Package: flowSpy

Version: 1.1.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:flowSpy.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings flowSpy_1.1.0.tar.gz

StartedAt: 2020-01-16 04:32:27 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 04:41:12 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 525.0 seconds

RetCode: 0

Status:  OK

CheckDir: flowSpy.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:flowSpy.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings flowSpy_1.1.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/flowSpy.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowSpy/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowSpy’ version ‘1.1.0’
* 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 ‘flowSpy’ can be installed ... OK
* checking installed package size ... OK
* 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 line endings in C/C++/Fortran sources/headers ... 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 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/flowSpy.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL flowSpy
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘flowSpy’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/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/4.0/Resources/library/Rcpp/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c jaccard_coeff.cpp -o jaccard_coeff.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 flowSpy.so RcppExports.o jaccard_coeff.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-flowSpy/00new/flowSpy/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘ncdfFlow::filter’ by ‘dplyr::filter’ when loading ‘CytoML’
No methods found in package ‘flowCore’ for requests: ‘action’, ‘assign’, ‘Data’, ‘gate’, ‘tree’ when loading ‘flowUtils’
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘Quick_start.Rmd’ using ‘UTF-8’ 
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘ncdfFlow::filter’ by ‘dplyr::filter’ when loading ‘CytoML’
No methods found in package ‘flowCore’ for requests: ‘action’, ‘assign’, ‘Data’, ‘gate’, ‘tree’ when loading ‘flowUtils’
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘ncdfFlow::filter’ by ‘dplyr::filter’ when loading ‘CytoML’
No methods found in package ‘flowCore’ for requests: ‘action’, ‘assign’, ‘Data’, ‘gate’, ‘tree’ when loading ‘flowUtils’
** testing if installed package keeps a record of temporary installation path
* DONE (flowSpy)

name	user	system	elapsed
Rphenograph	4.308	0.025	4.335
buildTree	0.003	0.001	0.002
constraintMatrix	0.050	0.001	0.050
correctBatchFSPY	0.000	0.001	0.000
createFSPY	0.002	0.000	0.001
defLeafCells	0.002	0.000	0.002
defRootCells	0.002	0.000	0.002
fetchCell	0.001	0.000	0.001
fetchClustMeta	0.001	0.001	0.001
fetchPlotMeta	0.000	0.000	0.001
find_neighbors	0.002	0.001	0.002
flowSpy-package	0.000	0.000	0.001
gatingMatrix	0.025	0.001	0.026
plot2D	0.027	0.001	0.029
plot3D	0.000	0.001	0.001
plotBranchHeatmap	0.001	0.001	0.002
plotCluster	0.003	0.001	0.003
plotClusterHeatmap	0.001	0.001	0.002
plotHeatmap	0.001	0.000	0.001
plotMarkerDensity	0.000	0.000	0.001
plotPieCluster	0.003	0.000	0.003
plotPieTree	0.001	0.000	0.001
plotPseudotimeDensity	0.002	0.000	0.002
plotPseudotimeTraj	0.002	0.000	0.003
plotTrajHeatmap	0.001	0.000	0.001
plotTree	0.003	0.000	0.003
plotViolin	0.001	0.000	0.001
processingCluster	0.002	0.000	0.003
runClara	0.001	0.000	0.001
runCluster	0.002	0.001	0.003
runDiff	0.000	0.000	0.001
runDiffusionMap	0.000	0.000	0.001
runExprsExtract	0.001	0.000	0.002
runExprsMerge	0.001	0.000	0.001
runFastPCA	0	0	0
runKNN	0.001	0.001	0.001
runKmeans	0.001	0.000	0.000
runMclust	0.000	0.000	0.001
runPhenograph	0	0	0
runPseudotime	0.004	0.001	0.005
runSOM	0	0	0
runTSNE	0.001	0.000	0.002
runUMAP	0.001	0.000	0.001
runWalk	0.000	0.001	0.001
show-FSPY-method	0.000	0.000	0.001
subsetFSPY	0.000	0.000	0.001
updateClustMeta	0.000	0.000	0.001
updatePlotMeta	0.001	0.000	0.001