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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:openCyto.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings openCyto_2.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/openCyto.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'openCyto/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'openCyto' version '2.2.0'
* 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 ... NOTE
Found the following hidden files and directories:
.travis.yml
.github
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'openCyto' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpueYXhT/R.INSTALL265c4b346a09/openCyto/man/add.Rd:15: file link 'add' in package 'flowWorkspace' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpueYXhT/R.INSTALL265c4b346a09/openCyto/man/add.Rd:17: file link 'add' in package 'flowWorkspace' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpueYXhT/R.INSTALL265c4b346a09/openCyto/man/add.Rd:19: file link 'add' in package 'flowWorkspace' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpueYXhT/R.INSTALL265c4b346a09/openCyto/man/gs_add_gating_method.Rd:46: file link 'load_gs' in package 'flowWorkspace' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/openCyto.Rcheck/00install.out' for details.
* 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
* 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 ... NOTE
Namespace in Imports field not imported from: 'flowViz'
All declared Imports should be used.
Unexported objects imported by ':::' calls:
'flowClust:::.ellipsePoints' 'flowStats:::drvkde'
'flowWorkspace:::.addGate' 'flowWorkspace:::.cpp_addGate'
'flowWorkspace:::.cpp_boolGating' 'flowWorkspace:::.cpp_setIndices'
'flowWorkspace:::.getAllDescendants'
'flowWorkspace:::filter_to_list.booleanFilter'
'flowWorkspace:::filter_to_list.rectangleGate' 'lattice:::updateList'
'ncdfFlow:::toBitVec' 'ncdfFlow:::toLogical'
See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
'groupBy' 'isCollapse' 'ppMethod' 'unlockNamespace'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Found the following possibly unsafe calls:
File 'openCyto/R/pluginFramework.R':
unlockBinding(methodName, ENV)
unlockBinding(methodName, ENV)
.boundary: no visible global function definition for 'rectangleGate'
.center_mode: no visible global function definition for 'density'
.find_peaks: no visible global function definition for 'density'
.find_peaks: no visible global function definition for 'points'
.find_valleys: no visible global function definition for 'density'
.gateToFilterResult: no visible global function definition for 'exprs'
.gateToFilterResult: no visible global function definition for 'as'
.gate_tail: no visible global function definition for 'exprs'
.gate_tail: no visible global function definition for 'exprs<-'
.gate_tail: no visible global function definition for 'rectangleGate'
.gatingTemplate: no visible global function definition for 'as'
.gatingTemplate: no visible global function definition for 'new'
.gatingTemplate: no visible binding for global variable 'pop'
.gatingTemplate: no visible binding for global variable 'gating_method'
.gatingTemplate: no visible binding for global variable 'gating_args'
.gatingTemplate: no visible binding for global variable
'collapseDataForGating'
.gatingTemplate: no visible binding for global variable
'preprocessing_method'
.gatingTemplate: no visible binding for global variable
'preprocessing_args'
.gatingTemplate: no visible global function definition for 'extends'
.gating_adaptor: no visible global function definition for 'as'
.gating_adaptor: no visible global function definition for 'na.omit'
.gating_adaptor: no visible global function definition for
'rectangleGate'
.gating_adaptor: no visible global function definition for 'filters'
.gating_adaptor: no visible global function definition for 'extends'
.gating_gtMethod: no visible global function definition for 'na.omit'
.gating_gtMethod : <anonymous>: no visible global function definition
for 'extends'
.gating_gtMethod: no visible global function definition for 'extends'
.gating_gtMethod: no visible global function definition for 'is'
.gating_gtMethod : <anonymous>: no visible global function definition
for 'filters'
.gating_refGate : <anonymous>: no visible global function definition
for 'rectangleGate'
.gating_refGate: no visible global function definition for 'filterList'
.gating_refGate: no visible global function definition for 'is'
.gen_1dgate : <anonymous>: no visible binding for global variable
'parent'
.gen_1dgate : <anonymous>: no visible binding for global variable
'gating_method'
.gen_1dgate : <anonymous>: no visible binding for global variable
'gating_args'
.gen_1dgate : <anonymous>: no visible binding for global variable
'collapseDataForGating'
.gen_1dgate : <anonymous>: no visible binding for global variable
'preprocessing_method'
.gen_1dgate : <anonymous>: no visible binding for global variable
'preprocessing_args'
.gen_dummy_ref_gate: no visible binding for global variable 'parent'
.gen_dummy_ref_gate : <anonymous>: no visible binding for global
variable 'pop'
.gen_dummy_ref_gate : <anonymous>: no visible binding for global
variable 'gating_method'
.gen_dummy_ref_gate : <anonymous>: no visible binding for global
variable 'gating_args'
.gen_dummy_ref_gate : <anonymous>: no visible binding for global
variable 'collapseDataForGating'
.gen_dummy_ref_gate : <anonymous>: no visible binding for global
variable 'preprocessing_method'
.gen_dummy_ref_gate : <anonymous>: no visible binding for global
variable 'preprocessing_args'
.gen_refGate: no visible binding for global variable 'parent'
.gen_refGate: no visible binding for global variable 'gating_args'
.getEllipse: no visible global function definition for 'qf'
.getEllipse: no visible global function definition for 'qchisq'
.getEllipseGate: no visible global function definition for 'qf'
.getEllipseGate: no visible global function definition for 'qchisq'
.getEllipseGate: no visible global function definition for
'polygonGate'
.getEllipseGate: no visible global function definition for
'ellipsoidGate'
.getFullPath: no visible binding for global variable 'parent'
.improvedMindensity: no visible global function definition for
'density'
.improvedMindensity: no visible global function definition for
'smooth.spline'
.improvedMindensity: no visible global function definition for
'predict'
.improvedMindensity: no visible global function definition for 'median'
.improvedMindensity : .plots: no visible global function definition for
'abline'
.improvedMindensity: no visible global function definition for 'par'
.improvedMindensity: no visible global function definition for 'abline'
.plotTree: no visible global function definition for 'as'
.plotTree: no visible global function definition for 'par'
.plotTree: no visible global function definition for 'legend'
.preprocess_csv: no visible binding for global variable 'pop'
.preprocess_csv: no visible binding for global variable 'parent'
.preprocess_csv: no visible binding for global variable 'gating_method'
.preprocess_csv: no visible binding for global variable 'gating_args'
.preprocess_csv: no visible binding for global variable
'collapseDataForGating'
.preprocess_csv: no visible binding for global variable
'preprocessing_method'
.preprocess_csv: no visible binding for global variable
'preprocessing_args'
.preprocess_row: no visible binding for global variable 'pop'
.preprocess_row: no visible binding for global variable 'gating_method'
.preprocess_row: no visible binding for global variable 'parent'
.preprocess_row: no visible binding for global variable 'gating_args'
.preprocess_row: no visible binding for global variable
'preprocessing_method'
.preprocess_row: no visible binding for global variable
'preprocessing_args'
.prior_flowClust1d: no visible global function definition for 'fsApply'
.prior_flowClust1d : <anonymous>: no visible global function definition
for 'exprs'
.prior_flowClust1d: no visible global function definition for 'hclust'
.prior_flowClust1d: no visible global function definition for 'dist'
.prior_flowClust1d: no visible global function definition for 'median'
.prior_flowClust1d: no visible global function definition for 'cutree'
.prior_flowClust1d: no visible global function definition for 'kmeans'
.prior_flowClust1d : <anonymous>: no visible global function definition
for 'sd'
.prior_flowClust1d: no visible binding for global variable 'var'
.prior_flowClust1d : <anonymous>: no visible global function definition
for 'embed'
.prior_flowClust1d : <anonymous>: no visible binding for global
variable 'var'
.prior_kmeans : <anonymous>: no visible global function definition for
'exprs'
.prior_kmeans : <anonymous>: no visible global function definition for
'kmeans'
.prior_kmeans : <anonymous> : <anonymous>: no visible global function
definition for 'cov'
.prior_kmeans : <anonymous>: no visible global function definition for
'dist'
.prior_kmeans: no visible binding for global variable 'cov.wt'
.quadGate2rectangleGates: no visible global function definition for
'rectangleGate'
.quadGate2rectangleGates: no visible global function definition for
'filters'
.quantile_flowClust : cdf_target : <anonymous>: no visible global
function definition for 'pt'
.quantile_flowClust : cdf_target: no visible global function definition
for 'weighted.mean'
.quantile_flowClust: no visible global function definition for
'uniroot'
.read.FCS.csv: no visible global function definition for 'new'
.read.FCS.csv: no visible global function definition for 'parameters<-'
.read.flowSet.csv: no visible global function definition for 'flowSet'
.standardize_flowFrame: no visible global function definition for
'exprs'
.standardize_flowFrame: no visible global function definition for
'exprs<-'
.standardize_flowset: no visible global function definition for
'fsApply'
.standardize_flowset: no visible global function definition for
'flowSet'
.standardize_flowset: no visible global function definition for 'as'
.tailgate: no visible global function definition for 'exprs'
.tailgate: no visible global function definition for 'exprs<-'
.tailgate: no visible global function definition for 'rectangleGate'
.truncate_flowframe: no visible global function definition for
'rectangleGate'
.truncate_flowframe: no visible global function definition for 'Subset'
.truncate_flowset: no visible global function definition for
'rectangleGate'
.truncate_flowset: no visible global function definition for 'Subset'
.unique_check_alias: no visible binding for global variable 'parent'
as.data.table.gatingTemplate : <anonymous>: no visible global function
definition for 'extends'
fast_coerce: no visible global function definition for 'fsApply'
fast_coerce : <anonymous>: no visible global function definition for
'exprs'
fast_coerce: no visible global function definition for 'new'
fcEllipsoidGate: no visible global function definition for 'as'
fcFilterList : <anonymous>: no visible global function definition for
'extends'
fcFilterList: no visible global function definition for 'filterList'
fcFilterList: no visible global function definition for 'as'
fcPolygonGate: no visible global function definition for 'as'
fcRectangleGate: no visible global function definition for 'as'
fcTree: no visible global function definition for 'as'
fcTree: no visible global function definition for 'new'
gate_flowclust_1d: no visible global function definition for 'exprs'
gate_flowclust_1d: no visible global function definition for
'rectangleGate'
gate_flowclust_1d: no visible global function definition for 'abline'
gate_flowclust_1d: no visible global function definition for 'rainbow'
gate_flowclust_1d: no visible global function definition for 'lines'
gate_flowclust_2d: no visible global function definition for 'new'
gate_flowclust_2d: no visible global function definition for 'dist'
gate_flowclust_2d: no visible global function definition for 'qchisq'
gate_flowclust_2d: no visible global function definition for 'exprs'
gate_flowclust_2d: no visible global function definition for 'sd'
gate_flowclust_2d: no visible global function definition for
'polygonGate'
gate_flowclust_2d: no visible global function definition for 'lines'
gate_flowclust_2d: no visible global function definition for 'points'
gate_mindensity: no visible global function definition for 'exprs'
gate_mindensity: no visible global function definition for
'rectangleGate'
gate_mindensity2: no visible global function definition for 'exprs'
gate_mindensity2: no visible global function definition for
'rectangleGate'
gate_quad_sequential : <anonymous>: no visible global function
definition for 'exprs'
gate_quad_sequential: no visible global function definition for
'filter'
gate_quad_sequential: no visible global function definition for 'as'
gate_quad_sequential : <anonymous>: no visible global function
definition for 'rectangleGate'
gate_quad_sequential: no visible global function definition for
'filters'
gate_quad_tmix: no visible global function definition for 'filter'
gate_quad_tmix: no visible global function definition for 'as'
gate_quad_tmix: no visible global function definition for 'polygonGate'
gate_quad_tmix: no visible global function definition for 'filters'
gate_quantile: no visible global function definition for 'exprs'
gate_quantile: no visible global function definition for 'quantile'
gate_quantile: no visible global function definition for 'hist'
gate_quantile: no visible global function definition for 'density'
gate_quantile: no visible global function definition for 'abline'
gate_quantile: no visible global function definition for 'text'
gate_quantile: no visible global function definition for
'rectangleGate'
gate_tail: no visible global function definition for 'exprs'
gate_tail: no visible global function definition for 'rectangleGate'
gate_tautstring: no visible global function definition for 'exprs'
gate_tautstring: no visible global function definition for
'rectangleGate'
gs_add_gating_method: no visible global function definition for 'is'
gs_add_gating_method_init: no visible global function definition for
'is'
gs_remove_gating_method: no visible global function definition for 'is'
mindensity: no visible global function definition for 'exprs'
mindensity: no visible global function definition for 'rectangleGate'
ocRectRefGate: no visible global function definition for 'as'
quadGate.tmix: no visible global function definition for
'quad_gate_tmix'
tailgate: no visible global function definition for 'exprs'
tailgate: no visible global function definition for 'rectangleGate'
coerce,ncdfFlowList-flowFrame: no visible global function definition
for 'selectMethod'
gatingTemplate,character: no visible binding for global variable
'isMultiPops'
gatingTemplate,character: no visible binding for global variable 'pop'
gatingTemplate,character: no visible binding for global variable
'gating_args'
plot,fcFilterList-ANY : <anonymous>: no visible global function
definition for 'dnorm'
plot,fcFilterList-ANY: no visible global function definition for 'hist'
plot,fcFilterList-ANY: no visible global function definition for
'exprs'
plot,fcFilterList-ANY: no visible global function definition for
'lines'
plot,fcFilterList-ANY: no visible global function definition for
'rainbow'
plot,fcFilterList-ANY: no visible global function definition for
'abline'
show,fcFilter: no visible global function definition for
'callNextMethod'
Undefined global functions or variables:
Subset abline as callNextMethod collapseDataForGating cov cov.wt
cutree density dist dnorm ellipsoidGate embed exprs exprs<- extends
filter filterList filters flowSet fsApply gating_args gating_method
hclust hist is isMultiPops kmeans legend lines median na.omit new par
parameters<- parent points polygonGate pop predict preprocessing_args
preprocessing_method pt qchisq qf quad_gate_tmix quantile rainbow
rectangleGate sd selectMethod smooth.spline text uniroot var
weighted.mean
Consider adding
importFrom("grDevices", "rainbow")
importFrom("graphics", "abline", "hist", "legend", "lines", "par",
"points", "text")
importFrom("methods", "as", "callNextMethod", "extends", "is", "new",
"selectMethod")
importFrom("stats", "cov", "cov.wt", "cutree", "density", "dist",
"dnorm", "embed", "filter", "hclust", "kmeans", "median",
"na.omit", "predict", "pt", "qchisq", "qf", "quantile",
"sd", "smooth.spline", "uniroot", "var", "weighted.mean")
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 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 use of PKG_*FLAGS in Makefiles ... 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-3.12-bioc/R/library/openCyto/libs/i386/openCyto.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/openCyto/libs/x64/openCyto.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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* 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-3.12-bioc/meat/openCyto.Rcheck/00check.log'
for details.
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/openCyto_2.2.0.tar.gz && rm -rf openCyto.buildbin-libdir && mkdir openCyto.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=openCyto.buildbin-libdir openCyto_2.2.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL openCyto_2.2.0.zip && rm openCyto_2.2.0.tar.gz openCyto_2.2.0.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
100 1106k 100 1106k 0 0 34.1M 0 --:--:-- --:--:-- --:--:-- 34.8M
install for i386
* installing *source* package 'openCyto' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cpPmden.cpp -o cpPmden.o
cpPmden.cpp: In function 'stringInfo cpPmden(const std::vector<double>&)':
cpPmden.cpp:88:22: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare]
for (auto i = 0; i < (nsamp-1); i++) {
~~^~~~~~~~~~~
cpPmden.cpp:100:17: warning: variable 'newaccx' set but not used [-Wunused-but-set-variable]
double rhs, newaccx;
^~~~~~~
cpPmden.cpp:157:24: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare]
for (auto i = 0; i < nsamp; i++) {
~~^~~~~~~
cpPmden.cpp:164:22: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare]
for (auto i=0; i < (nsamp-2); i++) {
~~^~~~~~~~~~~
cpPmden.cpp:193:24: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare]
for (auto i = 0; i < nsamp; i++) {
~~^~~~~~~
cpPmden.cpp:219:26: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare]
for (auto i = 0; i < nsamp; i++) {
~~^~~~~~~
cpPmden.cpp:251:26: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare]
for (auto i = 0; i < nsamp; i++) {
~~^~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cppApprox.cpp -o cppApprox.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cppdip.cpp -o cppdip.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c dynamic_prog.cpp -o dynamic_prog.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fill_SMAWK.cpp -o fill_SMAWK.o
fill_SMAWK.cpp: In function 'void reduce_in_place(int, int, int, int, const std::vector<unsigned int>&, std::vector<unsigned int>&, const std::vector<std::vector<double> >&, const std::vector<std::vector<unsigned int> >&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, DISSIMILARITY)':
fill_SMAWK.cpp:80:8: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<unsigned int>::size_type' {aka 'unsigned int'} [-Wsign-compare]
if(N >= js.size()) {
~~^~~~~~~~~~~~
fill_SMAWK.cpp:90:11: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'int' [-Wsign-compare]
while(m > N) { // js_reduced has more than N positions / columns
~~^~~
fill_SMAWK.cpp:121:25: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
for(int r=(left+1); r < m; ++r) {
~~^~~
fill_SMAWK.cpp: In function 'void fill_even_positions(int, int, int, int, const std::vector<unsigned int>&, std::vector<std::vector<double> >&, std::vector<std::vector<unsigned int> >&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, DISSIMILARITY)':
fill_SMAWK.cpp:164:17: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
for(++ r; r < n && js[r]<=jmax; r++) {
~~^~~
fill_SMAWK.cpp:164:29: warning: comparison of integer expressions of different signedness: 'const value_type' {aka 'const unsigned int'} and 'int' [-Wsign-compare]
for(++ r; r < n && js[r]<=jmax; r++) {
fill_SMAWK.cpp:168:15: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const unsigned int'} and 'int' [-Wsign-compare]
if(jabs > i) break;
~~~~~^~~
fill_SMAWK.cpp: In function 'void find_min_from_candidates(int, int, int, int, const std::vector<unsigned int>&, std::vector<std::vector<double> >&, std::vector<std::vector<unsigned int> >&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, DISSIMILARITY)':
fill_SMAWK.cpp:218:16: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const unsigned int'} and 'int' [-Wsign-compare]
if(j_abs > i) break;
~~~~~~^~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c getTautStringApprox.cpp -o getTautStringApprox.o
getTautStringApprox.cpp: In function 'Rcpp::List getTautStringApprox(std::vector<double>)':
getTautStringApprox.cpp:32:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wsign-compare]
for (int i = 1; i != fullString.size(); ++i) {
~~^~~~~~~~~~~~~~~~~~~~
getTautStringApprox.cpp:56:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<stringPairs>::size_type' {aka 'unsigned int'} [-Wsign-compare]
for (int i = 0; i != plotSpecs.size(); ++i) {
~~^~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c kMedDP.cpp -o kMedDP.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c kkuiper.cpp -o kkuiper.o
kkuiper.cpp: In function 'void difficultmax(std::vector<double>&, long int, long int, long int, long int*, long int*, double*)':
kkuiper.cpp:77:10: warning: variable 'min' set but not used [-Wunused-but-set-variable]
double min, max;
^~~
kkuiper.cpp: In function 'void easymax(std::vector<double>&, long int, long int, long int, long int*, long int*, double*)':
kkuiper.cpp:64:10: warning: 'maxi' may be used uninitialized in this function [-Wmaybe-uninitialized]
*erga=maxi;
~~~~~^~~~~
kkuiper.cpp:63:10: warning: 'mini' may be used uninitialized in this function [-Wmaybe-uninitialized]
*ergb=mini;
~~~~~^~~~~
kkuiper.cpp: In function 'void difficultmax(std::vector<double>&, long int, long int, long int, long int*, long int*, double*)':
kkuiper.cpp:161:23: warning: 'maxi' may be used uninitialized in this function [-Wmaybe-uninitialized]
*erga=minis[maxi];
^
kkuiper.cpp: In function 'std::vector<double> kkuiper(std::vector<double>&, long int, int)':
kkuiper.cpp:64:10: warning: 'maxi' may be used uninitialized in this function [-Wmaybe-uninitialized]
*erga=maxi;
~~~~~^~~~~
kkuiper.cpp:44:15: note: 'maxi' was declared here
long i,mini,maxi;
^~~~
kkuiper.cpp:63:10: warning: 'mini' may be used uninitialized in this function [-Wmaybe-uninitialized]
*ergb=mini;
~~~~~^~~~~
kkuiper.cpp:44:10: note: 'mini' was declared here
long i,mini,maxi;
^~~~
kkuiper.cpp:64:10: warning: 'maxi' may be used uninitialized in this function [-Wmaybe-uninitialized]
*erga=maxi;
~~~~~^~~~~
kkuiper.cpp:44:15: note: 'maxi' was declared here
long i,mini,maxi;
^~~~
kkuiper.cpp:63:10: warning: 'mini' may be used uninitialized in this function [-Wmaybe-uninitialized]
*ergb=mini;
~~~~~^~~~~
kkuiper.cpp:44:10: note: 'mini' was declared here
long i,mini,maxi;
^~~~
kkuiper.cpp:58:3: warning: 'maxi' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(mini<maxi) {
^~
kkuiper.cpp:44:15: note: 'maxi' was declared here
long i,mini,maxi;
^~~~
kkuiper.cpp:58:3: warning: 'mini' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(mini<maxi) {
^~
kkuiper.cpp:44:10: note: 'mini' was declared here
long i,mini,maxi;
^~~~
kkuiper.cpp:197:9: warning: 'maxi' may be used uninitialized in this function [-Wmaybe-uninitialized]
a[0]=maxi;
kkuiper.cpp:196:9: warning: 'mini' may be used uninitialized in this function [-Wmaybe-uninitialized]
b[0]=mini;
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c local_density.cpp -o local_density.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c medianAbsoluteDeviation.cpp -o medianAbsoluteDeviation.o
medianAbsoluteDeviation.cpp: In function 'double medianAbsoluteDeviation(const std::vector<double>&)':
medianAbsoluteDeviation.cpp:28:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wsign-compare]
for (auto i = 0; i != devs.size(); ++i)
~~^~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c misc.cpp -o misc.o
misc.cpp: In function 'Rcpp::NumericMatrix collapseData(Rcpp::List, Rcpp::StringVector)':
misc.cpp:10:24: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
for(unsigned i = 0; i < mat_list.size(); i++){
~~^~~~~~~~~~~~~~~~~
misc.cpp:21:31: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
for(unsigned ind = 0; ind < mat_list.size(); ind++){
~~~~^~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rQuantile.cpp -o rQuantile.o
rQuantile.cpp: In function 'std::vector<double> rQuantile(const std::vector<double>&, std::vector<double>)':
rQuantile.cpp:35:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wsign-compare]
for (auto i = 0; i != lowInd.size(); ++i) {
~~^~~~~~~~~~~~~~~~
rQuantile.cpp:41:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wsign-compare]
for (auto i = 0; i != lowInd.size(); ++i) {
~~^~~~~~~~~~~~~~~~
rQuantile.cpp:47:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<bool>::size_type' {aka 'unsigned int'} [-Wsign-compare]
for (auto i = 0; i != offSet.size(); ++i)
~~^~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c singleDip.cpp -o singleDip.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c tautstring.cpp -o tautstring.o
tautstring.cpp: In function 'stringInfo tautString(const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, double, double, long int, int)':
tautstring.cpp:148:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wsign-compare]
for (auto i = 0; i < knotst.size(); i++) {
~~^~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c tsGates.cpp -o tsGates.o
tsGates.cpp: In function 'std::vector<double> findKmedGates(const std::vector<double>&, const std::vector<int>&, int)':
tsGates.cpp:41:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'unsigned int'} [-Wsign-compare]
for (auto j = 0; j != classVector.size(); j++)
~~^~~~~~~~~~~~~~~~~~~~~
tsGates.cpp: In function 'std::vector<double> tsGates(const std::vector<double>&, int)':
tsGates.cpp:81:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<bool>::size_type' {aka 'unsigned int'} [-Wsign-compare]
for (auto i = 1; i != (localMins.size()-1); ++i) {
~~^~~~~~~~~~~~~~~~~~~~~~~
tsGates.cpp:86:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wsign-compare]
for (auto i = 0; i != yvals.size(); ++i)
~~^~~~~~~~~~~~~~~
tsGates.cpp:96:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wsign-compare]
for (auto j = 0; j != cutValues.size(); ++j) {
~~^~~~~~~~~~~~~~~~~~~
tsGates.cpp:99:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wsign-compare]
for (auto i = 0; i != ys.size(); ++i)
~~^~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c unlockNamespace.c -o unlockNamespace.o
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o openCyto.dll tmp.def RcppExports.o cpPmden.o cppApprox.o cppdip.o dynamic_prog.o fill_SMAWK.o getTautStringApprox.o kMedDP.o kkuiper.o local_density.o medianAbsoluteDeviation.o misc.o rQuantile.o singleDip.o tautstring.o tsGates.o unlockNamespace.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/openCyto.buildbin-libdir/00LOCK-openCyto/00new/openCyto/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'openCyto'
finding HTML links ... done
CytoExploreR_exports html
add html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpueYXhT/R.INSTALL265c4b346a09/openCyto/man/add.Rd:15: file link 'add' in package 'flowWorkspace' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpueYXhT/R.INSTALL265c4b346a09/openCyto/man/add.Rd:17: file link 'add' in package 'flowWorkspace' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpueYXhT/R.INSTALL265c4b346a09/openCyto/man/add.Rd:19: file link 'add' in package 'flowWorkspace' does not exist and so has been treated as a topic
as.data.table html
boolMethod-class html
dims-gtMethod-method html
dummyMethod-class html
fcEllipsoidGate-class html
fcEllipsoidGate html
fcFilter-class html
fcFilterList-class html
fcFilterList html
fcPolygonGate-class html
fcPolygonGate html
fcRectangleGate-class html
fcRectangleGate html
fcTree-class html
fcTree html
gate_flowclust_1d html
finding level-2 HTML links ... done
gate_flowclust_2d html
gate_mindensity html
gate_mindensity2 html
gate_quad_sequential html
gate_quad_tmix html
gate_quantile html
gate_tail html
gate_tautstring html
gatingTemplate-class html
getGate-fcTree-character-method html
getNodes-fcTree-method html
gh_generate_template html
groupBy-gtMethod-method html
gs_add_gating_method html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpueYXhT/R.INSTALL265c4b346a09/openCyto/man/gs_add_gating_method.Rd:46: file link 'load_gs' in package 'flowWorkspace' does not exist and so has been treated as a topic
gs_add_gating_method_init html
gs_remove_gating_method html
gtMethod-class html
gtPopulation-class html
gtSubsets-class html
gt_gating html
gt_get_children html
gt_get_gate html
gt_get_nodes html
gt_get_parent html
gt_list_methods html
gt_toggle_helpergates html
isCollapse-gtMethod-method html
names-gtMethod-method html
names-gtPopulation-method html
ocRectRefGate-class html
ocRectRefGate html
ocRectangleGate-class html
openCyto-deprecated html
openCyto html
openCyto.options html
parameters-gtMethod-method html
plot-fcFilterList-ANY-method html
plot-fcTree-character-method html
plot-gatingTemplate-missing-method html
polyFunctions-class html
posteriors-fcFilter-ANY-method html
ppMethod-class html
ppMethod-gatingTemplate-character-method
html
preprocessing-ppMethod-GatingSet-method
html
prior_flowclust html
priors-fcFilter-ANY-method html
refGate-class html
register_plugins html
show-boolMethod-method html
show-fcFilter-method html
show-gatingTemplate-method html
show-gtMethod-method html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'openCyto' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cpPmden.cpp -o cpPmden.o
cpPmden.cpp: In function 'stringInfo cpPmden(const std::vector<double>&)':
cpPmden.cpp:88:22: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare]
for (auto i = 0; i < (nsamp-1); i++) {
~~^~~~~~~~~~~
cpPmden.cpp:100:17: warning: variable 'newaccx' set but not used [-Wunused-but-set-variable]
double rhs, newaccx;
^~~~~~~
cpPmden.cpp:157:24: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare]
for (auto i = 0; i < nsamp; i++) {
~~^~~~~~~
cpPmden.cpp:164:22: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare]
for (auto i=0; i < (nsamp-2); i++) {
~~^~~~~~~~~~~
cpPmden.cpp:193:24: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare]
for (auto i = 0; i < nsamp; i++) {
~~^~~~~~~
cpPmden.cpp:219:26: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare]
for (auto i = 0; i < nsamp; i++) {
~~^~~~~~~
cpPmden.cpp:251:26: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare]
for (auto i = 0; i < nsamp; i++) {
~~^~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cppApprox.cpp -o cppApprox.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cppdip.cpp -o cppdip.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c dynamic_prog.cpp -o dynamic_prog.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fill_SMAWK.cpp -o fill_SMAWK.o
fill_SMAWK.cpp: In function 'void reduce_in_place(int, int, int, int, const std::vector<long long unsigned int>&, std::vector<long long unsigned int>&, const std::vector<std::vector<double> >&, const std::vector<std::vector<long long unsigned int> >&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, DISSIMILARITY)':
fill_SMAWK.cpp:80:8: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<long long unsigned int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
if(N >= js.size()) {
~~^~~~~~~~~~~~
fill_SMAWK.cpp:90:11: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
while(m > N) { // js_reduced has more than N positions / columns
~~^~~
fill_SMAWK.cpp:121:25: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
for(int r=(left+1); r < m; ++r) {
~~^~~
fill_SMAWK.cpp: In function 'void fill_even_positions(int, int, int, int, const std::vector<long long unsigned int>&, std::vector<std::vector<double> >&, std::vector<std::vector<long long unsigned int> >&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, DISSIMILARITY)':
fill_SMAWK.cpp:164:17: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
for(++ r; r < n && js[r]<=jmax; r++) {
~~^~~
fill_SMAWK.cpp:164:29: warning: comparison of integer expressions of different signedness: 'const value_type' {aka 'const long long unsigned int'} and 'int' [-Wsign-compare]
for(++ r; r < n && js[r]<=jmax; r++) {
fill_SMAWK.cpp:168:15: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long long unsigned int'} and 'int' [-Wsign-compare]
if(jabs > i) break;
~~~~~^~~
fill_SMAWK.cpp: In function 'void find_min_from_candidates(int, int, int, int, const std::vector<long long unsigned int>&, std::vector<std::vector<double> >&, std::vector<std::vector<long long unsigned int> >&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, DISSIMILARITY)':
fill_SMAWK.cpp:218:16: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long long unsigned int'} and 'int' [-Wsign-compare]
if(j_abs > i) break;
~~~~~~^~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c getTautStringApprox.cpp -o getTautStringApprox.o
getTautStringApprox.cpp: In function 'Rcpp::List getTautStringApprox(std::vector<double>)':
getTautStringApprox.cpp:32:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
for (int i = 1; i != fullString.size(); ++i) {
~~^~~~~~~~~~~~~~~~~~~~
getTautStringApprox.cpp:56:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<stringPairs>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
for (int i = 0; i != plotSpecs.size(); ++i) {
~~^~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c kMedDP.cpp -o kMedDP.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c kkuiper.cpp -o kkuiper.o
kkuiper.cpp: In function 'void difficultmax(std::vector<double>&, long int, long int, long int, long int*, long int*, double*)':
kkuiper.cpp:77:10: warning: variable 'min' set but not used [-Wunused-but-set-variable]
double min, max;
^~~
kkuiper.cpp: In function 'void easymax(std::vector<double>&, long int, long int, long int, long int*, long int*, double*)':
kkuiper.cpp:64:10: warning: 'maxi' may be used uninitialized in this function [-Wmaybe-uninitialized]
*erga=maxi;
~~~~~^~~~~
kkuiper.cpp:63:10: warning: 'mini' may be used uninitialized in this function [-Wmaybe-uninitialized]
*ergb=mini;
~~~~~^~~~~
kkuiper.cpp: In function 'void difficultmax(std::vector<double>&, long int, long int, long int, long int*, long int*, double*)':
kkuiper.cpp:161:23: warning: 'maxi' may be used uninitialized in this function [-Wmaybe-uninitialized]
*erga=minis[maxi];
^
kkuiper.cpp: In function 'std::vector<double> kkuiper(std::vector<double>&, long int, int)':
kkuiper.cpp:64:10: warning: 'maxi' may be used uninitialized in this function [-Wmaybe-uninitialized]
*erga=maxi;
~~~~~^~~~~
kkuiper.cpp:44:15: note: 'maxi' was declared here
long i,mini,maxi;
^~~~
kkuiper.cpp:63:10: warning: 'mini' may be used uninitialized in this function [-Wmaybe-uninitialized]
*ergb=mini;
~~~~~^~~~~
kkuiper.cpp:44:10: note: 'mini' was declared here
long i,mini,maxi;
^~~~
kkuiper.cpp:64:10: warning: 'maxi' may be used uninitialized in this function [-Wmaybe-uninitialized]
*erga=maxi;
~~~~~^~~~~
kkuiper.cpp:44:15: note: 'maxi' was declared here
long i,mini,maxi;
^~~~
kkuiper.cpp:63:10: warning: 'mini' may be used uninitialized in this function [-Wmaybe-uninitialized]
*ergb=mini;
~~~~~^~~~~
kkuiper.cpp:44:10: note: 'mini' was declared here
long i,mini,maxi;
^~~~
kkuiper.cpp:58:3: warning: 'maxi' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(mini<maxi) {
^~
kkuiper.cpp:44:15: note: 'maxi' was declared here
long i,mini,maxi;
^~~~
kkuiper.cpp:58:3: warning: 'mini' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(mini<maxi) {
^~
kkuiper.cpp:44:10: note: 'mini' was declared here
long i,mini,maxi;
^~~~
kkuiper.cpp:197:9: warning: 'maxi' may be used uninitialized in this function [-Wmaybe-uninitialized]
a[0]=maxi;
kkuiper.cpp:196:9: warning: 'mini' may be used uninitialized in this function [-Wmaybe-uninitialized]
b[0]=mini;
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c local_density.cpp -o local_density.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c medianAbsoluteDeviation.cpp -o medianAbsoluteDeviation.o
medianAbsoluteDeviation.cpp: In function 'double medianAbsoluteDeviation(const std::vector<double>&)':
medianAbsoluteDeviation.cpp:28:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
for (auto i = 0; i != devs.size(); ++i)
~~^~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c misc.cpp -o misc.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rQuantile.cpp -o rQuantile.o
rQuantile.cpp: In function 'std::vector<double> rQuantile(const std::vector<double>&, std::vector<double>)':
rQuantile.cpp:35:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
for (auto i = 0; i != lowInd.size(); ++i) {
~~^~~~~~~~~~~~~~~~
rQuantile.cpp:41:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
for (auto i = 0; i != lowInd.size(); ++i) {
~~^~~~~~~~~~~~~~~~
rQuantile.cpp:47:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<bool>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
for (auto i = 0; i != offSet.size(); ++i)
~~^~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c singleDip.cpp -o singleDip.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c tautstring.cpp -o tautstring.o
tautstring.cpp: In function 'stringInfo tautString(const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, double, double, long int, int)':
tautstring.cpp:148:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
for (auto i = 0; i < knotst.size(); i++) {
~~^~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c tsGates.cpp -o tsGates.o
tsGates.cpp: In function 'std::vector<double> findKmedGates(const std::vector<double>&, const std::vector<int>&, int)':
tsGates.cpp:41:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
for (auto j = 0; j != classVector.size(); j++)
~~^~~~~~~~~~~~~~~~~~~~~
tsGates.cpp: In function 'std::vector<double> tsGates(const std::vector<double>&, int)':
tsGates.cpp:81:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<bool>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
for (auto i = 1; i != (localMins.size()-1); ++i) {
~~^~~~~~~~~~~~~~~~~~~~~~~
tsGates.cpp:86:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
for (auto i = 0; i != yvals.size(); ++i)
~~^~~~~~~~~~~~~~~
tsGates.cpp:96:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
for (auto j = 0; j != cutValues.size(); ++j) {
~~^~~~~~~~~~~~~~~~~~~
tsGates.cpp:99:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
for (auto i = 0; i != ys.size(); ++i)
~~^~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c unlockNamespace.c -o unlockNamespace.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o openCyto.dll tmp.def RcppExports.o cpPmden.o cppApprox.o cppdip.o dynamic_prog.o fill_SMAWK.o getTautStringApprox.o kMedDP.o kkuiper.o local_density.o medianAbsoluteDeviation.o misc.o rQuantile.o singleDip.o tautstring.o tsGates.o unlockNamespace.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/openCyto.buildbin-libdir/openCyto/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'openCyto' as openCyto_2.2.0.zip
* DONE (openCyto)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'openCyto' successfully unpacked and MD5 sums checked
