	0.131	0.015	0.157
Subset-methods	1.714	0.077	1.840
actionItem-class	0.007	0.004	0.012
arcsinhTransform	0.108	0.013	0.121
asinht-class	0.075	0.006	0.082
biexponentialTransform	13.882	2.131	16.982
boundaryFilter-class	0.212	0.036	0.264
characterOrTransformation-class	0.003	0.004	0.008
coerce	0.153	0.044	0.242
compensateActionItem-class	0.004	0.005	0.013
compensateView-class	0.003	0.005	0.008
compensatedParameter-class	0.407	0.154	0.599
compensation-class	0.813	0.248	1.079
curv1Filter-class	0.705	0.217	0.943
curv2Filter-class	3.016	0.508	3.564
dg1polynomial-class	0.075	0.019	0.096
each_col-methods	0.080	0.017	0.097
ellipsoidGate	0.175	0.078	0.254
exponential-class	0.069	0.015	0.085
expressionFilter-class	0.207	0.063	0.276
fcReference-class	0.011	0.035	0.048
filter-methods	1.230	0.185	1.431
filter-on-methods	0.267	0.043	0.309
filterList-class	0.018	0.009	0.027
filterResult-class	0.004	0.006	0.010
filterResultList-class	2.304	0.806	3.148
filterSet-class	0.090	0.032	0.125
filterSummary-class	0.279	0.106	0.390
filterSummaryList-class	1.610	0.458	2.093
flowFrame-class	5.401	0.550	6.194
flowSet-class	5.047	0.602	5.763
fsApply	0.387	0.098	0.485
gateActionItem-class	0.004	0.005	0.010
gateView-class	0.004	0.006	0.010
hyperlog-class	2.270	0.045	2.325
identifier-methods	0.064	0.018	0.082
inverseLogicleTransform	0.923	0.171	1.109
invsplitscale-class	0.084	0.029	0.112
keyword-methods	1.389	0.348	1.763
kmeansFilter	0.402	0.079	0.487
linearTransform	0.105	0.030	0.148
lnTransform	4.991	1.267	6.385
logTransform	0.094	0.021	0.117
logarithm-class	0.075	0.031	0.108
logicalFilterResult-class	0.003	0.004	0.008
logicleTransform	1.008	0.172	1.183
manyFilterResult-class	0.004	0.005	0.009
multipleFilterResult-class	0.004	0.007	0.011
norm2Filter-class	0.336	0.070	0.438
normalizeActionItem-class	0.004	0.006	0.009
normalizeView-class	0.008	0.010	0.018
parameters-methods	0.073	0.025	0.100
polygonGate	0.176	0.050	0.229
quadGate	0.469	0.083	0.564
quadratic-class	0.074	0.015	0.087
quadraticTransform	0.098	0.020	0.120
ratio-class	0.072	0.016	0.089
read.FCS	0.127	0.038	0.170
read.FCSheader	0.012	0.011	0.025
read.flowSet	0.288	0.085	0.382
rectangleGate	0.234	0.050	0.283
sampleFilter-class	0.134	0.038	0.173
scaleTransform	0.095	0.021	0.116
singleParameterTransform-class	0.004	0.005	0.009
sinht-class	0.076	0.026	0.102
split-methods	2.242	0.438	2.710
splitScaleTransform	3.561	1.298	4.950
splitscale-class	0.070	0.013	0.085
squareroot-class	0.076	0.017	0.096
subsettingActionItem-class	0.004	0.005	0.009
subsettingView-class	0.004	0.005	0.009
timeFilter-class	2.690	0.364	3.105
transform-class	0.007	0.008	0.014
transformActionItem-class	0.004	0.006	0.010
transformFilter-class	0.240	0.034	0.279
transformList-class	0.905	0.168	1.095
transformMap-class	0.008	0.027	0.036
transformView-class	0.003	0.004	0.008
truncateTransform	0.100	0.033	0.135
unitytransform-class	0.066	0.017	0.085
view-class	0.004	0.006	0.011
workFlow-class	0.007	0.013	0.020
write.FCS	0.228	0.040	0.277
write.flowSet	1.911	0.290	2.227