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 08:33:02 -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: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowCore.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings flowCore_1.46.2.tar.gz |
| StartedAt: 2018-10-17 02:00:48 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 02:04:20 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 211.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: flowCore.Rcheck |
| Warnings: 1 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowCore.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings flowCore_1.46.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/flowCore.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'flowCore' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpIBfl0e/R.INSTALLea876f83bc7/flowCore/man/FCSTransTransform.Rd:42: file link 'estimateLogicle' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpIBfl0e/R.INSTALLea876f83bc7/flowCore/man/filters-class.Rd:13: file link 'filterList' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpIBfl0e/R.INSTALLea876f83bc7/flowCore/man/logicleTransform.Rd:50: file link 'estimateLogicle' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpIBfl0e/R.INSTALLea876f83bc7/flowCore/man/normalization-class.Rd:82: file link 'normalize-methods' in package 'flowStats' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/flowCore.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 11.2Mb
sub-directories of 1Mb or more:
R 1.2Mb
data 5.0Mb
extdata 1.1Mb
libs 1.7Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/flowCore/libs/i386/flowCore.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
biexponentialTransform 6.38 0.09 6.46
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
biexponentialTransform 6.41 0.08 6.48
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
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
'C:/Users/biocbuild/bbs-3.7-bioc/meat/flowCore.Rcheck/00check.log'
for details.
flowCore.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/flowCore_1.46.2.tar.gz && rm -rf flowCore.buildbin-libdir && mkdir flowCore.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowCore.buildbin-libdir flowCore_1.46.2.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL flowCore_1.46.2.zip && rm flowCore_1.46.2.tar.gz flowCore_1.46.2.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
24 8352k 24 2064k 0 0 23.0M 0 --:--:-- --:--:-- --:--:-- 24.8M
100 8352k 100 8352k 0 0 56.7M 0 --:--:-- --:--:-- --:--:-- 59.5M
install for i386
* installing *source* package 'flowCore' ...
** libs
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c FastLogicle.cpp -o FastLogicle.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c Hyperlog.cpp -o Hyperlog.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c Logicle.cpp -o Logicle.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c biexponential.cpp -o biexponential.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c convertRawBytes.cpp -o convertRawBytes.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c fcsTextParse.cpp -o fcsTextParse.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c hyperlogTransform.cpp -o hyperlogTransform.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c inPolygon.cpp -o inPolygon.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c inPolytope.cpp -o inPolytope.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c logicleTransform.cpp -o logicleTransform.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c pairVectorRcppWrap.cpp -o pairVectorRcppWrap.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c sortBytes.cpp -o sortBytes.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c uint2double.cpp -o uint2double.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c zeroin.cpp -o zeroin.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o flowCore.dll tmp.def 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 -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
if [ `uname -s` = 'Darwin' ]; then install_name_tool -change /usr/local/clang4/lib/libc++.1.dylib /usr/lib/libc++.1.dylib flowCore.dll; fi
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/flowCore.buildbin-libdir/flowCore/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'flowCore'
finding HTML links ... done
EHtrans-class html
FCSTransTransform html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpIBfl0e/R.INSTALLea876f83bc7/flowCore/man/FCSTransTransform.Rd:42: file link 'estimateLogicle' in package 'flowCore' does not exist and so has been treated as a topic
GvHD html
Subset-methods html
actionItem-class html
arcsinhTransform html
asinht-class html
asinhtGml2-class html
biexponentialTransform html
boundaryFilter-class html
characterOrTransformation-class html
checkOffset html
coerce html
compensateActionItem-class html
compensateView-class html
compensatedParameter-class html
compensation-class html
concreteFilter-class html
dg1polynomial-class html
each_col-methods html
ellipsoidGate html
estimateMedianLogicle html
exponential-class html
expressionFilter-class html
fcReference-class html
filter-and-methods html
filter-class html
filter-in-methods html
filter-methods html
filter-on-methods html
filterDetails-methods html
filterList-class html
filterReference-class html
filterResult-class html
filterResultList-class html
filterSet-class html
filterSummary-class html
filterSummaryList-class html
filters-class html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpIBfl0e/R.INSTALLea876f83bc7/flowCore/man/filters-class.Rd:13: file link 'filterList' in package 'flowCore' does not exist and so has been treated as a topic
flowCore-package html
flowFrame-class html
flowSet-class html
fsApply html
gateActionItem-class html
gateView-class html
getChannelMarker html
getIndexSort-methods html
hyperlog-class html
hyperlogtGml2-class html
identifier-methods html
inverseLogicleTransform html
invsplitscale-class html
keyword-methods html
kmeansFilter html
linearTransform html
lintGml2-class html
lnTransform html
logTransform html
logarithm-class html
logicalFilterResult-class html
logicleTransform html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpIBfl0e/R.INSTALLea876f83bc7/flowCore/man/logicleTransform.Rd:50: file link 'estimateLogicle' in package 'flowCore' does not exist and so has been treated as a topic
logicletGml2-class html
logtGml2-class html
manyFilterResult-class html
markernames html
multipleFilterResult-class html
norm2Filter-class html
normalization-class html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpIBfl0e/R.INSTALLea876f83bc7/flowCore/man/normalization-class.Rd:82: file link 'normalize-methods' in package 'flowStats' does not exist and so has been treated as a topic
normalizeActionItem-class html
normalizeView-class html
parameterFilter-class html
parameterTransform-class html
parameters-class html
parameters-methods html
polygonGate html
polytopeGate html
quadGate html
quadratic-class html
quadraticTransform html
randomFilterResult-class html
ratio-class html
ratiotGml2-class html
read.FCS html
read.FCSheader html
read.flowSet html
rectangleGate html
sampleFilter-class html
scaleTransform html
setOperationFilter-class html
singleParameterTransform-class html
sinht-class html
spillover-flowSet html
split-methods html
splitScaleTransform html
splitscale-class html
squareroot-class html
subsetting-class html
subsettingActionItem-class html
subsettingView-class html
summarizeFilter-methods html
timeFilter-class html
transform-class html
transformActionItem-class html
transformFilter-class html
transformList-class html
transformMap-class html
transformReference-class html
transformView-class html
transformation-class html
truncateTransform html
unitytransform-class html
validFilters html
view-class html
workFlow-class html
write.FCS html
write.flowSet html
** building package indices
** installing vignettes
'HowTo-flowCore.Rnw'
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'flowCore' ...
** libs
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c FastLogicle.cpp -o FastLogicle.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c Hyperlog.cpp -o Hyperlog.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c Logicle.cpp -o Logicle.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c biexponential.cpp -o biexponential.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c convertRawBytes.cpp -o convertRawBytes.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c fcsTextParse.cpp -o fcsTextParse.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c hyperlogTransform.cpp -o hyperlogTransform.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c inPolygon.cpp -o inPolygon.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c inPolytope.cpp -o inPolytope.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c logicleTransform.cpp -o logicleTransform.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c pairVectorRcppWrap.cpp -o pairVectorRcppWrap.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c sortBytes.cpp -o sortBytes.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c uint2double.cpp -o uint2double.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c zeroin.cpp -o zeroin.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o flowCore.dll tmp.def 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 -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
if [ `uname -s` = 'Darwin' ]; then install_name_tool -change /usr/local/clang4/lib/libc++.1.dylib /usr/lib/libc++.1.dylib flowCore.dll; fi
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/flowCore.buildbin-libdir/flowCore/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowCore' as flowCore_1.46.2.zip
* DONE (flowCore)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'flowCore' successfully unpacked and MD5 sums checked
In R CMD INSTALL
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flowCore.Rcheck/tests_i386/testthat.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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
18.57 1.21 19.84
|
flowCore.Rcheck/tests_x64/testthat.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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
13.62 1.31 17.92
|
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flowCore.Rcheck/examples_i386/flowCore-Ex.timings
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flowCore.Rcheck/examples_x64/flowCore-Ex.timings
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