Back to Multiple platform build/check report for BioC 3.7 |
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This page was generated on 2018-10-17 08:47:09 -0400 (Wed, 17 Oct 2018).
Package 502/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
flowCore 1.46.2 M.Jiang
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK |
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 |
############################################################################## ############################################################################## ### ### 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 ### ############################################################################## ############################################################################## * 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.
flowCore.Rcheck/00install.out
############################################################################## ############################################################################## ### ### 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)
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
flowCore.Rcheck/flowCore-Ex.timings
name | user | system | elapsed | |
EHtrans-class | 0.064 | 0.006 | 0.073 | |
FCSTransTransform | 0.661 | 0.059 | 0.724 | |
Subset-methods | 0.190 | 0.021 | 0.212 | |
actionItem-class | 0.002 | 0.001 | 0.002 | |
arcsinhTransform | 0.063 | 0.007 | 0.070 | |
asinht-class | 0.030 | 0.005 | 0.035 | |
asinhtGml2-class | 0.037 | 0.008 | 0.045 | |
biexponentialTransform | 2.821 | 0.112 | 2.941 | |
boundaryFilter-class | 0.084 | 0.004 | 0.088 | |
characterOrTransformation-class | 0.001 | 0.001 | 0.001 | |
coerce | 0.064 | 0.004 | 0.069 | |
compensateActionItem-class | 0.002 | 0.001 | 0.003 | |
compensateView-class | 0.001 | 0.000 | 0.002 | |
compensatedParameter-class | 0.143 | 0.014 | 0.157 | |
compensation-class | 0.326 | 0.028 | 0.355 | |
dg1polynomial-class | 0.031 | 0.003 | 0.033 | |
each_col-methods | 0.030 | 0.002 | 0.032 | |
ellipsoidGate | 0.062 | 0.005 | 0.067 | |
exponential-class | 0.038 | 0.004 | 0.044 | |
expressionFilter-class | 0.106 | 0.003 | 0.108 | |
fcReference-class | 0.002 | 0.000 | 0.002 | |
filter-methods | 0.917 | 0.079 | 1.002 | |
filter-on-methods | 0.110 | 0.009 | 0.120 | |
filterList-class | 0.009 | 0.001 | 0.011 | |
filterResult-class | 0.002 | 0.000 | 0.003 | |
filterResultList-class | 0.004 | 0.001 | 0.004 | |
filterSummary-class | 0.002 | 0.000 | 0.002 | |
filterSummaryList-class | 0.001 | 0.000 | 0.002 | |
flowFrame-class | 2.797 | 0.156 | 2.969 | |
flowSet-class | 2.334 | 0.113 | 2.462 | |
fsApply | 0.112 | 0.011 | 0.125 | |
gateActionItem-class | 0.002 | 0.000 | 0.001 | |
gateView-class | 0.002 | 0.000 | 0.002 | |
getIndexSort-methods | 0.020 | 0.003 | 0.023 | |
hyperlog-class | 1.115 | 0.009 | 1.133 | |
hyperlogtGml2-class | 0.027 | 0.001 | 0.028 | |
identifier-methods | 0.023 | 0.000 | 0.023 | |
inverseLogicleTransform | 0.599 | 0.047 | 0.648 | |
invsplitscale-class | 0.023 | 0.003 | 0.025 | |
keyword-methods | 0.536 | 0.038 | 0.574 | |
kmeansFilter | 0.173 | 0.003 | 0.176 | |
linearTransform | 0.028 | 0.002 | 0.031 | |
lintGml2-class | 0.029 | 0.003 | 0.032 | |
lnTransform | 0.946 | 0.078 | 1.028 | |
logTransform | 0.026 | 0.002 | 0.028 | |
logarithm-class | 0.023 | 0.002 | 0.024 | |
logicalFilterResult-class | 0.001 | 0.001 | 0.001 | |
logicleTransform | 0.613 | 0.055 | 0.670 | |
logicletGml2-class | 0.037 | 0.000 | 0.037 | |
logtGml2-class | 0.024 | 0.003 | 0.026 | |
manyFilterResult-class | 0.002 | 0.000 | 0.002 | |
markernames | 0.611 | 0.064 | 0.679 | |
multipleFilterResult-class | 0.001 | 0.000 | 0.001 | |
norm2Filter-class | 0.150 | 0.004 | 0.154 | |
normalizeActionItem-class | 0.002 | 0.001 | 0.002 | |
normalizeView-class | 0.002 | 0.000 | 0.002 | |
parameters-methods | 0.022 | 0.002 | 0.024 | |
polygonGate | 0.052 | 0.003 | 0.056 | |
quadGate | 0.141 | 0.011 | 0.153 | |
quadratic-class | 0.023 | 0.001 | 0.024 | |
quadraticTransform | 0.027 | 0.002 | 0.029 | |
ratio-class | 0.026 | 0.002 | 0.028 | |
ratiotGml2-class | 0.022 | 0.002 | 0.023 | |
read.FCS | 0.075 | 0.004 | 0.080 | |
read.FCSheader | 0.006 | 0.001 | 0.007 | |
read.flowSet | 0.081 | 0.006 | 0.087 | |
rectangleGate | 0.087 | 0.006 | 0.094 | |
sampleFilter-class | 0.048 | 0.001 | 0.050 | |
scaleTransform | 0.032 | 0.002 | 0.033 | |
singleParameterTransform-class | 0.002 | 0.000 | 0.002 | |
sinht-class | 0.026 | 0.001 | 0.028 | |
split-methods | 0.792 | 0.066 | 0.862 | |
splitScaleTransform | 0.932 | 0.083 | 1.017 | |
splitscale-class | 0.024 | 0.002 | 0.025 | |
squareroot-class | 0.023 | 0.002 | 0.025 | |
subsettingActionItem-class | 0.003 | 0.000 | 0.003 | |
subsettingView-class | 0.002 | 0.001 | 0.003 | |
timeFilter-class | 1.150 | 0.079 | 1.232 | |
transform-class | 0.003 | 0.000 | 0.003 | |
transformActionItem-class | 0.002 | 0.000 | 0.002 | |
transformFilter-class | 0.091 | 0.004 | 0.096 | |
transformList-class | 0.542 | 0.051 | 0.594 | |
transformMap-class | 0.001 | 0.000 | 0.001 | |
transformView-class | 0.002 | 0.000 | 0.001 | |
truncateTransform | 0.031 | 0.002 | 0.033 | |
unitytransform-class | 0.028 | 0.002 | 0.031 | |
view-class | 0.003 | 0.001 | 0.003 | |
workFlow-class | 0.004 | 0.000 | 0.004 | |
write.FCS | 0.056 | 0.012 | 0.069 | |
write.flowSet | 0.794 | 0.060 | 0.856 | |