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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/openCyto_1.24.0.tar.gz && rm -rf openCyto.buildbin-libdir && mkdir openCyto.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=openCyto.buildbin-libdir openCyto_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL openCyto_1.24.0.zip && rm openCyto_1.24.0.tar.gz openCyto_1.24.0.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 481k 100 481k 0 0 4321k 0 --:--:-- --:--:-- --:--:-- 4502k
install for i386
* installing *source* package 'openCyto' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c cpPmden.cpp -o cpPmden.o
cpPmden.cpp: In function 'stringInfo cpPmden(const std::vector<double>&)':
cpPmden.cpp:88:22: warning: comparison between signed and unsigned integer expressions [-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:156:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (auto i = 0; i < nsamp; i++) {
^
cpPmden.cpp:162:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (auto i=0; i < (nsamp-2); i++) {
^
cpPmden.cpp:186:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (auto i = 0; i < nsamp; i++) {
^
cpPmden.cpp:212:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (auto i = 0; i < nsamp; i++) {
^
cpPmden.cpp:244:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (auto i = 0; i < nsamp; i++) {
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c cppApprox.cpp -o cppApprox.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c cppdip.cpp -o cppdip.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c dynamic_prog.cpp -o dynamic_prog.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -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 between signed and unsigned integer expressions [-Wsign-compare]
if(N >= js.size()) {
^
fill_SMAWK.cpp:90:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while(m > N) { // js_reduced has more than N positions / columns
^
fill_SMAWK.cpp:121:25: warning: comparison between signed and unsigned integer expressions [-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 between signed and unsigned integer expressions [-Wsign-compare]
for(++ r; r < n && js[r]<=jmax; r++) {
^
fill_SMAWK.cpp:164:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(++ r; r < n && js[r]<=jmax; r++) {
^
fill_SMAWK.cpp:168:15: warning: comparison between signed and unsigned integer expressions [-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 between signed and unsigned integer expressions [-Wsign-compare]
if(j_abs > i) break;
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c getTautStringApprox.cpp -o getTautStringApprox.o
getTautStringApprox.cpp: In function 'Rcpp::List getTautStringApprox(std::vector<double>)':
getTautStringApprox.cpp:32:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 1; i != fullString.size(); ++i) {
^
getTautStringApprox.cpp:56:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i != plotSpecs.size(); ++i) {
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c kMedDP.cpp -o kMedDP.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -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:64:15: warning: 'maxi' may be used uninitialized in this function [-Wmaybe-uninitialized]
*erga=maxi;
^
kkuiper.cpp:63:15: 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:64:15: 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:63:15: 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:64:15: 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:63:15: 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:242:36: warning: 'maxb' may be used uninitialized in this function [-Wmaybe-uninitialized]
norm[k]=norm[k-1]+std::fabs(x[maxb]-x[maxa]);
^
kkuiper.cpp:242:44: warning: 'maxa' may be used uninitialized in this function [-Wmaybe-uninitialized]
norm[k]=norm[k-1]+std::fabs(x[maxb]-x[maxa]);
^
kkuiper.cpp:197:14: warning: 'maxi' may be used uninitialized in this function [-Wmaybe-uninitialized]
a[0]=maxi;
^
kkuiper.cpp:196:14: warning: 'mini' may be used uninitialized in this function [-Wmaybe-uninitialized]
b[0]=mini;
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c local_density.cpp -o local_density.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c medianAbsoluteDeviation.cpp -o medianAbsoluteDeviation.o
medianAbsoluteDeviation.cpp: In function 'double medianAbsoluteDeviation(const std::vector<double>&)':
medianAbsoluteDeviation.cpp:28:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (auto i = 0; i != devs.size(); ++i)
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c misc.cpp -o misc.o
misc.cpp: In function 'Rcpp::NumericMatrix collapseData(Rcpp::List, Rcpp::StringVector)':
misc.cpp:10:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned i = 0; i < mat_list.size(); i++){
^
misc.cpp:21:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned ind = 0; ind < mat_list.size(); ind++){
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -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 between signed and unsigned integer expressions [-Wsign-compare]
for (auto i = 0; i != lowInd.size(); ++i) {
^
rQuantile.cpp:41:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (auto i = 0; i != lowInd.size(); ++i) {
^
rQuantile.cpp:47:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (auto i = 0; i != offSet.size(); ++i)
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c singleDip.cpp -o singleDip.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -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 between signed and unsigned integer expressions [-Wsign-compare]
for (auto i = 0; i < knotst.size(); i++) {
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -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 between signed and unsigned integer expressions [-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 between signed and unsigned integer expressions [-Wsign-compare]
for (auto i = 1; i != (localMins.size()-1); ++i) {
^
tsGates.cpp:86:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (auto i = 0; i != yvals.size(); ++i)
^
tsGates.cpp:96:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (auto j = 0; j != cutValues.size(); ++j) {
^
tsGates.cpp:99:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (auto i = 0; i != ys.size(); ++i)
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c unlockNamespace.c -o unlockNamespace.o
C:/Rtools/mingw_32/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-3~1.10-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.10-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
add html
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpSIaAaw/R.INSTALL89834b64edc/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-3.10-bioc/tmpdir/RtmpSIaAaw/R.INSTALL89834b64edc/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-3.10-bioc/tmpdir/RtmpSIaAaw/R.INSTALL89834b64edc/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.gatingTemplate 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
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-3.10-bioc/tmpdir/RtmpSIaAaw/R.INSTALL89834b64edc/openCyto/man/gs_add_gating_method.Rd:40: 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
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpSIaAaw/R.INSTALL89834b64edc/openCyto/man/openCyto.Rd:28: missing file link 'gating-methods'
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
tautstring 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:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c cpPmden.cpp -o cpPmden.o
cpPmden.cpp: In function 'stringInfo cpPmden(const std::vector<double>&)':
cpPmden.cpp:88:22: warning: comparison between signed and unsigned integer expressions [-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:156:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (auto i = 0; i < nsamp; i++) {
^
cpPmden.cpp:162:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (auto i=0; i < (nsamp-2); i++) {
^
cpPmden.cpp:186:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (auto i = 0; i < nsamp; i++) {
^
cpPmden.cpp:212:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (auto i = 0; i < nsamp; i++) {
^
cpPmden.cpp:244:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (auto i = 0; i < nsamp; i++) {
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c cppApprox.cpp -o cppApprox.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c cppdip.cpp -o cppdip.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c dynamic_prog.cpp -o dynamic_prog.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -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 between signed and unsigned integer expressions [-Wsign-compare]
if(N >= js.size()) {
^
fill_SMAWK.cpp:90:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while(m > N) { // js_reduced has more than N positions / columns
^
fill_SMAWK.cpp:121:25: warning: comparison between signed and unsigned integer expressions [-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 between signed and unsigned integer expressions [-Wsign-compare]
for(++ r; r < n && js[r]<=jmax; r++) {
^
fill_SMAWK.cpp:164:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(++ r; r < n && js[r]<=jmax; r++) {
^
fill_SMAWK.cpp:168:15: warning: comparison between signed and unsigned integer expressions [-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 between signed and unsigned integer expressions [-Wsign-compare]
if(j_abs > i) break;
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c getTautStringApprox.cpp -o getTautStringApprox.o
getTautStringApprox.cpp: In function 'Rcpp::List getTautStringApprox(std::vector<double>)':
getTautStringApprox.cpp:32:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 1; i != fullString.size(); ++i) {
^
getTautStringApprox.cpp:56:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i != plotSpecs.size(); ++i) {
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c kMedDP.cpp -o kMedDP.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -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:64:15: warning: 'maxi' may be used uninitialized in this function [-Wmaybe-uninitialized]
*erga=maxi;
^
kkuiper.cpp:63:15: 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:64:15: 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:63:15: 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:64:15: 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:63:15: 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:242:36: warning: 'maxb' may be used uninitialized in this function [-Wmaybe-uninitialized]
norm[k]=norm[k-1]+std::fabs(x[maxb]-x[maxa]);
^
kkuiper.cpp:242:44: warning: 'maxa' may be used uninitialized in this function [-Wmaybe-uninitialized]
norm[k]=norm[k-1]+std::fabs(x[maxb]-x[maxa]);
^
kkuiper.cpp:197:14: warning: 'maxi' may be used uninitialized in this function [-Wmaybe-uninitialized]
a[0]=maxi;
^
kkuiper.cpp:196:14: warning: 'mini' may be used uninitialized in this function [-Wmaybe-uninitialized]
b[0]=mini;
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c local_density.cpp -o local_density.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c medianAbsoluteDeviation.cpp -o medianAbsoluteDeviation.o
medianAbsoluteDeviation.cpp: In function 'double medianAbsoluteDeviation(const std::vector<double>&)':
medianAbsoluteDeviation.cpp:28:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (auto i = 0; i != devs.size(); ++i)
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c misc.cpp -o misc.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -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 between signed and unsigned integer expressions [-Wsign-compare]
for (auto i = 0; i != lowInd.size(); ++i) {
^
rQuantile.cpp:41:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (auto i = 0; i != lowInd.size(); ++i) {
^
rQuantile.cpp:47:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (auto i = 0; i != offSet.size(); ++i)
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c singleDip.cpp -o singleDip.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -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 between signed and unsigned integer expressions [-Wsign-compare]
for (auto i = 0; i < knotst.size(); i++) {
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -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 between signed and unsigned integer expressions [-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 between signed and unsigned integer expressions [-Wsign-compare]
for (auto i = 1; i != (localMins.size()-1); ++i) {
^
tsGates.cpp:86:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (auto i = 0; i != yvals.size(); ++i)
^
tsGates.cpp:96:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (auto j = 0; j != cutValues.size(); ++j) {
^
tsGates.cpp:99:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (auto i = 0; i != ys.size(); ++i)
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c unlockNamespace.c -o unlockNamespace.o
C:/Rtools/mingw_64/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-3~1.10-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/openCyto.buildbin-libdir/openCyto/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'openCyto' as openCyto_1.24.0.zip
* DONE (openCyto)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'openCyto' successfully unpacked and MD5 sums checked
