Greg Finak
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/flowWorkspace |
| Branch: RELEASE_3_6 |
| Last Commit: 8cbfbca |
| Last Changed Date: 2018-04-04 13:28:25 -0400 (Wed, 04 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:34:20 -0400 (Thu, 12 Apr 2018).
| Package 500/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| flowWorkspace 3.26.9 Greg Finak
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: flowWorkspace |
| Version: 3.26.9 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings flowWorkspace_3.26.9.tar.gz |
| StartedAt: 2018-04-12 03:52:22 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 03:57:05 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 282.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: flowWorkspace.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings flowWorkspace_3.26.9.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/flowWorkspace.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowWorkspace/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowWorkspace’ version ‘3.26.9’
* 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 ‘flowWorkspace’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 24.9Mb
sub-directories of 1Mb or more:
doc 2.9Mb
lib 18.4Mb
libs 2.9Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Versioned 'LinkingTo' values for
‘BH’ ‘cytolib’
are 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 ... NOTE
Namespaces in Imports field not imported from:
‘RBGL’ ‘grDevices’ ‘graphics’
All declared Imports should be used.
Unexported objects imported by ':::' calls:
‘flowCore:::.estimateLogicle’ ‘flowCore:::checkClass’
‘flowCore:::copyFlowSet’ ‘flowCore:::guid’
‘flowCore:::logicle_transform’ ‘graph:::.makeEdgeKeys’
‘lattice:::updateList’ ‘ncdfFlow:::.isValidSamples’
‘stats:::.splinefun’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getGate,GatingSetList-character: warning in unlist(res, recur = FALSE):
partial argument match of 'recur' to 'recursive'
.addGatingHierarchies: no visible global function definition for ‘is’
.addGatingHierarchies : <anonymous>: no visible global function
definition for ‘tolower<-’
.computeCV : <anonymous>: no visible binding for global variable
‘xml.count’
.computeCV : <anonymous>: no visible binding for global variable
‘openCyto.count’
.computeCV : <anonymous> : <anonymous>: no visible global function
definition for ‘IQR’
.computeCV : <anonymous> : <anonymous>: no visible global function
definition for ‘median’
.computeCV_gh : <anonymous>: no visible global function definition for
‘IQR’
.computeCV_gh : <anonymous>: no visible global function definition for
‘median’
.convertTrans : <anonymous> : f : <anonymous>: no visible binding for
global variable ‘max_val’
.convertTrans : <anonymous> : f : <anonymous>: no visible binding for
global variable ‘decade’
.convertTrans : <anonymous> : f : <anonymous>: no visible binding for
global variable ‘offset’
.convertTrans : <anonymous> : f : <anonymous>: no visible binding for
global variable ‘min_val’
.convertTrans : <anonymous>: multiple local function definitions for
‘f’ with different formal arguments
.dropRedundantNodes : <anonymous>: no visible global function
definition for ‘is’
.getSingleCellExpression: no visible binding for global variable
‘parallel’
.graph_handler : asGraphNEL: no visible global function definition for
‘new’
.graph_handler : asGraphNEL: no visible global function definition for
‘validObject’
.load_gs: no visible global function definition for ‘new’
.load_gs: no visible global function definition for ‘.hasSlot’
.load_gs: no visible global function definition for ‘slot’
.mergeGates : <anonymous>: no visible global function definition for
‘extends’
.parse.pData: no visible binding for global variable ‘.’
.plotGate: no visible global function definition for ‘new’
.plotGate: no visible global function definition for ‘as.formula’
.preplot: no visible global function definition for ‘as’
.preprocessMap: no visible binding for global variable ‘old’
.preprocessMap: no visible binding for global variable ‘.’
.preprocessor: no visible binding for global variable ‘groupName’
GatingSetList: no visible global function definition for ‘as’
GatingSetList: no visible global function definition for ‘validObject’
booleanFilter: no visible global function definition for ‘new’
char2booleanFilter: no visible global function definition for ‘new’
dropRedundantNodes : <anonymous>: no visible global function definition
for ‘is’
flowWorkspace.par.init: no visible global function definition for
‘gray’
getMergedStats: no visible binding for global variable ‘sampleName’
mkformula: no visible global function definition for ‘as.formula’
save_gslist: no visible binding for global variable ‘slot’
transformerList: no visible global function definition for ‘is’
transformerList: no visible binding for global variable ‘is’
GatingSet,GatingHierarchy-character: no visible global function
definition for ‘new’
GatingSet,character-character: no visible global function definition
for ‘new’
GatingSet,flowSet-ANY: no visible global function definition for ‘new’
Rm,character-GatingSetList-character: no visible global function
definition for ‘selectMethod’
[,GatingSet-ANY: no visible global function definition for ‘extends’
[,GatingSetList-ANY: no visible global function definition for
‘callNextMethod’
[,GatingSetList-ANY: no visible global function definition for ‘as’
[[,GatingSet-character: no visible global function definition for ‘new’
add,GatingHierarchy-logicalFilterResult: no visible global function
definition for ‘selectMethod’
add,GatingSet-filtersList: no visible global function definition for
‘selectMethod’
add,GatingSet-list: no visible global function definition for
‘selectMethod’
add,GatingSetList-filter: no visible global function definition for
‘selectMethod’
add,GatingSetList-filterList: no visible global function definition for
‘selectMethod’
add,GatingSetList-filters: no visible global function definition for
‘selectMethod’
add,GatingSetList-filtersList: no visible global function definition
for ‘selectMethod’
add,GatingSetList-list: no visible global function definition for
‘selectMethod’
getPopStats,GatingHierarchy: no visible binding for global variable
‘node’
keyword,GatingSetList-character: no visible global function definition
for ‘selectMethod’
keyword,GatingSetList-missing: no visible global function definition
for ‘selectMethod’
openWorkspace,character: no visible global function definition for
‘new’
pData<-,GatingSetList-data.frame: no visible global function definition
for ‘callNextMethod’
pData<-,GatingSetList-data.frame: no visible global function definition
for ‘as’
plotGate,GatingSetList-character: no visible global function definition
for ‘selectMethod’
rbind2,GatingSetList-missing: no visible global function definition for
‘new’
rbind2,GatingSetList-missing: no visible binding for global variable
‘slot’
recompute,GatingSetList: no visible global function definition for
‘selectMethod’
show,flowJoWorkspace: no visible global function definition for ‘.’
show,flowJoWorkspace: no visible binding for global variable
‘groupName’
transform,GatingSet: no visible global function definition for ‘is’
Undefined global functions or variables:
. .hasSlot IQR as as.formula callNextMethod decade extends gray
groupName is max_val median min_val new node offset old
openCyto.count parallel sampleName selectMethod slot tolower<-
validObject xml.count
Consider adding
importFrom("grDevices", "gray")
importFrom("methods", ".hasSlot", "as", "callNextMethod", "extends",
"is", "new", "selectMethod", "slot", "validObject")
importFrom("stats", "IQR", "as.formula", "median", "offset")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 shell scripts ... 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 ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘flowWorkspace/libs/flowWorkspace.so’:
Found ‘__ZNSt3__14coutE’, possibly from ‘std::cout’ (C++)
Objects: ‘flowJoWorkspace.o’, ‘macFlowJoWorkspace.o’,
‘winFlowJoWorkspace.o’, ‘workspace.o’, ‘ws2gh.o’, ‘ws2gs.o’
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.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* 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: 6 NOTEs
See
‘/Users/biocbuild/bbs-3.6-bioc/meat/flowWorkspace.Rcheck/00check.log’
for details.
flowWorkspace.Rcheck/00install.out
* installing *source* package ‘flowWorkspace’ ...
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether clang++ -std=gnu++11 accepts -g... yes
checking for gcc... clang
checking whether we are using the GNU C compiler... yes
checking whether clang accepts -g... yes
checking for clang option to accept ISO C89... none needed
configure: setting xml2 flags...
configure: No directory was specified for --with-xml2. Trying to find xml2 using other methods.
checking for xml2-config... /usr/bin/xml2-config
configure: Using the following compilation and linking flags for flowWorkspace
configure: PKG_CPPFLAGS=-I/usr/include/libxml2 -ftemplate-depth=900
configure: PKG_LIBS=-lxml2 -lz -lpthread -licucore -lm
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I../inst/include/ -I/usr/include/libxml2 -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/cytolib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c R_API.cpp -o R_API.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I../inst/include/ -I/usr/include/libxml2 -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/cytolib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c R_GatingHierarchy.cpp -o R_GatingHierarchy.o
R_GatingHierarchy.cpp:357:6: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
if(u<0)
˜^˜
R_GatingHierarchy.cpp:476:6: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
if(u<0)throw(domain_error("not valid vertexID!"));
˜^˜
R_GatingHierarchy.cpp:506:6: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
if(u<0)throw(domain_error("not valid vertexID!"));
˜^˜
R_GatingHierarchy.cpp:517:6: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
if(u<0)throw(domain_error("not valid vertexID!"));
˜^˜
R_GatingHierarchy.cpp:526:6: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
if(u<0)throw(domain_error("not valid vertexID!"));
˜^˜
5 warnings generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I../inst/include/ -I/usr/include/libxml2 -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/cytolib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c R_GatingSet.cpp -o R_GatingSet.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I../inst/include/ -I/usr/include/libxml2 -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/cytolib/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 -DROUT -I../inst/include/ -I/usr/include/libxml2 -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/cytolib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c flowJoWorkspace.cpp -o flowJoWorkspace.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I../inst/include/ -I/usr/include/libxml2 -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/cytolib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c getSingleCellExpression.cpp -o getSingleCellExpression.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I../inst/include/ -I/usr/include/libxml2 -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/cytolib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c macFlowJoWorkspace.cpp -o macFlowJoWorkspace.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I../inst/include/ -I/usr/include/libxml2 -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/cytolib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c setCounts.cpp -o setCounts.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I../inst/include/ -I/usr/include/libxml2 -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/cytolib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c winFlowJoWorkspace.cpp -o winFlowJoWorkspace.o
winFlowJoWorkspace.cpp:113:11: warning: unused variable 'minRange' [-Wunused-variable]
double minRange=atof(transNode.getProperty("minRange").c_str());
^
winFlowJoWorkspace.cpp:562:27: warning: '/*' within block comment [-Wcomment]
* "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate
^
winFlowJoWorkspace.cpp:546:10: warning: variable 'quad' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
else if(quadPattern == "--")
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
winFlowJoWorkspace.cpp:554:42: note: uninitialized use occurs here
CurlyGuadGate * g=new CurlyGuadGate(pp, quad);
^˜˜˜
winFlowJoWorkspace.cpp:546:7: note: remove the 'if' if its condition is always true
else if(quadPattern == "--")
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
winFlowJoWorkspace.cpp:539:2: note: variable 'quad' is declared here
QUAD quad;
^
3 warnings generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I../inst/include/ -I/usr/include/libxml2 -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/cytolib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c workspace.cpp -o workspace.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I../inst/include/ -I/usr/include/libxml2 -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/cytolib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c ws2gh.cpp -o ws2gh.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I../inst/include/ -I/usr/include/libxml2 -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/cytolib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c ws2gs.cpp -o ws2gs.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I../inst/include/ -I/usr/include/libxml2 -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/cytolib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c wsNode.cpp -o wsNode.o
mkdir -p "/Users/biocbuild/bbs-3.6-bioc/meat/flowWorkspace.Rcheck/flowWorkspace/lib"
ar rs "/Users/biocbuild/bbs-3.6-bioc/meat/flowWorkspace.Rcheck/flowWorkspace/lib/libflowWorkspace.a" R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o flowJoWorkspace.o getSingleCellExpression.o macFlowJoWorkspace.o setCounts.o winFlowJoWorkspace.o workspace.o ws2gh.o ws2gs.o wsNode.o
ar: creating archive /Users/biocbuild/bbs-3.6-bioc/meat/flowWorkspace.Rcheck/flowWorkspace/lib/libflowWorkspace.a
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 flowWorkspace.so R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o flowJoWorkspace.o getSingleCellExpression.o macFlowJoWorkspace.o setCounts.o winFlowJoWorkspace.o workspace.o ws2gh.o ws2gs.o wsNode.o /Library/Frameworks/R.framework/Versions/3.4/Resources/library/cytolib/lib/libcytolib.a /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/lib/libprotobuf.a -lxml2 -lz -lpthread -licucore -lm -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 flowWorkspace.so; fi
installing to /Users/biocbuild/bbs-3.6-bioc/meat/flowWorkspace.Rcheck/flowWorkspace/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (flowWorkspace)
flowWorkspace.Rcheck/tests/testthat.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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(flowWorkspace)
Loading required package: flowCore
Attaching package: 'flowCore'
The following object is masked from 'package:base':
sort
Loading required package: ncdfFlow
Loading required package: RcppArmadillo
Loading required package: BH
>
> test_check("flowWorkspace")
Attaching package: 'dplyr'
The following objects are masked from 'package:data.table':
between, first, last
The following object is masked from 'package:ncdfFlow':
filter
The following object is masked from 'package:flowCore':
filter
The following object is masked from 'package:testthat':
matches
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
mac version of flowJo workspace recognized.
mac version of flowJo workspace recognized.
mac version of flowJo workspace recognized.
mac version of flowJo workspace recognized.
mac version of flowJo workspace recognized.
mac version of flowJo workspace recognized.
mac version of flowJo workspace recognized.
mac version of flowJo workspace recognized.
mac version of flowJo workspace recognized.
mac version of flowJo workspace recognized.
mac version of flowJo workspace recognized.
mac version of flowJo workspace recognized.
mac version of flowJo workspace recognized.
mac version of flowJo workspace recognized.
mac version of flowJo workspace recognized.
mac version of flowJo workspace recognized.
mac version of flowJo workspace recognized.
mac version of flowJo workspace recognized.
mac version of flowJo workspace recognized.
mac version of flowJo workspace recognized.
══ testthat results ═══════════════════════════════════════════════════════════
OK: 770 SKIPPED: 3 FAILED: 0
>
> #devtools::test("˜/rglab/workspace/flowWorkspace")
> #devtools::check_man()
> #test_file("/home/wjiang2/rglab/workspace/flowWorkspace/tests/testthat/test-archive.R")
> #test_file("/home/wjiang2/rglab/workspace/flowWorkspace/tests/testthat/test-parseWorkspace.R")
>
> #test_file("/home/wjiang2/rglab/workspace/flowWorkspace/tests/testthat/InternalTestSuite.R")
>
>
> proc.time()
user system elapsed
38.155 3.180 40.876
flowWorkspace.Rcheck/flowWorkspace-Ex.timings
| name | user | system | elapsed | |
| GatingHierarchy-class | 3.958 | 0.211 | 4.247 | |
| GatingSet-class | 2.476 | 0.140 | 2.665 | |
| GatingSet-methods | 0.001 | 0.000 | 0.001 | |
| GatingSetList-class | 0.003 | 0.000 | 0.003 | |
| add | 0.003 | 0.000 | 0.004 | |
| asinh_Gml2 | 0.001 | 0.001 | 0.002 | |
| asinhtGml2_trans | 0.002 | 0.000 | 0.002 | |
| booleanFilter-class | 0.002 | 0.000 | 0.003 | |
| checkRedundantNodes | 0.000 | 0.000 | 0.001 | |
| clone | 0.000 | 0.000 | 0.001 | |
| compensate | 0.001 | 0.000 | 0.001 | |
| dropRedundantChannels | 0 | 0 | 0 | |
| dropRedundantNodes | 0.001 | 0.000 | 0.001 | |
| estimateLogicle.GatingHierarchy | 0.001 | 0.000 | 0.000 | |
| flowJo.fasinh | 0.000 | 0.000 | 0.001 | |
| flowJoTrans | 0.002 | 0.001 | 0.002 | |
| flowJoWorkspace-class | 0.040 | 0.005 | 0.045 | |
| flowJo_biexp_trans | 0.717 | 0.053 | 0.774 | |
| flowJo_fasinh_trans | 0.002 | 0.000 | 0.001 | |
| flowWorkspace.par.get | 0.002 | 0.000 | 0.002 | |
| flow_breaks | 0.714 | 0.045 | 0.762 | |
| getCompensationMatrices | 0.001 | 0.000 | 0.000 | |
| getData-methods | 0.001 | 0.000 | 0.001 | |
| getGate | 0.001 | 0.000 | 0.001 | |
| getIndices-GatingSet-name-method | 0.001 | 0.000 | 0.001 | |
| getIndices | 0 | 0 | 0 | |
| getKeywords | 0.226 | 0.033 | 0.262 | |
| getMergedStats | 0.001 | 0.000 | 0.000 | |
| getParent | 0.001 | 0.000 | 0.001 | |
| getPopStats | 0.001 | 0.001 | 0.002 | |
| getSampleGroups | 0.000 | 0.000 | 0.001 | |
| getSamples | 0 | 0 | 0 | |
| getSingleCellExpression | 0.001 | 0.001 | 0.001 | |
| getTransformations | 0.001 | 0.000 | 0.001 | |
| groupByChannels | 0.001 | 0.000 | 0.001 | |
| groupByTree | 0.000 | 0.000 | 0.001 | |
| insertGate | 0.000 | 0.000 | 0.001 | |
| keyword | 0.001 | 0.000 | 0.002 | |
| logicleGml2_trans | 0.002 | 0.001 | 0.002 | |
| logicle_trans | 0.02 | 0.00 | 0.02 | |
| loglevel | 0.001 | 0.000 | 0.001 | |
| markernames | 0.000 | 0.000 | 0.001 | |
| mkformula | 0.002 | 0.000 | 0.001 | |
| moveNode | 0.111 | 0.017 | 0.128 | |
| openWorkspace | 0.001 | 0.000 | 0.001 | |
| parseWorkspace | 0.002 | 0.000 | 0.002 | |
| plot-methods | 0.001 | 0.000 | 0.000 | |
| plotGate-methods | 0.001 | 0.001 | 0.001 | |
| plotPopCV | 0.000 | 0.000 | 0.001 | |
| prettyAxis | 0.000 | 0.000 | 0.001 | |
| sampleNames | 0.001 | 0.000 | 0.001 | |
| save_gs | 0.001 | 0.000 | 0.000 | |
| set.count.xml | 0 | 0 | 0 | |
| setGate | 0.000 | 0.000 | 0.001 | |
| setNode-methods | 0.000 | 0.001 | 0.001 | |
| transform | 0.001 | 0.000 | 0.001 | |
| transformerList | 0.013 | 0.001 | 0.013 | |
| updateChannels | 0.001 | 0.000 | 0.001 | |