Mike Jiang
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/flowCore |
| Branch: RELEASE_3_9 |
| Last Commit: c8610b3 |
| Last Changed Date: 2019-05-02 11:53:07 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:46:15 -0400 (Wed, 16 Oct 2019).
| Package 563/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| flowCore 1.50.0 Mike Jiang
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: flowCore |
| Version: 1.50.0 |
| 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_1.50.0.tar.gz |
| StartedAt: 2019-10-16 02:50:49 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 02:54:09 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 199.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: flowCore.Rcheck |
| Warnings: 0 |
##############################################################################
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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_1.50.0.tar.gz
###
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##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/flowCore.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.50.0’
* package encoding: UTF-8
* 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 ... OK
* checking installed package size ... NOTE
installed size is 8.6Mb
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 ... 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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
Examples with CPU or elapsed time > 5s
user system elapsed
flowFrame-class 5.315 0.467 5.793
filterResultList-class 5.258 0.513 5.784
* 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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.9-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/3.6/Resources/library’ * installing *source* package ‘flowCore’ ... ** using staged installation ** libs clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c fcsTextParse.cpp -o fcsTextParse.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c poly_centroid.cpp -o poly_centroid.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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 poly_centroid.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/3.6/Resources/library/00LOCK-flowCore/00new/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’ using ‘UTF-8’ ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (flowCore)
flowCore.Rcheck/tests/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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")
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following object is masked from 'package:flowCore':
normalize
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
orig_channel_name new_channel_name
$P5N B710-A FL1
$P9N V545-A FL1
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 316 | SKIPPED: 0 | WARNINGS: 2 | 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
19.740 3.251 22.998
flowCore.Rcheck/flowCore-Ex.timings
| name | user | system | elapsed | |
| EHtrans-class | 0.091 | 0.019 | 0.112 | |
| FCSTransTransform | 0.938 | 0.149 | 1.087 | |
| Subset-methods | 0.491 | 0.047 | 0.540 | |
| actionItem-class | 0.003 | 0.001 | 0.004 | |
| arcsinhTransform | 0.089 | 0.015 | 0.103 | |
| asinht-class | 0.045 | 0.010 | 0.054 | |
| asinhtGml2-class | 0.046 | 0.015 | 0.060 | |
| biexponentialTransform | 3.741 | 0.252 | 3.994 | |
| boundaryFilter-class | 0.107 | 0.017 | 0.123 | |
| characterOrNumeric-class | 0.001 | 0.001 | 0.002 | |
| characterOrParameters-class | 0.001 | 0.001 | 0.002 | |
| characterOrTransformation-class | 0.003 | 0.001 | 0.003 | |
| coerce | 0.080 | 0.011 | 0.091 | |
| collapse_desc | 0.825 | 0.134 | 0.959 | |
| compensateActionItem-class | 0.002 | 0.000 | 0.002 | |
| compensateView-class | 0.001 | 0.000 | 0.002 | |
| compensatedParameter-class | 0.181 | 0.020 | 0.203 | |
| compensation-class | 0.441 | 0.087 | 0.527 | |
| decompensate-methods | 0.061 | 0.020 | 0.081 | |
| dg1polynomial-class | 0.023 | 0.003 | 0.027 | |
| each_col | 0.037 | 0.010 | 0.046 | |
| ellipsoidGate-class | 0.094 | 0.012 | 0.105 | |
| exponential-class | 0.029 | 0.005 | 0.034 | |
| expressionFilter-class | 0.140 | 0.029 | 0.169 | |
| fcReference-class | 0.002 | 0.002 | 0.003 | |
| filter-methods | 0.945 | 0.144 | 1.089 | |
| filter-on-methods | 0.130 | 0.019 | 0.150 | |
| filterList-class | 0.012 | 0.000 | 0.012 | |
| filterResult-class | 0.002 | 0.000 | 0.002 | |
| filterResultList-class | 5.258 | 0.513 | 5.784 | |
| filterSummary-class | 0.227 | 0.052 | 0.279 | |
| filterSummaryList-class | 1.694 | 0.203 | 1.898 | |
| filter_keywords | 0.767 | 0.130 | 0.898 | |
| flowFrame-class | 5.315 | 0.467 | 5.793 | |
| flowSet-class | 3.339 | 0.359 | 3.701 | |
| fr_append_cols | 0.761 | 0.131 | 0.893 | |
| fsApply | 0.136 | 0.052 | 0.188 | |
| gateActionItem-class | 0.001 | 0.000 | 0.002 | |
| gateView-class | 0.001 | 0.000 | 0.002 | |
| getIndexSort-methods | 0.02 | 0.00 | 0.02 | |
| hyperlog-class | 1.463 | 0.006 | 1.469 | |
| hyperlogtGml2-class | 0.025 | 0.001 | 0.029 | |
| identifier-methods | 0.032 | 0.003 | 0.035 | |
| inverseLogicleTransform | 0.834 | 0.134 | 0.967 | |
| invsplitscale-class | 0.038 | 0.004 | 0.043 | |
| keyword-methods | 0.764 | 0.104 | 0.868 | |
| kmeansFilter-class | 0.167 | 0.007 | 0.174 | |
| linearTransform | 0.037 | 0.004 | 0.041 | |
| lintGml2-class | 0.026 | 0.004 | 0.030 | |
| lnTransform | 1.636 | 0.216 | 1.852 | |
| logTransform | 0.050 | 0.006 | 0.056 | |
| logarithm-class | 0.024 | 0.003 | 0.027 | |
| logicalFilterResult-class | 0.001 | 0.000 | 0.001 | |
| logicleTransform | 0.836 | 0.135 | 0.971 | |
| logicletGml2-class | 0.056 | 0.007 | 0.063 | |
| logtGml2-class | 0.039 | 0.006 | 0.044 | |
| manyFilterResult-class | 0.002 | 0.001 | 0.002 | |
| markernames | 0.618 | 0.097 | 0.716 | |
| multipleFilterResult-class | 0.001 | 0.001 | 0.002 | |
| norm2Filter-class | 0.183 | 0.008 | 0.191 | |
| normalizeActionItem-class | 0.001 | 0.001 | 0.002 | |
| normalizeView-class | 0.002 | 0.001 | 0.003 | |
| parameters-methods | 0.038 | 0.004 | 0.041 | |
| polygonGate-class | 0.090 | 0.009 | 0.099 | |
| quadGate-class | 0.244 | 0.012 | 0.259 | |
| quadratic-class | 0.039 | 0.005 | 0.043 | |
| quadraticTransform | 0.048 | 0.005 | 0.053 | |
| ratio-class | 0.053 | 0.020 | 0.072 | |
| ratiotGml2-class | 0.026 | 0.002 | 0.028 | |
| read.FCS | 0.100 | 0.008 | 0.108 | |
| read.FCSheader | 0.008 | 0.005 | 0.013 | |
| read.flowSet | 0.124 | 0.012 | 0.136 | |
| rectangleGate-class | 0.109 | 0.009 | 0.118 | |
| rotate_gate | 0.000 | 0.001 | 0.001 | |
| sampleFilter-class | 0.067 | 0.008 | 0.074 | |
| scaleTransform | 0.063 | 0.019 | 0.082 | |
| scale_gate | 0.001 | 0.000 | 0.001 | |
| shift_gate | 0.001 | 0.000 | 0.001 | |
| singleParameterTransform-class | 0.002 | 0.000 | 0.002 | |
| sinht-class | 0.031 | 0.001 | 0.032 | |
| split-methods | 1.636 | 0.203 | 1.839 | |
| splitScaleTransform | 1.612 | 0.210 | 1.823 | |
| splitscale-class | 0.041 | 0.005 | 0.045 | |
| squareroot-class | 0.035 | 0.006 | 0.040 | |
| subsettingActionItem-class | 0.001 | 0.001 | 0.002 | |
| subsettingView-class | 0.001 | 0.001 | 0.002 | |
| timeFilter-class | 1.718 | 0.193 | 1.911 | |
| transform-class | 0.001 | 0.000 | 0.002 | |
| transformActionItem-class | 0.001 | 0.000 | 0.002 | |
| transformFilter-class | 0.139 | 0.009 | 0.147 | |
| transformList-class | 0.756 | 0.140 | 0.896 | |
| transformMap-class | 0.001 | 0.000 | 0.001 | |
| transformView-class | 0.002 | 0.001 | 0.003 | |
| transform_gate | 0 | 0 | 0 | |
| truncateTransform | 0.034 | 0.004 | 0.039 | |
| unitytransform-class | 0.022 | 0.004 | 0.027 | |
| view-class | 0.001 | 0.000 | 0.002 | |
| workFlow-class | 0.002 | 0.001 | 0.004 | |
| write.FCS | 0.073 | 0.035 | 0.108 | |
| write.flowSet | 1.016 | 0.162 | 1.178 | |