openCyto 2.0.0
Mike Jiang ,Jake Wagner
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/openCyto |
| Branch: RELEASE_3_11 |
| Last Commit: 74d58ec |
| Last Changed Date: 2020-04-27 14:37:01 -0400 (Mon, 27 Apr 2020) |
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | WARNINGS | OK | |
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/openCyto_2.0.0.tar.gz && rm -rf openCyto.buildbin-libdir && mkdir openCyto.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=openCyto.buildbin-libdir openCyto_2.0.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL openCyto_2.0.0.zip && rm openCyto_2.0.0.tar.gz openCyto_2.0.0.zip
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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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/tmpdir/RtmpYtLNoU/R.INSTALL24083834506c/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-3.11-bioc/tmpdir/RtmpYtLNoU/R.INSTALL24083834506c/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-3.11-bioc/tmpdir/RtmpYtLNoU/R.INSTALL24083834506c/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-3.11-bioc/tmpdir/RtmpYtLNoU/R.INSTALL24083834506c/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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/openCyto.buildbin-libdir/openCyto/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'openCyto' as openCyto_2.0.0.zip
* DONE (openCyto)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'openCyto' successfully unpacked and MD5 sums checked