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CHECK report for flowCore on merida2

This page was generated on 2018-10-17 08:47:09 -0400 (Wed, 17 Oct 2018).

Package 502/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowCore 1.46.2
M.Jiang
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/flowCore
Branch: RELEASE_3_7
Last Commit: d99c7f6
Last Changed Date: 2018-09-11 18:20:06 -0400 (Tue, 11 Sep 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: flowCore
Version: 1.46.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:flowCore.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings flowCore_1.46.2.tar.gz
StartedAt: 2018-10-16 21:23:30 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 21:25:27 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 116.9 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: flowCore.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:flowCore.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings flowCore_1.46.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/flowCore.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowCore/DESCRIPTION’ ... OK
* this is package ‘flowCore’ version ‘1.46.2’
* 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 ... WARNING
Found the following significant warnings:
  fcsTextParse.cpp:39:17: warning: comparison of constant 256 with expression of type 'char' is always true [-Wtautological-constant-out-of-range-compare]
  fcsTextParse.cpp:47:13: warning: comparison of constant 256 with expression of type 'char' is always false [-Wtautological-constant-out-of-range-compare]
See ‘/Users/biocbuild/bbs-3.7-bioc/meat/flowCore.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is  9.0Mb
  sub-directories of 1Mb or more:
    R         1.3Mb
    data      5.0Mb
    extdata   1.1Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Versioned 'LinkingTo' value for ‘BH’ is only usable in R >= 3.0.2
* 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 ... OK
* 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: warning in assign(i, x[[i]], env = env):
  partial argument match of 'env' to 'envir'
rbind2,flowSet-flowSet: 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’
plot,workFlow-missing: no visible binding for global variable
  ‘Rgraphviz’
spillover,flowSet: no visible global function definition for
  ‘devAskNewPage’
spillover,flowSet : <anonymous>: no visible global function definition
  for ‘rangeGate’
spillover,flowSet : <anonymous>: no visible global function definition
  for ‘density’
spillover,flowSet : <anonymous>: no visible global function definition
  for ‘abline’
spillover,flowSet : <anonymous> : <anonymous>: no visible global
  function definition for ‘density’
split,flowFrame-factor: no visible binding for global variable ‘i’
summary,workFlow: no visible binding for global variable ‘wf’
Undefined global functions or variables:
  Rgraphviz abline cov.rob density devAskNewPage i rangeGate wf
Consider adding
  importFrom("grDevices", "devAskNewPage")
  importFrom("graphics", "abline")
  importFrom("stats", "density")
to your NAMESPACE file.
* 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 ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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: 1 WARNING, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/flowCore.Rcheck/00check.log’
for details.



Installation output

flowCore.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL flowCore
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘flowCore’ ...
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c FastLogicle.cpp -o FastLogicle.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c Hyperlog.cpp -o Hyperlog.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c Logicle.cpp -o Logicle.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c biexponential.cpp -o biexponential.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c convertRawBytes.cpp -o convertRawBytes.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c fcsTextParse.cpp -o fcsTextParse.o
fcsTextParse.cpp:39:17: warning: comparison of constant 256 with expression of type 'char' is always true [-Wtautological-constant-out-of-range-compare]
                for(; oddChar < 256; oddChar++)
                      ˜˜˜˜˜˜˜ ^ ˜˜˜
fcsTextParse.cpp:47:13: warning: comparison of constant 256 with expression of type 'char' is always false [-Wtautological-constant-out-of-range-compare]
                if(oddChar==256)
                   ˜˜˜˜˜˜˜^ ˜˜˜
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c hyperlogTransform.cpp -o hyperlogTransform.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c inPolygon.cpp -o inPolygon.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c inPolytope.cpp -o inPolytope.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c logicleTransform.cpp -o logicleTransform.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c pairVectorRcppWrap.cpp -o pairVectorRcppWrap.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c sortBytes.cpp -o sortBytes.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c uint2double.cpp -o uint2double.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c zeroin.cpp -o zeroin.o
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o flowCore.so FastLogicle.o Hyperlog.o Logicle.o RcppExports.o biexponential.o convertRawBytes.o fcsTextParse.o hyperlogTransform.o inPolygon.o inPolytope.o logicleTransform.o pairVectorRcppWrap.o sortBytes.o uint2double.o zeroin.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
if [ `uname -s` = 'Darwin' ]; then install_name_tool -change /usr/local/clang4/lib/libc++.1.dylib /usr/lib/libc++.1.dylib flowCore.so; fi
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/flowCore/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘HowTo-flowCore.Rnw’ 
** testing if installed package can be loaded
* DONE (flowCore)

Tests output

flowCore.Rcheck/tests/testthat.Rout


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(flowCore)
> 
> 
> test_check("flowCore")
     orig_channel_name new_channel_name
$P5N            B710-A              FL1
$P9N            V545-A              FL1
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 199 SKIPPED: 0 FAILED: 0
> 
> #devtools::test("˜/rglab/workspace/flowCore")
> #the FCS files are not included in package due to the size , thus only for internal testing
> #test_file("/home/wjiang2/rglab/workspace/flowCore/tests/testthat/IO-testSuite.R")
> 
> proc.time()
   user  system elapsed 
 13.344   1.283  14.686 

Example timings

flowCore.Rcheck/flowCore-Ex.timings

nameusersystemelapsed
EHtrans-class0.0640.0060.073
FCSTransTransform0.6610.0590.724
Subset-methods0.1900.0210.212
actionItem-class0.0020.0010.002
arcsinhTransform0.0630.0070.070
asinht-class0.0300.0050.035
asinhtGml2-class0.0370.0080.045
biexponentialTransform2.8210.1122.941
boundaryFilter-class0.0840.0040.088
characterOrTransformation-class0.0010.0010.001
coerce0.0640.0040.069
compensateActionItem-class0.0020.0010.003
compensateView-class0.0010.0000.002
compensatedParameter-class0.1430.0140.157
compensation-class0.3260.0280.355
dg1polynomial-class0.0310.0030.033
each_col-methods0.0300.0020.032
ellipsoidGate0.0620.0050.067
exponential-class0.0380.0040.044
expressionFilter-class0.1060.0030.108
fcReference-class0.0020.0000.002
filter-methods0.9170.0791.002
filter-on-methods0.1100.0090.120
filterList-class0.0090.0010.011
filterResult-class0.0020.0000.003
filterResultList-class0.0040.0010.004
filterSummary-class0.0020.0000.002
filterSummaryList-class0.0010.0000.002
flowFrame-class2.7970.1562.969
flowSet-class2.3340.1132.462
fsApply0.1120.0110.125
gateActionItem-class0.0020.0000.001
gateView-class0.0020.0000.002
getIndexSort-methods0.0200.0030.023
hyperlog-class1.1150.0091.133
hyperlogtGml2-class0.0270.0010.028
identifier-methods0.0230.0000.023
inverseLogicleTransform0.5990.0470.648
invsplitscale-class0.0230.0030.025
keyword-methods0.5360.0380.574
kmeansFilter0.1730.0030.176
linearTransform0.0280.0020.031
lintGml2-class0.0290.0030.032
lnTransform0.9460.0781.028
logTransform0.0260.0020.028
logarithm-class0.0230.0020.024
logicalFilterResult-class0.0010.0010.001
logicleTransform0.6130.0550.670
logicletGml2-class0.0370.0000.037
logtGml2-class0.0240.0030.026
manyFilterResult-class0.0020.0000.002
markernames0.6110.0640.679
multipleFilterResult-class0.0010.0000.001
norm2Filter-class0.1500.0040.154
normalizeActionItem-class0.0020.0010.002
normalizeView-class0.0020.0000.002
parameters-methods0.0220.0020.024
polygonGate0.0520.0030.056
quadGate0.1410.0110.153
quadratic-class0.0230.0010.024
quadraticTransform0.0270.0020.029
ratio-class0.0260.0020.028
ratiotGml2-class0.0220.0020.023
read.FCS0.0750.0040.080
read.FCSheader0.0060.0010.007
read.flowSet0.0810.0060.087
rectangleGate0.0870.0060.094
sampleFilter-class0.0480.0010.050
scaleTransform0.0320.0020.033
singleParameterTransform-class0.0020.0000.002
sinht-class0.0260.0010.028
split-methods0.7920.0660.862
splitScaleTransform0.9320.0831.017
splitscale-class0.0240.0020.025
squareroot-class0.0230.0020.025
subsettingActionItem-class0.0030.0000.003
subsettingView-class0.0020.0010.003
timeFilter-class1.1500.0791.232
transform-class0.0030.0000.003
transformActionItem-class0.0020.0000.002
transformFilter-class0.0910.0040.096
transformList-class0.5420.0510.594
transformMap-class0.0010.0000.001
transformView-class0.0020.0000.001
truncateTransform0.0310.0020.033
unitytransform-class0.0280.0020.031
view-class0.0030.0010.003
workFlow-class0.0040.0000.004
write.FCS0.0560.0120.069
write.flowSet0.7940.0600.856