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) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:21:52 -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: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:flowCore.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings flowCore_1.46.2.tar.gz |
| StartedAt: 2018-10-16 00:25:10 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 00:26:40 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 90.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: flowCore.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:flowCore.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings flowCore_1.46.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/flowCore.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.46.2’
* 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 ... OK
* checking installed package size ... NOTE
installed size is 11.9Mb
sub-directories of 1Mb or more:
R 1.3Mb
data 5.0Mb
extdata 1.1Mb
libs 3.1Mb
* 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 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: 4 NOTEs
See
‘/home/biocbuild/bbs-3.7-bioc/meat/flowCore.Rcheck/00check.log’
for details.
flowCore.Rcheck/00install.out
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### Running command:
###
### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL flowCore
###
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘flowCore’ ...
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I/usr/local/include -fpic -g -O2 -c FastLogicle.cpp -o FastLogicle.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I/usr/local/include -fpic -g -O2 -c Hyperlog.cpp -o Hyperlog.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I/usr/local/include -fpic -g -O2 -c Logicle.cpp -o Logicle.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I/usr/local/include -fpic -g -O2 -c biexponential.cpp -o biexponential.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I/usr/local/include -fpic -g -O2 -c convertRawBytes.cpp -o convertRawBytes.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I/usr/local/include -fpic -g -O2 -c fcsTextParse.cpp -o fcsTextParse.o
In file included from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/function.hpp:30,
from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
from fcsTextParse.cpp:8:
/home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
template<class T> T * get_pointer(std::auto_ptr<T> const& p)
^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
from /usr/include/c++/5/locale:43,
from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/algorithm/string/classification.hpp:15,
from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:23,
from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from fcsTextParse.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I/usr/local/include -fpic -g -O2 -c hyperlogTransform.cpp -o hyperlogTransform.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I/usr/local/include -fpic -g -O2 -c inPolygon.cpp -o inPolygon.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I/usr/local/include -fpic -g -O2 -c inPolytope.cpp -o inPolytope.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I/usr/local/include -fpic -g -O2 -c logicleTransform.cpp -o logicleTransform.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I/usr/local/include -fpic -g -O2 -c pairVectorRcppWrap.cpp -o pairVectorRcppWrap.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I/usr/local/include -fpic -g -O2 -c sortBytes.cpp -o sortBytes.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I/usr/local/include -fpic -g -O2 -c uint2double.cpp -o uint2double.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I/usr/local/include -fpic -g -O2 -c zeroin.cpp -o zeroin.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.7-bioc/R/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 -L/home/biocbuild/bbs-3.7-bioc/R/lib -lR
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 /home/biocbuild/bbs-3.7-bioc/R/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-pc-linux-gnu (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
10.068 0.388 10.499
flowCore.Rcheck/flowCore-Ex.timings
| name | user | system | elapsed | |
| EHtrans-class | 0.052 | 0.004 | 0.067 | |
| FCSTransTransform | 0.612 | 0.016 | 0.631 | |
| Subset-methods | 0.176 | 0.008 | 0.207 | |
| actionItem-class | 0.004 | 0.000 | 0.002 | |
| arcsinhTransform | 0.040 | 0.004 | 0.043 | |
| asinht-class | 0.020 | 0.000 | 0.022 | |
| asinhtGml2-class | 0.024 | 0.000 | 0.027 | |
| biexponentialTransform | 3.196 | 0.044 | 3.243 | |
| boundaryFilter-class | 0.052 | 0.000 | 0.051 | |
| characterOrTransformation-class | 0.000 | 0.000 | 0.001 | |
| coerce | 0.036 | 0.000 | 0.038 | |
| compensateActionItem-class | 0.004 | 0.000 | 0.001 | |
| compensateView-class | 0 | 0 | 0 | |
| compensatedParameter-class | 0.096 | 0.008 | 0.121 | |
| compensation-class | 0.232 | 0.004 | 0.235 | |
| dg1polynomial-class | 0.020 | 0.000 | 0.019 | |
| each_col-methods | 0.024 | 0.000 | 0.023 | |
| ellipsoidGate | 0.044 | 0.000 | 0.046 | |
| exponential-class | 0.020 | 0.000 | 0.022 | |
| expressionFilter-class | 0.064 | 0.000 | 0.063 | |
| fcReference-class | 0.004 | 0.000 | 0.001 | |
| filter-methods | 0.720 | 0.012 | 0.734 | |
| filter-on-methods | 0.068 | 0.000 | 0.067 | |
| filterList-class | 0.004 | 0.000 | 0.005 | |
| filterResult-class | 0.000 | 0.000 | 0.001 | |
| filterResultList-class | 0.000 | 0.000 | 0.001 | |
| filterSummary-class | 0.000 | 0.000 | 0.001 | |
| filterSummaryList-class | 0.000 | 0.000 | 0.001 | |
| flowFrame-class | 2.220 | 0.016 | 2.241 | |
| flowSet-class | 1.720 | 0.044 | 1.767 | |
| fsApply | 0.092 | 0.000 | 0.093 | |
| gateActionItem-class | 0.004 | 0.000 | 0.001 | |
| gateView-class | 0.000 | 0.000 | 0.002 | |
| getIndexSort-methods | 0.020 | 0.000 | 0.016 | |
| hyperlog-class | 0.752 | 0.000 | 0.755 | |
| hyperlogtGml2-class | 0.020 | 0.000 | 0.023 | |
| identifier-methods | 0.016 | 0.000 | 0.014 | |
| inverseLogicleTransform | 0.520 | 0.020 | 0.539 | |
| invsplitscale-class | 0.02 | 0.00 | 0.02 | |
| keyword-methods | 0.528 | 0.016 | 0.542 | |
| kmeansFilter | 0.140 | 0.000 | 0.139 | |
| linearTransform | 0.024 | 0.000 | 0.023 | |
| lintGml2-class | 0.020 | 0.000 | 0.019 | |
| lnTransform | 0.932 | 0.012 | 0.945 | |
| logTransform | 0.024 | 0.000 | 0.023 | |
| logarithm-class | 0.020 | 0.000 | 0.019 | |
| logicalFilterResult-class | 0.004 | 0.000 | 0.001 | |
| logicleTransform | 0.560 | 0.004 | 0.566 | |
| logicletGml2-class | 0.036 | 0.000 | 0.036 | |
| logtGml2-class | 0.02 | 0.00 | 0.02 | |
| manyFilterResult-class | 0.000 | 0.000 | 0.001 | |
| markernames | 0.504 | 0.016 | 0.518 | |
| multipleFilterResult-class | 0.000 | 0.000 | 0.001 | |
| norm2Filter-class | 0.112 | 0.000 | 0.110 | |
| normalizeActionItem-class | 0.000 | 0.000 | 0.001 | |
| normalizeView-class | 0.004 | 0.000 | 0.001 | |
| parameters-methods | 0.016 | 0.000 | 0.018 | |
| polygonGate | 0.036 | 0.000 | 0.037 | |
| quadGate | 0.112 | 0.000 | 0.113 | |
| quadratic-class | 0.020 | 0.000 | 0.017 | |
| quadraticTransform | 0.020 | 0.000 | 0.021 | |
| ratio-class | 0.024 | 0.000 | 0.021 | |
| ratiotGml2-class | 0.016 | 0.000 | 0.016 | |
| read.FCS | 0.056 | 0.000 | 0.055 | |
| read.FCSheader | 0.004 | 0.000 | 0.004 | |
| read.flowSet | 0.056 | 0.000 | 0.058 | |
| rectangleGate | 0.060 | 0.000 | 0.061 | |
| sampleFilter-class | 0.020 | 0.008 | 0.030 | |
| scaleTransform | 0.020 | 0.000 | 0.021 | |
| singleParameterTransform-class | 0.000 | 0.000 | 0.001 | |
| sinht-class | 0.016 | 0.000 | 0.017 | |
| split-methods | 0.752 | 0.008 | 0.762 | |
| splitScaleTransform | 0.864 | 0.036 | 0.901 | |
| splitscale-class | 0.020 | 0.000 | 0.019 | |
| squareroot-class | 0.020 | 0.000 | 0.018 | |
| subsettingActionItem-class | 0.000 | 0.000 | 0.001 | |
| subsettingView-class | 0.004 | 0.000 | 0.001 | |
| timeFilter-class | 1.252 | 0.040 | 1.297 | |
| transform-class | 0.004 | 0.000 | 0.002 | |
| transformActionItem-class | 0.000 | 0.000 | 0.001 | |
| transformFilter-class | 0.088 | 0.000 | 0.087 | |
| transformList-class | 0.604 | 0.024 | 0.628 | |
| transformMap-class | 0.004 | 0.000 | 0.001 | |
| transformView-class | 0.000 | 0.000 | 0.001 | |
| truncateTransform | 0.020 | 0.000 | 0.021 | |
| unitytransform-class | 0.012 | 0.000 | 0.015 | |
| view-class | 0.000 | 0.000 | 0.001 | |
| workFlow-class | 0.004 | 0.000 | 0.001 | |
| write.FCS | 0.040 | 0.000 | 0.041 | |
| write.flowSet | 0.684 | 0.016 | 0.699 | |