##############################################################################
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###
### Running command:
###
### rm -rf scater.buildbin-libdir && mkdir scater.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=scater.buildbin-libdir scater_1.10.1.tar.gz
###
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install for i386
* installing *source* package 'scater' ...
** libs
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c calc_exprs.cpp -o calc_exprs.o
calc_exprs.cpp: In instantiation of 'normalizer<V, M>::normalizer(M, Rcpp::List, Rcpp::IntegerVector, Rcpp::RObject) [with V = Rcpp::Vector<13>; M = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; Rcpp::List = Rcpp::Vector<19>; Rcpp::IntegerVector = Rcpp::Vector<13>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
calc_exprs.cpp:86:64: required from 'Rcpp::RObject norm_exprs_internal(M, Rcpp::List, Rcpp::IntegerVector, Rcpp::RObject, Rcpp::RObject, Rcpp::RObject) [with V = Rcpp::Vector<13>; M = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; Rcpp::List = Rcpp::Vector<19>; Rcpp::IntegerVector = Rcpp::Vector<13>]'
calc_exprs.cpp:126:110: required from here
calc_exprs.cpp:14:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (i < 0 || i >= nsets) {
^
calc_exprs.cpp:29:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (current.size() != ncells) {
^
calc_exprs.cpp:41:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (set_id.size()!=ptr->get_nrow()) {
^
calc_exprs.cpp: In instantiation of 'normalizer<V, M>::normalizer(M, Rcpp::List, Rcpp::IntegerVector, Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; Rcpp::List = Rcpp::Vector<19>; Rcpp::IntegerVector = Rcpp::Vector<13>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
calc_exprs.cpp:86:64: required from 'Rcpp::RObject norm_exprs_internal(M, Rcpp::List, Rcpp::IntegerVector, Rcpp::RObject, Rcpp::RObject, Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; Rcpp::List = Rcpp::Vector<19>; Rcpp::IntegerVector = Rcpp::Vector<13>]'
calc_exprs.cpp:129:110: required from here
calc_exprs.cpp:14:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (i < 0 || i >= nsets) {
^
calc_exprs.cpp:29:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (current.size() != ncells) {
^
calc_exprs.cpp:41:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (set_id.size()!=ptr->get_nrow()) {
^
In file included from C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:238:0,
from C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
from scater.h:5,
from calc_exprs.cpp:1:
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h: In instantiation of 'beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; beachmat::const_col_indexed_info<V> = std::tuple<unsigned int, int*, double*>; typename V::iterator = double*; size_t = unsigned int; typename V::iterator = double*]':
calc_exprs.cpp:172:1: required from here
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (indices.size()!=this->get_nrow()) {
^
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h: In instantiation of 'beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<13>; beachmat::const_col_indexed_info<V> = std::tuple<unsigned int, int*, int*>; typename V::iterator = int*; size_t = unsigned int; typename V::iterator = int*]':
calc_exprs.cpp:172:1: required from here
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c combined_qc.cpp -o combined_qc.o
combined_qc.cpp: In function 'void check_topset(const IntegerVector&)':
combined_qc.cpp:6:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t t=1; t<top.size(); ++t) {
^
combined_qc.cpp: In instantiation of 'void compute_cumsum(typename V::iterator, size_t, const IntegerVector&, IT) [with T = int; V = Rcpp::Vector<13>; IT = double*; typename V::iterator = int*; size_t = unsigned int; Rcpp::IntegerVector = Rcpp::Vector<13>]':
combined_qc.cpp:257:77: required from 'SEXPREC* top_cumprop_internal(M, Rcpp::IntegerVector) [with T = int; V = Rcpp::Vector<13>; M = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; SEXP = SEXPREC*; Rcpp::IntegerVector = Rcpp::Vector<13>]'
combined_qc.cpp:269:77: required from here
combined_qc.cpp:26:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while (x<target_index && x<ngenes) { // '<' as top contains 1-based indices.
^
combined_qc.cpp: In instantiation of 'void compute_cumsum(typename V::iterator, size_t, const IntegerVector&, IT) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; IT = double*; typename V::iterator = double*; size_t = unsigned int; Rcpp::IntegerVector = Rcpp::Vector<13>]':
combined_qc.cpp:257:77: required from 'SEXPREC* top_cumprop_internal(M, Rcpp::IntegerVector) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; SEXP = SEXPREC*; Rcpp::IntegerVector = Rcpp::Vector<13>]'
combined_qc.cpp:272:80: required from here
combined_qc.cpp:26:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
In file included from C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:238:0,
from C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
from scater.h:5,
from combined_qc.cpp:1:
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h: In instantiation of 'beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; beachmat::const_col_indexed_info<V> = std::tuple<unsigned int, int*, double*>; typename V::iterator = double*; size_t = unsigned int; typename V::iterator = double*]':
combined_qc.cpp:277:1: required from here
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (indices.size()!=this->get_nrow()) {
^
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h: In instantiation of 'beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<13>; beachmat::const_col_indexed_info<V> = std::tuple<unsigned int, int*, int*>; typename V::iterator = int*; size_t = unsigned int; typename V::iterator = int*]':
combined_qc.cpp:277:1: required from here
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c init.cpp -o init.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c num_exprs.cpp -o num_exprs.o
In file included from C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:238:0,
from C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
from scater.h:5,
from num_exprs.cpp:1:
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h: In instantiation of 'beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; beachmat::const_col_indexed_info<V> = std::tuple<unsigned int, int*, double*>; typename V::iterator = double*; size_t = unsigned int; typename V::iterator = double*]':
num_exprs.cpp:137:1: required from here
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (indices.size()!=this->get_nrow()) {
^
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h: In instantiation of 'beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<13>; beachmat::const_col_indexed_info<V> = std::tuple<unsigned int, int*, int*>; typename V::iterator = int*; size_t = unsigned int; typename V::iterator = int*]':
num_exprs.cpp:137:1: required from here
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c sum_counts.cpp -o sum_counts.o
In file included from C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:238:0,
from C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
from scater.h:5,
from sum_counts.cpp:1:
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h: In instantiation of 'beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; beachmat::const_col_indexed_info<V> = std::tuple<unsigned int, int*, double*>; typename V::iterator = double*; size_t = unsigned int; typename V::iterator = double*]':
sum_counts.cpp:61:1: required from here
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (indices.size()!=this->get_nrow()) {
^
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h: In instantiation of 'beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<13>; beachmat::const_col_indexed_info<V> = std::tuple<unsigned int, int*, int*>; typename V::iterator = int*; size_t = unsigned int; typename V::iterator = int*]':
sum_counts.cpp:61:1: required from here
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c utils.cpp -o utils.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o scater.dll tmp.def calc_exprs.o combined_qc.o init.o num_exprs.o sum_counts.o utils.o -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/library/beachmat/lib/i386 -lbeachmat -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/library/Rhdf5lib/lib/i386 -lhdf5_cpp -lhdf5 -lszip -lz -lpsapi -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/scater.buildbin-libdir/scater/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'mutate' in package 'scater'
Creating a new generic function for 'filter' in package 'scater'
** help
*** installing help indices
converting help for package 'scater'
finding HTML links ... done
SCESet html
accessors html
finding level-2 HTML links ... done
arrange html
bootstraps html
calcIsExprs html
calculateAverage html
calculateCPM html
calculateFPKM html
calculateQCMetrics html
calculateTPM html
centreSizeFactors html
filter html
getBMFeatureAnnos html
getExplanatoryPCs html
getVarianceExplained html
isOutlier html
librarySizeFactors html
multiplot html
mutate html
nexprs html
normalize html
normalizeCounts html
plotColData html
plotExplanatoryPCs html
plotExplanatoryVariables html
plotExpression html
plotExprsFreqVsMean html
plotExprsVsTxLength html
plotHeatmap html
plotHighestExprs html
plotPlatePosition html
plotQC html
plotRLE html
plotReducedDim html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpEXgkMi/R.INSTALL30a44feb460a/scater/man/plotReducedDim.Rd:21: file link 'plotPCA' in package 'scater' does not exist and so has been treated as a topic
plotRowData html
plotScater html
plot_reddim html
readSparseCounts html
readTxResults html
rename html
runDiffusionMap html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpEXgkMi/R.INSTALL30a44feb460a/scater/man/runDiffusionMap.Rd:26: file link 'DiffusionMap' in package 'destiny' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpEXgkMi/R.INSTALL30a44feb460a/scater/man/runDiffusionMap.Rd:34: file link 'DiffusionMap' in package 'destiny' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpEXgkMi/R.INSTALL30a44feb460a/scater/man/runDiffusionMap.Rd:44: file link 'DiffusionMap' in package 'destiny' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpEXgkMi/R.INSTALL30a44feb460a/scater/man/runDiffusionMap.Rd:49: file link 'DiffusionMap' in package 'destiny' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpEXgkMi/R.INSTALL30a44feb460a/scater/man/runDiffusionMap.Rd:71: file link 'plotDiffusionMap' in package 'scater' does not exist and so has been treated as a topic
runMDS html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpEXgkMi/R.INSTALL30a44feb460a/scater/man/runMDS.Rd:62: file link 'plotMDS' in package 'scater' does not exist and so has been treated as a topic
runPCA html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpEXgkMi/R.INSTALL30a44feb460a/scater/man/runPCA.Rd:90: file link 'plotPCA' in package 'scater' does not exist and so has been treated as a topic
runTSNE html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpEXgkMi/R.INSTALL30a44feb460a/scater/man/runTSNE.Rd:82: file link 'plotTSNE' in package 'scater' does not exist and so has been treated as a topic
runUMAP html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpEXgkMi/R.INSTALL30a44feb460a/scater/man/runUMAP.Rd:69: file link 'plotUMAP' in package 'scater' does not exist and so has been treated as a topic
sc_example_cell_info html
sc_example_counts html
scater-package html
scater-plot-args html
scater-vis-var html
sumCountsAcrossFeatures html
summariseExprsAcrossFeatures html
toSingleCellExperiment html
uniquifyFeatureNames html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'scater' ...
** libs
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c calc_exprs.cpp -o calc_exprs.o
calc_exprs.cpp: In instantiation of 'normalizer<V, M>::normalizer(M, Rcpp::List, Rcpp::IntegerVector, Rcpp::RObject) [with V = Rcpp::Vector<13>; M = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; Rcpp::List = Rcpp::Vector<19>; Rcpp::IntegerVector = Rcpp::Vector<13>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
calc_exprs.cpp:86:64: required from 'Rcpp::RObject norm_exprs_internal(M, Rcpp::List, Rcpp::IntegerVector, Rcpp::RObject, Rcpp::RObject, Rcpp::RObject) [with V = Rcpp::Vector<13>; M = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; Rcpp::List = Rcpp::Vector<19>; Rcpp::IntegerVector = Rcpp::Vector<13>]'
calc_exprs.cpp:126:110: required from here
calc_exprs.cpp:14:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (i < 0 || i >= nsets) {
^
calc_exprs.cpp:29:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (current.size() != ncells) {
^
calc_exprs.cpp:41:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (set_id.size()!=ptr->get_nrow()) {
^
calc_exprs.cpp: In instantiation of 'normalizer<V, M>::normalizer(M, Rcpp::List, Rcpp::IntegerVector, Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; Rcpp::List = Rcpp::Vector<19>; Rcpp::IntegerVector = Rcpp::Vector<13>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
calc_exprs.cpp:86:64: required from 'Rcpp::RObject norm_exprs_internal(M, Rcpp::List, Rcpp::IntegerVector, Rcpp::RObject, Rcpp::RObject, Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; Rcpp::List = Rcpp::Vector<19>; Rcpp::IntegerVector = Rcpp::Vector<13>]'
calc_exprs.cpp:129:110: required from here
calc_exprs.cpp:14:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (i < 0 || i >= nsets) {
^
calc_exprs.cpp:29:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (current.size() != ncells) {
^
calc_exprs.cpp:41:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (set_id.size()!=ptr->get_nrow()) {
^
In file included from C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:238:0,
from C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
from scater.h:5,
from calc_exprs.cpp:1:
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h: In instantiation of 'beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; beachmat::const_col_indexed_info<V> = std::tuple<long long unsigned int, int*, double*>; typename V::iterator = double*; size_t = long long unsigned int; typename V::iterator = double*]':
calc_exprs.cpp:172:1: required from here
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (indices.size()!=this->get_nrow()) {
^
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h: In instantiation of 'beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<13>; beachmat::const_col_indexed_info<V> = std::tuple<long long unsigned int, int*, int*>; typename V::iterator = int*; size_t = long long unsigned int; typename V::iterator = int*]':
calc_exprs.cpp:172:1: required from here
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c combined_qc.cpp -o combined_qc.o
combined_qc.cpp: In function 'void check_topset(const IntegerVector&)':
combined_qc.cpp:6:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t t=1; t<top.size(); ++t) {
^
combined_qc.cpp: In instantiation of 'void compute_cumsum(typename V::iterator, size_t, const IntegerVector&, IT) [with T = int; V = Rcpp::Vector<13>; IT = double*; typename V::iterator = int*; size_t = long long unsigned int; Rcpp::IntegerVector = Rcpp::Vector<13>]':
combined_qc.cpp:257:77: required from 'SEXPREC* top_cumprop_internal(M, Rcpp::IntegerVector) [with T = int; V = Rcpp::Vector<13>; M = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; SEXP = SEXPREC*; Rcpp::IntegerVector = Rcpp::Vector<13>]'
combined_qc.cpp:269:77: required from here
combined_qc.cpp:26:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while (x<target_index && x<ngenes) { // '<' as top contains 1-based indices.
^
combined_qc.cpp: In instantiation of 'void compute_cumsum(typename V::iterator, size_t, const IntegerVector&, IT) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; IT = double*; typename V::iterator = double*; size_t = long long unsigned int; Rcpp::IntegerVector = Rcpp::Vector<13>]':
combined_qc.cpp:257:77: required from 'SEXPREC* top_cumprop_internal(M, Rcpp::IntegerVector) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; SEXP = SEXPREC*; Rcpp::IntegerVector = Rcpp::Vector<13>]'
combined_qc.cpp:272:80: required from here
combined_qc.cpp:26:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
In file included from C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:238:0,
from C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
from scater.h:5,
from combined_qc.cpp:1:
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h: In instantiation of 'beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; beachmat::const_col_indexed_info<V> = std::tuple<long long unsigned int, int*, double*>; typename V::iterator = double*; size_t = long long unsigned int; typename V::iterator = double*]':
combined_qc.cpp:277:1: required from here
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (indices.size()!=this->get_nrow()) {
^
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h: In instantiation of 'beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<13>; beachmat::const_col_indexed_info<V> = std::tuple<long long unsigned int, int*, int*>; typename V::iterator = int*; size_t = long long unsigned int; typename V::iterator = int*]':
combined_qc.cpp:277:1: required from here
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c init.cpp -o init.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c num_exprs.cpp -o num_exprs.o
In file included from C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:238:0,
from C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
from scater.h:5,
from num_exprs.cpp:1:
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h: In instantiation of 'beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; beachmat::const_col_indexed_info<V> = std::tuple<long long unsigned int, int*, double*>; typename V::iterator = double*; size_t = long long unsigned int; typename V::iterator = double*]':
num_exprs.cpp:137:1: required from here
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (indices.size()!=this->get_nrow()) {
^
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h: In instantiation of 'beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<13>; beachmat::const_col_indexed_info<V> = std::tuple<long long unsigned int, int*, int*>; typename V::iterator = int*; size_t = long long unsigned int; typename V::iterator = int*]':
num_exprs.cpp:137:1: required from here
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c sum_counts.cpp -o sum_counts.o
In file included from C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:238:0,
from C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
from scater.h:5,
from sum_counts.cpp:1:
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h: In instantiation of 'beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; beachmat::const_col_indexed_info<V> = std::tuple<long long unsigned int, int*, double*>; typename V::iterator = double*; size_t = long long unsigned int; typename V::iterator = double*]':
sum_counts.cpp:61:1: required from here
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (indices.size()!=this->get_nrow()) {
^
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h: In instantiation of 'beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<13>; beachmat::const_col_indexed_info<V> = std::tuple<long long unsigned int, int*, int*>; typename V::iterator = int*; size_t = long long unsigned int; typename V::iterator = int*]':
sum_counts.cpp:61:1: required from here
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c utils.cpp -o utils.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o scater.dll tmp.def calc_exprs.o combined_qc.o init.o num_exprs.o sum_counts.o utils.o -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/library/beachmat/lib/x64 -lbeachmat -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/library/Rhdf5lib/lib/x64 -lhdf5_cpp -lhdf5 -lszip -lz -lpsapi -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/scater.buildbin-libdir/scater/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'scater' as scater_1.10.1.zip
* DONE (scater)
In R CMD INSTALL
In R CMD INSTALL
