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BioC 3.2: CHECK report for flowCore on zin1

This page was generated on 2015-08-24 10:47:12 -0700 (Mon, 24 Aug 2015).

Package 344/1071HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowCore 1.35.10
M.Jiang
Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowCore
Last Changed Rev: 107618 / Revision: 107696
Last Changed Date: 2015-08-20 09:51:56 -0700 (Thu, 20 Aug 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: flowCore
Version: 1.35.10
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings flowCore_1.35.10.tar.gz
StartedAt: 2015-08-23 23:48:29 -0700 (Sun, 23 Aug 2015)
EndedAt: 2015-08-23 23:51:16 -0700 (Sun, 23 Aug 2015)
EllapsedTime: 167.0 seconds
RetCode: 0
Status:  OK 
CheckDir: flowCore.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings flowCore_1.35.10.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/flowCore.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowCore/DESCRIPTION’ ... OK
* this is package ‘flowCore’ version ‘1.35.10’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... NOTE
Found the following apparent object files/libraries:
  src/boost_regex/c_regex_traits.o src/boost_regex/cpp_regex_traits.o
  src/boost_regex/cregex.o src/boost_regex/fileiter.o
  src/boost_regex/icu.o src/boost_regex/instances.o
  src/boost_regex/posix_api.o src/boost_regex/regex.o
  src/boost_regex/regex_debug.o src/boost_regex/regex_raw_buffer.o
  src/boost_regex/regex_traits_defaults.o
  src/boost_regex/static_mutex.o src/boost_regex/usinstances.o
  src/boost_regex/w32_regex_traits.o src/boost_regex/wc_regex_traits.o
  src/boost_regex/wide_posix_api.o src/boost_regex/winstances.o
Object files/libraries should not be included in a source package.
* 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 ... [69s/70s] OK
* checking installed package size ... NOTE
  installed size is 32.0Mb
  sub-directories of 1Mb or more:
    data      5.0Mb
    doc       1.3Mb
    extdata   1.1Mb
    lib      19.6Mb
    libs      3.5Mb
* 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
* 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
'library' or 'require' call to ‘Rgraphviz’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in 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
rbind2,flowSet-flowSet : .local: warning in assign(i, x[[i]], env =
  env): partial argument match of 'env' to 'envir'
rbind2,flowSet-flowSet : .local: warning in assign(i, y[[i]], env =
  env): partial argument match of 'env' to 'envir'
%in%,flowFrame-norm2Filter: no visible global function definition for
  ‘cov.rob’
spillover,flowSet : .local : <anonymous>: no visible global function
  definition for ‘rangeGate’
split,flowFrame-factor : .local: no visible binding for global variable
  ‘i’
summary,workFlow : .local: no visible binding for global variable ‘wf’
* 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 compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [27s/27s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘run-all.R’ [6s/6s]
 [6s/6s] OK
* 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
* DONE

Status: 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/flowCore.Rcheck/00check.log’
for details.


flowCore.Rcheck/00install.out:

* installing *source* package ‘flowCore’ ...
** libs
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c FastLogicle.cpp -o FastLogicle.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c Hyperlog.cpp -o Hyperlog.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c Logicle.cpp -o Logicle.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c biexponential.c -o biexponential.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c fcsTextParse.cpp -o fcsTextParse.o
fcsTextParse.cpp:44:80: warning: multi-line comment [-Wcomment]
    txt = boost::regex_replace(txt, boost::regex(doubleDelimiter), magicString);//somehow boost::replace_all won't do the job for \\\\
                                                                                ^
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c hyperlogTransform.cpp -o hyperlogTransform.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c inPolygon.c -o inPolygon.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c inPolytope.c -o inPolytope.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c init.c -o init.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c logicleTransform.cpp -o logicleTransform.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c pairVectorRcppWrap.cpp -o pairVectorRcppWrap.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c zeroin.c -o zeroin.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c boost_regex/c_regex_traits.cpp -o boost_regex/c_regex_traits.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c boost_regex/cpp_regex_traits.cpp -o boost_regex/cpp_regex_traits.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c boost_regex/cregex.cpp -o boost_regex/cregex.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c boost_regex/fileiter.cpp -o boost_regex/fileiter.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c boost_regex/icu.cpp -o boost_regex/icu.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c boost_regex/instances.cpp -o boost_regex/instances.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c boost_regex/posix_api.cpp -o boost_regex/posix_api.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c boost_regex/regex.cpp -o boost_regex/regex.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c boost_regex/regex_debug.cpp -o boost_regex/regex_debug.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c boost_regex/regex_raw_buffer.cpp -o boost_regex/regex_raw_buffer.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c boost_regex/regex_traits_defaults.cpp -o boost_regex/regex_traits_defaults.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c boost_regex/static_mutex.cpp -o boost_regex/static_mutex.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c boost_regex/usinstances.cpp -o boost_regex/usinstances.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c boost_regex/w32_regex_traits.cpp -o boost_regex/w32_regex_traits.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c boost_regex/wc_regex_traits.cpp -o boost_regex/wc_regex_traits.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c boost_regex/wide_posix_api.cpp -o boost_regex/wide_posix_api.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c boost_regex/winstances.cpp -o boost_regex/winstances.o
mkdir -p "/home/biocbuild/bbs-3.2-bioc/meat/flowCore.Rcheck/flowCore/lib"
ar rs "/home/biocbuild/bbs-3.2-bioc/meat/flowCore.Rcheck/flowCore/lib/libboost_regex.a" boost_regex/c_regex_traits.o boost_regex/cpp_regex_traits.o boost_regex/cregex.o boost_regex/fileiter.o boost_regex/icu.o boost_regex/instances.o boost_regex/posix_api.o boost_regex/regex.o boost_regex/regex_debug.o boost_regex/regex_raw_buffer.o boost_regex/regex_traits_defaults.o boost_regex/static_mutex.o boost_regex/usinstances.o boost_regex/w32_regex_traits.o boost_regex/wc_regex_traits.o boost_regex/wide_posix_api.o boost_regex/winstances.o
ar: creating /home/biocbuild/bbs-3.2-bioc/meat/flowCore.Rcheck/flowCore/lib/libboost_regex.a
g++ -shared -L/home/biocbuild/bbs-3.2-bioc/R/lib -L/usr/local/lib -o flowCore.so FastLogicle.o Hyperlog.o Logicle.o RcppExports.o biexponential.o fcsTextParse.o hyperlogTransform.o inPolygon.o inPolytope.o init.o logicleTransform.o pairVectorRcppWrap.o zeroin.o /home/biocbuild/bbs-3.2-bioc/meat/flowCore.Rcheck/flowCore/lib/libboost_regex.a -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-bioc/meat/flowCore.Rcheck/flowCore/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (flowCore)

flowCore.Rcheck/flowCore-Ex.timings:

nameusersystemelapsed
EHtrans-class0.0490.0040.052
FCSTransTransform0.9900.0161.007
Subset-methods0.2990.0040.304
actionItem-class0.0010.0030.001
arcsinhTransform0.0350.0010.037
asinht-class0.0320.0000.032
asinhtGml2-class0.0540.0000.055
biexponentialTransform4.4950.0354.540
boundaryFilter-class0.0760.0040.081
characterOrTransformation-class0.0010.0000.001
coerce0.1460.0000.147
compensateActionItem-class0.0010.0000.001
compensateView-class0.0010.0000.001
compensatedParameter-class0.1290.0000.132
compensation-class0.3290.0080.337
dg1polynomial-class0.030.000.03
each_col-methods0.0400.0000.041
ellipsoidGate0.0610.0000.061
exponential-class0.0310.0000.032
expressionFilter-class0.0660.0000.067
fcReference-class0.0020.0000.002
filter-methods0.6800.0080.688
filter-on-methods0.0910.0000.091
filterList-class0.0060.0000.006
filterResult-class0.0000.0000.001
filterResultList-class0.0010.0000.001
filterSummary-class0.0010.0000.001
filterSummaryList-class0.0010.0000.001
flowFrame-class2.8170.0282.864
flowSet-class2.1670.0162.185
fsApply0.1520.0000.152
gateActionItem-class0.0010.0000.001
gateView-class0.0010.0000.001
getIndexSort-methods0.0230.0000.023
hyperlog-class1.8110.0001.812
hyperlogtGml2-class0.0530.0000.054
identifier-methods0.0250.0000.025
inverseLogicleTransform0.6190.0040.623
invsplitscale-class0.0340.0000.034
keyword-methods0.6840.0080.692
kmeansFilter0.1650.0000.165
linearTransform0.0330.0040.037
lintGml2-class0.0530.0000.053
lnTransform1.0930.0081.102
logTransform0.040.000.04
logarithm-class0.030.000.03
logicalFilterResult-class0.0010.0000.001
logicleTransform0.7710.0120.783
logicletGml2-class0.0580.0000.058
logtGml2-class0.0550.0000.055
manyFilterResult-class0.0010.0000.001
multipleFilterResult-class0.0000.0040.001
norm2Filter-class0.1460.0000.148
normalizeActionItem-class0.0010.0000.001
normalizeView-class0.0010.0000.000
parameters-methods0.0240.0040.028
polygonGate0.0640.0000.063
quadGate0.1710.0000.171
quadratic-class0.0260.0000.027
quadraticTransform0.0340.0000.033
ratio-class0.0300.0000.031
ratiotGml2-class0.0520.0000.052
read.FCS0.0590.0000.058
read.FCSheader0.0010.0040.006
read.flowSet0.1030.0000.103
rectangleGate0.0930.0000.093
sampleFilter-class0.0540.0000.055
scaleTransform0.0360.0000.036
singleParameterTransform-class0.0010.0000.001
sinht-class0.030.000.03
split-methods1.2170.0241.259
splitScaleTransform1.1840.0041.193
splitscale-class0.1360.0040.143
squareroot-class0.0310.0000.032
subsettingActionItem-class0.0010.0000.002
subsettingView-class0.0010.0000.001
timeFilter-class1.3710.0001.385
transform-class0.0020.0000.002
transformActionItem-class0.0020.0000.001
transformFilter-class0.120.000.12
transformList-class0.7190.0160.739
transformMap-class0.0000.0000.001
transformView-class0.0010.0000.001
truncateTransform0.0370.0000.036
unitytransform-class0.0270.0000.027
view-class0.0010.0000.002
workFlow-class0.0010.0000.001
write.FCS0.0650.0000.064
write.flowSet0.980.000.98