BioC 2.13: CHECK report for flowCore on moscato1

Package: flowCore

Version: 1.28.24

Command: rm -rf flowCore.buildbin-libdir && mkdir flowCore.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=flowCore.buildbin-libdir flowCore_1.28.24.tar.gz >flowCore-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=flowCore.buildbin-libdir --install="check:flowCore-install.out" --force-multiarch --no-vignettes --timings flowCore_1.28.24.tar.gz && mv flowCore.buildbin-libdir/* flowCore.Rcheck/ && rmdir flowCore.buildbin-libdir

StartedAt: 2014-04-05 03:50:20 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 03:55:43 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 323.3 seconds

RetCode: 0

Status:  OK

CheckDir: flowCore.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/flowCore.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'flowCore/DESCRIPTION' ... OK
* this is package 'flowCore' version '1.28.24'
* 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 whether package 'flowCore' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  9.8Mb
  sub-directories of 1Mb or more:
    data      5.0Mb
    doc       1.1Mb
    extdata   1.1Mb
    libs      1.2Mb
* checking package directory ... OK
* checking 'build' 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 dependencies in R code ... NOTE
':::' calls which should be '::':
  'Rgraphviz:::layoutGraph' 'Rgraphviz:::renderGraph'
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'inpolygon'
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* 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 ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'D:/biocbld/bbs-2.13-bioc/meat/flowCore.buildbin-libdir/flowCore/libs/i386/flowCore.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'D:/biocbld/bbs-2.13-bioc/meat/flowCore.buildbin-libdir/flowCore/libs/x64/flowCore.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console.  The detected symbols
are linked into the code but might come from libraries and not actually
be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [64s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
biexponentialTransform 10.93   0.08   11.17
flowFrame-class         5.26   0.13    5.43
flowSet-class           4.89   0.03    5.32
** running examples for arch 'x64' ... [66s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
biexponentialTransform 11.84   0.19   12.06
flowFrame-class         5.97   0.03    8.85
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 4 notes.
See
  'D:/biocbld/bbs-2.13-bioc/meat/flowCore.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'flowCore' ...
** libs
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c FastLogicle.cpp -o FastLogicle.o
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c Hyperlog.cpp -o Hyperlog.o
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c Logicle.cpp -o Logicle.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c biexponential.c -o biexponential.o
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c hyperlogTransform.cpp -o hyperlogTransform.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c inPolygon.c -o inPolygon.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c inPolytope.c -o inPolytope.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c init.c -o init.o
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c logicleTransform.cpp -o logicleTransform.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c zeroin.c -o zeroin.o
g++ -m32 -shared -s -static-libgcc -o flowCore.dll tmp.def FastLogicle.o Hyperlog.o Logicle.o biexponential.o hyperlogTransform.o inPolygon.o inPolytope.o init.o logicleTransform.o zeroin.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-2˜1.13-/R/bin/i386 -lR
installing to D:/biocbld/bbs-2.13-bioc/meat/flowCore.buildbin-libdir/flowCore/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'flowCore' ...
** libs
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c FastLogicle.cpp -o FastLogicle.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c Hyperlog.cpp -o Hyperlog.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c Logicle.cpp -o Logicle.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c biexponential.c -o biexponential.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c hyperlogTransform.cpp -o hyperlogTransform.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c inPolygon.c -o inPolygon.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c inPolytope.c -o inPolytope.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c init.c -o init.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c logicleTransform.cpp -o logicleTransform.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c zeroin.c -o zeroin.o
g++ -m64 -shared -s -static-libgcc -o flowCore.dll tmp.def FastLogicle.o Hyperlog.o Logicle.o biexponential.o hyperlogTransform.o inPolygon.o inPolytope.o init.o logicleTransform.o zeroin.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-2˜1.13-/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.13-bioc/meat/flowCore.buildbin-libdir/flowCore/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowCore' as flowCore_1.28.24.zip
* DONE (flowCore)

name	user	system	elapsed
EHtrans-class	0.20	0.01	0.21
FCSTransTransform	2.09	0.03	2.14
Subset-methods	0.47	0.03	0.50
actionItem-class	0.01	0.00	0.01
arcsinhTransform	0.09	0.00	0.10
asinht-class	0.06	0.00	0.06
asinhtGml2-class	0.06	0.00	0.06
biexponentialTransform	10.93	0.08	11.17
boundaryFilter-class	0.18	0.00	0.18
characterOrTransformation-class	0.02	0.00	0.02
coerce	0.15	0.00	0.15
compensateActionItem-class	0	0	0
compensateView-class	0	0	0
compensatedParameter-class	0.39	0.00	0.39
compensation-class	0.78	0.01	0.79
curv1Filter-class	0.60	0.02	0.63
curv2Filter-class	3.17	0.00	3.18
dg1polynomial-class	0.06	0.00	0.06
each_col-methods	0.10	0.00	0.09
ellipsoidGate	0.14	0.00	0.14
exponential-class	0.07	0.00	0.06
expressionFilter-class	0.15	0.00	0.16
fcReference-class	0	0	0
filter-methods	1.10	0.03	1.14
filter-on-methods	0.14	0.02	0.16
filterList-class	0.02	0.00	0.01
filterResult-class	0	0	0
filterResultList-class	1.57	0.03	1.61
filterSet-class	0.08	0.00	0.07
filterSummary-class	0.28	0.00	0.28
filterSummaryList-class	1.93	0.01	2.06
flowFrame-class	5.26	0.13	5.43
flowSet-class	4.89	0.03	5.32
fsApply	0.38	0.00	0.37
gateActionItem-class	0	0	0
gateView-class	0	0	0
getIndexSort-methods	0.08	0.00	0.08
hyperlog-class	1.87	0.01	1.89
hyperlogtGml2-class	0.06	0.00	0.06
identifier-methods	0.05	0.00	0.04
inverseLogicleTransform	0.78	0.00	0.78
invsplitscale-class	0.05	0.00	0.05
keyword-methods	0.86	0.04	0.89
kmeansFilter	0.23	0.00	0.23
linearTransform	0.06	0.00	0.07
lintGml2-class	0.04	0.00	0.05
lnTransform	3.34	0.06	3.42
logTransform	0.26	0.00	0.27
logarithm-class	0.08	0.00	0.07
logicalFilterResult-class	0	0	0
logicleTransform	1.03	0.01	1.05
logicletGml2-class	0.06	0.00	0.06
logtGml2-class	0.05	0.00	0.04
manyFilterResult-class	0.01	0.00	0.02
multipleFilterResult-class	0	0	0
norm2Filter-class	0.27	0.00	0.52
normalizeActionItem-class	0	0	0
normalizeView-class	0	0	0
parameters-methods	0.05	0.00	0.05
polygonGate	0.12	0.00	0.12
quadGate	0.25	0.02	0.27
quadratic-class	0.03	0.02	0.04
quadraticTransform	0.06	0.00	0.06
ratio-class	0.05	0.00	0.05
ratiotGml2-class	0.05	0.00	0.05
read.FCS	0.07	0.01	0.09
read.FCSheader	0.02	0.00	0.02
read.flowSet	0.2	0.0	0.2
rectangleGate	0.24	0.00	0.23
sampleFilter-class	0.11	0.00	0.11
scaleTransform	0.08	0.00	0.07
singleParameterTransform-class	0.02	0.00	0.02
sinht-class	0.07	0.00	0.08
split-methods	1.73	0.03	1.76
splitScaleTransform	2.95	0.11	3.06
splitscale-class	0.06	0.00	0.07
squareroot-class	0.06	0.02	0.07
subsettingActionItem-class	0.02	0.00	0.02
subsettingView-class	0	0	0
timeFilter-class	2.92	0.07	3.03
transform-class	0.01	0.00	0.01
transformActionItem-class	0	0	0
transformFilter-class	0.17	0.00	0.17
transformList-class	0.91	0.05	1.05
transformMap-class	0	0	0
transformView-class	0	0	0
truncateTransform	0.08	0.02	0.46
unitytransform-class	0.08	0.00	0.08
view-class	0	0	0
workFlow-class	0.02	0.00	0.01
write.FCS	0.21	0.00	0.22
write.flowSet	1.89	0.00	1.98

name	user	system	elapsed
EHtrans-class	0.12	0.00	0.14
FCSTransTransform	2.50	0.01	2.57
Subset-methods	0.42	0.00	0.42
actionItem-class	0.02	0.00	0.02
arcsinhTransform	0.08	0.00	0.07
asinht-class	0.04	0.00	0.05
asinhtGml2-class	0.05	0.00	0.04
biexponentialTransform	11.84	0.19	12.06
boundaryFilter-class	0.2	0.0	0.2
characterOrTransformation-class	0	0	0
coerce	0.12	0.00	0.12
compensateActionItem-class	0.02	0.00	0.02
compensateView-class	0	0	0
compensatedParameter-class	0.25	0.01	0.27
compensation-class	0.58	0.02	0.59
curv1Filter-class	0.65	0.00	0.67
curv2Filter-class	3.54	0.04	3.62
dg1polynomial-class	0.03	0.00	0.03
each_col-methods	0.05	0.00	0.05
ellipsoidGate	0.10	0.00	0.11
exponential-class	0.05	0.00	0.04
expressionFilter-class	0.11	0.00	0.11
fcReference-class	0	0	0
filter-methods	0.87	0.02	0.89
filter-on-methods	0.17	0.00	0.17
filterList-class	0.02	0.00	0.01
filterResult-class	0	0	0
filterResultList-class	1.35	0.01	1.38
filterSet-class	0.08	0.00	0.08
filterSummary-class	0.21	0.00	0.20
filterSummaryList-class	1.62	0.03	1.65
flowFrame-class	5.97	0.03	8.85
flowSet-class	4.01	0.02	4.02
fsApply	0.36	0.01	0.42
gateActionItem-class	0.02	0.00	0.02
gateView-class	0	0	0
getIndexSort-methods	0.06	0.00	0.08
hyperlog-class	2.74	0.00	2.76
hyperlogtGml2-class	0.05	0.00	0.05
identifier-methods	0.03	0.00	0.03
inverseLogicleTransform	0.71	0.02	0.71
invsplitscale-class	0.04	0.00	0.05
keyword-methods	0.98	0.02	1.00
kmeansFilter	0.27	0.00	0.26
linearTransform	0.06	0.00	0.07
lintGml2-class	0.04	0.00	0.05
lnTransform	2.95	0.12	3.07
logTransform	0.11	0.00	0.11
logarithm-class	0.08	0.00	0.10
logicalFilterResult-class	0	0	0
logicleTransform	1.12	0.06	1.21
logicletGml2-class	0.08	0.00	0.08
logtGml2-class	0.06	0.00	0.06
manyFilterResult-class	0.02	0.00	0.01
multipleFilterResult-class	0	0	0
norm2Filter-class	0.23	0.02	0.28
normalizeActionItem-class	0	0	0
normalizeView-class	0	0	0
parameters-methods	0.05	0.00	0.05
polygonGate	0.10	0.00	0.09
quadGate	0.34	0.00	0.34
quadratic-class	0.10	0.00	0.09
quadraticTransform	0.09	0.01	0.11
ratio-class	0.06	0.00	0.08
ratiotGml2-class	0.07	0.00	0.06
read.FCS	0.14	0.02	0.47
read.FCSheader	0.02	0.00	0.01
read.flowSet	0.22	0.00	0.22
rectangleGate	0.17	0.00	0.17
sampleFilter-class	0.08	0.02	0.10
scaleTransform	0.08	0.00	0.08
singleParameterTransform-class	0	0	0
sinht-class	0.06	0.00	0.06
split-methods	1.53	0.04	1.58
splitScaleTransform	2.06	0.06	2.12
splitscale-class	0.05	0.00	0.05
squareroot-class	0.04	0.00	0.04
subsettingActionItem-class	0	0	0
subsettingView-class	0	0	0
timeFilter-class	2.80	0.05	2.95
transform-class	0	0	0
transformActionItem-class	0	0	0
transformFilter-class	0.27	0.00	0.26
transformList-class	0.97	0.08	1.05
transformMap-class	0.02	0.00	0.02
transformView-class	0	0	0
truncateTransform	0.07	0.02	0.09
unitytransform-class	0.08	0.00	0.08
view-class	0	0	0
workFlow-class	0.01	0.00	0.01
write.FCS	0.28	0.00	0.28
write.flowSet	1.63	0.00	1.64