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### Running command:
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### rm -rf scran.buildbin-libdir && mkdir scran.buildbin-libdir && C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.6/bioc/src/contrib/scran_1.6.9.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --library=scran.buildbin-libdir --merge-multiarch scran_1.6.9.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL scran_1.6.9.zip && rm scran_1.6.9.tar.gz scran_1.6.9.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
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 408k 100 408k 0 0 9788k 0 --:--:-- --:--:-- --:--:-- 9.9M
install for i386
* installing *source* package 'scran' ...
** libs
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c build_snn.cpp -o build_snn.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c compute_CV2.cpp -o compute_CV2.o
compute_CV2.cpp: In instantiation of 'SEXPREC* compute_CV2_internal(M, SEXP, SEXP, SEXP) [with M = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; SEXP = SEXPREC*]':
compute_CV2.cpp:78:83: required from here
compute_CV2.cpp:32:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (sizefacs.size()!=ncells) {
^
compute_CV2.cpp: In instantiation of 'SEXPREC* compute_CV2_internal(M, SEXP, SEXP, SEXP) [with M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; SEXP = SEXPREC*]':
compute_CV2.cpp:81:83: required from here
compute_CV2.cpp:32:28: 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˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c compute_rho.cpp -o compute_rho.o
compute_rho.cpp: In function 'SEXPREC* compute_rho(SEXP, SEXP, SEXP, SEXP)':
compute_rho.cpp:216:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (Npairs!=second.size()) {
^
compute_rho.cpp:244:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (g1x < 0 || g1x >= Ngenes) {
^
compute_rho.cpp:247:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (g2x < 0 || g2x >= Ngenes) {
^
compute_rho.cpp: In function 'SEXPREC* combine_corP(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
compute_rho.cpp:348:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (Npairs!=second.size()) {
^
compute_rho.cpp:353:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (Rho.size()!=Npairs) {
^
compute_rho.cpp:358:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (Pval.size()!=Npairs) {
^
compute_rho.cpp:363:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (Limited.size()!=Npairs) {
^
compute_rho.cpp:368:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (Order.size()!=Npairs) {
^
compute_rho.cpp: In instantiation of 'SEXPREC* rank_subset_internal(M, SEXP, SEXP, SEXP, T) [with T = int; V = Rcpp::Vector<13>; M = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; SEXP = SEXPREC*]':
compute_rho.cpp:190:117: required from here
compute_rho.cpp:171:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int cs=0; cs<cslen; ++cs, ++iIt){
^
compute_rho.cpp: In instantiation of 'SEXPREC* rank_subset_internal(M, SEXP, SEXP, SEXP, T) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; SEXP = SEXPREC*]':
compute_rho.cpp:198:120: required from here
compute_rho.cpp:171:26: 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˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c find_mutual_nns.cpp -o find_mutual_nns.o
find_mutual_nns.cpp: In function 'SEXPREC* smooth_gaussian_kernel(SEXP, SEXP, SEXP, SEXP)':
find_mutual_nns.cpp:128:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (i >= averages.size() || averages[i].empty()) {
^
find_mutual_nns.cpp:129:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (i >= averages.size()) {
^
find_mutual_nns.cpp: In function 'SEXPREC* adjust_shift_variance(SEXP, SEXP, SEXP, SEXP)':
find_mutual_nns.cpp:253:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (ngenes!=_data2.nrow() || ngenes!=_vect.ncol()) {
^
find_mutual_nns.cpp:253:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (ngenes!=_data2.nrow() || ngenes!=_vect.ncol()) {
^
find_mutual_nns.cpp:257:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (ncells2!=_vect.nrow()) {
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c fit_linear_model.cpp -o fit_linear_model.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c forge_system.cpp -o forge_system.o
forge_system.cpp: In function 'SEXPREC* forge_system(SEXP, SEXP, SEXP, SEXP)':
forge_system.cpp:136:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (SIZE < 1 || SIZE > ncells) { throw std::runtime_error("each element of sizes should be within [1, number of cells]"); }
^
forge_system.cpp:144:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (ngenes!=pseudo_cell.size()) { throw std::runtime_error("length of pseudo-cell vector is not the same as the number of cells"); }
^
forge_system.cpp:148:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (order.size() < ncells*2-1) { throw std::runtime_error("ordering vector is too short for number of cells"); }
^
forge_system.cpp:150:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (o < 0 || o > ncells) {
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c get_residuals.cpp -o get_residuals.o
get_residuals.cpp: In function 'SEXPREC* get_residuals(SEXP, SEXP, SEXP, SEXP, SEXP)':
get_residuals.cpp:43:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int c=0; c<ncells; ++c, ++tIt) {
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c get_scaled_ranks.cpp -o get_scaled_ranks.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c overlap_exprs.cpp -o overlap_exprs.o
overlap_exprs.cpp: In instantiation of 'SEXPREC* overlap_exprs_internal(M, const List&, SEXP, T) [with T = int; V = Rcpp::Vector<13>; M = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; SEXP = SEXPREC*; Rcpp::List = Rcpp::Vector<19>]':
overlap_exprs.cpp:141:99: required from here
overlap_exprs.cpp:63:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int j=0; j<ngroups; ++j, ++counter) {
^
overlap_exprs.cpp:65:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (i!=j) {
^
overlap_exprs.cpp: In instantiation of 'SEXPREC* overlap_exprs_internal(M, const List&, SEXP, T) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; SEXP = SEXPREC*; Rcpp::List = Rcpp::Vector<19>]':
overlap_exprs.cpp:148:102: required from here
overlap_exprs.cpp:63:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int j=0; j<ngroups; ++j, ++counter) {
^
overlap_exprs.cpp:65:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (i!=j) {
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c run_dormqr.cpp -o run_dormqr.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c shuffle_scores.cpp -o shuffle_scores.o
shuffle_scores.cpp: In instantiation of 'SEXPREC* shuffle_scores_internal(M, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector) [with V = Rcpp::Vector<13>; M = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; SEXP = SEXPREC*; Rcpp::IntegerVector = Rcpp::Vector<13>]':
shuffle_scores.cpp:96:130: required from here
shuffle_scores.cpp:28:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (npairs!=marker2.size()) { throw std::runtime_error("vectors of markers must be of the same length"); }
^
shuffle_scores.cpp:42:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (m1m >= nused || m1m < 0) { throw std::runtime_error("first marker indices are out of range"); }
^
shuffle_scores.cpp:44:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (m2m >= nused || m2m < 0) { throw std::runtime_error("second marker indices are out of range"); }
^
shuffle_scores.cpp:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (usedex >= ngenes || usedex < 0) { throw std::runtime_error("used gene indices are out of range"); }
^
shuffle_scores.cpp: In instantiation of 'SEXPREC* shuffle_scores_internal(M, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; SEXP = SEXPREC*; Rcpp::IntegerVector = Rcpp::Vector<13>]':
shuffle_scores.cpp:99:130: required from here
shuffle_scores.cpp:28:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (npairs!=marker2.size()) { throw std::runtime_error("vectors of markers must be of the same length"); }
^
shuffle_scores.cpp:42:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (m1m >= nused || m1m < 0) { throw std::runtime_error("first marker indices are out of range"); }
^
shuffle_scores.cpp:44:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (m2m >= nused || m2m < 0) { throw std::runtime_error("second marker indices are out of range"); }
^
shuffle_scores.cpp:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (usedex >= ngenes || usedex < 0) { throw std::runtime_error("used gene indices are out of range"); }
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c sum_spikes.cpp -o sum_spikes.o
sum_spikes.cpp: In instantiation of 'SEXPREC* sum_spikes_internal(M, Rcpp::IntegerVector) [with V = Rcpp::Vector<13>; M = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; SEXP = SEXPREC*; Rcpp::IntegerVector = Rcpp::Vector<13>]':
sum_spikes.cpp:32:76: required from here
sum_spikes.cpp:9:49: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (curdex <= last || curdex<0 || curdex>=ngenes) {
^
sum_spikes.cpp: In instantiation of 'SEXPREC* sum_spikes_internal(M, Rcpp::IntegerVector) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; SEXP = SEXPREC*; Rcpp::IntegerVector = Rcpp::Vector<13>]':
sum_spikes.cpp:35:76: required from here
sum_spikes.cpp:9:49: 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˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c utils.cpp -o utils.o
utils.cpp: In function 'Rcpp::IntegerVector check_subset_vector(SEXP, size_t)':
utils.cpp:6:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (*sIt < 0 || *sIt>=len) {
^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o scran.dll tmp.def build_snn.o compute_CV2.o compute_rho.o find_mutual_nns.o fit_linear_model.o forge_system.o get_residuals.o get_scaled_ranks.o init.o overlap_exprs.o run_dormqr.o shuffle_scores.o sum_spikes.o utils.o -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/library/beachmat/lib/i386 -lbeachmat -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/library/Rhdf5lib/lib/i386 -lhdf5_cpp -lhdf5 -lszip -lz -lpsapi -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/scran.buildbin-libdir/scran/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'scran'
finding HTML links ... done
DM html
buildSNNGraph html
combineVar html
computeSpikeFactors html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpQP4U4u/R.INSTALL158852e8df4/scran/man/computeSpikeFactors.Rd:34: missing file link 'normalize,SingleCellExperiment-method'
computeSumFactors html
convertTo html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpQP4U4u/R.INSTALL158852e8df4/scran/man/convertTo.Rd:72: missing file link 'DESeqDataSetFromMatrix'
correlatePairs html
finding level-2 HTML links ... done
cyclone html
decomposeVar html
denoisePCA html
exploreData html
findMarkers html
improvedCV2 html
mnnCorrect html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpQP4U4u/R.INSTALL158852e8df4/scran/man/mnnCorrect.Rd:115: missing file link 'get.knnx'
overlapExprs html
quickCluster html
sandbag html
selectorPlot html
technicalCV2 html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpQP4U4u/R.INSTALL158852e8df4/scran/man/technicalCV2.Rd:33: missing file link 'glmgam.fit'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpQP4U4u/R.INSTALL158852e8df4/scran/man/technicalCV2.Rd:79: missing file link 'glmgam.fit'
testVar html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpQP4U4u/R.INSTALL158852e8df4/scran/man/testVar.Rd:50: missing file link 'fitFDistRobustly'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpQP4U4u/R.INSTALL158852e8df4/scran/man/testVar.Rd:63: missing file link 'fitFDistRobustly'
trendVar html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'scran' ...
** libs
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c build_snn.cpp -o build_snn.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c compute_CV2.cpp -o compute_CV2.o
compute_CV2.cpp: In instantiation of 'SEXPREC* compute_CV2_internal(M, SEXP, SEXP, SEXP) [with M = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; SEXP = SEXPREC*]':
compute_CV2.cpp:78:83: required from here
compute_CV2.cpp:32:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (sizefacs.size()!=ncells) {
^
compute_CV2.cpp: In instantiation of 'SEXPREC* compute_CV2_internal(M, SEXP, SEXP, SEXP) [with M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; SEXP = SEXPREC*]':
compute_CV2.cpp:81:83: required from here
compute_CV2.cpp:32:28: 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˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c compute_rho.cpp -o compute_rho.o
compute_rho.cpp: In function 'SEXPREC* compute_rho(SEXP, SEXP, SEXP, SEXP)':
compute_rho.cpp:216:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (Npairs!=second.size()) {
^
compute_rho.cpp:244:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (g1x < 0 || g1x >= Ngenes) {
^
compute_rho.cpp:247:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (g2x < 0 || g2x >= Ngenes) {
^
compute_rho.cpp: In function 'SEXPREC* combine_corP(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
compute_rho.cpp:348:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (Npairs!=second.size()) {
^
compute_rho.cpp:353:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (Rho.size()!=Npairs) {
^
compute_rho.cpp:358:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (Pval.size()!=Npairs) {
^
compute_rho.cpp:363:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (Limited.size()!=Npairs) {
^
compute_rho.cpp:368:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (Order.size()!=Npairs) {
^
compute_rho.cpp: In instantiation of 'SEXPREC* rank_subset_internal(M, SEXP, SEXP, SEXP, T) [with T = int; V = Rcpp::Vector<13>; M = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; SEXP = SEXPREC*]':
compute_rho.cpp:190:117: required from here
compute_rho.cpp:171:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int cs=0; cs<cslen; ++cs, ++iIt){
^
compute_rho.cpp: In instantiation of 'SEXPREC* rank_subset_internal(M, SEXP, SEXP, SEXP, T) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; SEXP = SEXPREC*]':
compute_rho.cpp:198:120: required from here
compute_rho.cpp:171:26: 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˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c find_mutual_nns.cpp -o find_mutual_nns.o
find_mutual_nns.cpp: In function 'SEXPREC* smooth_gaussian_kernel(SEXP, SEXP, SEXP, SEXP)':
find_mutual_nns.cpp:128:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (i >= averages.size() || averages[i].empty()) {
^
find_mutual_nns.cpp:129:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (i >= averages.size()) {
^
find_mutual_nns.cpp: In function 'SEXPREC* adjust_shift_variance(SEXP, SEXP, SEXP, SEXP)':
find_mutual_nns.cpp:253:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (ngenes!=_data2.nrow() || ngenes!=_vect.ncol()) {
^
find_mutual_nns.cpp:253:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (ngenes!=_data2.nrow() || ngenes!=_vect.ncol()) {
^
find_mutual_nns.cpp:257:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (ncells2!=_vect.nrow()) {
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c fit_linear_model.cpp -o fit_linear_model.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c forge_system.cpp -o forge_system.o
forge_system.cpp: In function 'SEXPREC* forge_system(SEXP, SEXP, SEXP, SEXP)':
forge_system.cpp:136:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (SIZE < 1 || SIZE > ncells) { throw std::runtime_error("each element of sizes should be within [1, number of cells]"); }
^
forge_system.cpp:144:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (ngenes!=pseudo_cell.size()) { throw std::runtime_error("length of pseudo-cell vector is not the same as the number of cells"); }
^
forge_system.cpp:148:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (order.size() < ncells*2-1) { throw std::runtime_error("ordering vector is too short for number of cells"); }
^
forge_system.cpp:150:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (o < 0 || o > ncells) {
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c get_residuals.cpp -o get_residuals.o
get_residuals.cpp: In function 'SEXPREC* get_residuals(SEXP, SEXP, SEXP, SEXP, SEXP)':
get_residuals.cpp:43:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int c=0; c<ncells; ++c, ++tIt) {
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c get_scaled_ranks.cpp -o get_scaled_ranks.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c overlap_exprs.cpp -o overlap_exprs.o
overlap_exprs.cpp: In instantiation of 'SEXPREC* overlap_exprs_internal(M, const List&, SEXP, T) [with T = int; V = Rcpp::Vector<13>; M = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; SEXP = SEXPREC*; Rcpp::List = Rcpp::Vector<19>]':
overlap_exprs.cpp:141:99: required from here
overlap_exprs.cpp:63:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int j=0; j<ngroups; ++j, ++counter) {
^
overlap_exprs.cpp:65:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (i!=j) {
^
overlap_exprs.cpp: In instantiation of 'SEXPREC* overlap_exprs_internal(M, const List&, SEXP, T) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; SEXP = SEXPREC*; Rcpp::List = Rcpp::Vector<19>]':
overlap_exprs.cpp:148:102: required from here
overlap_exprs.cpp:63:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int j=0; j<ngroups; ++j, ++counter) {
^
overlap_exprs.cpp:65:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (i!=j) {
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c run_dormqr.cpp -o run_dormqr.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c shuffle_scores.cpp -o shuffle_scores.o
shuffle_scores.cpp: In instantiation of 'SEXPREC* shuffle_scores_internal(M, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector) [with V = Rcpp::Vector<13>; M = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; SEXP = SEXPREC*; Rcpp::IntegerVector = Rcpp::Vector<13>]':
shuffle_scores.cpp:96:130: required from here
shuffle_scores.cpp:28:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (npairs!=marker2.size()) { throw std::runtime_error("vectors of markers must be of the same length"); }
^
shuffle_scores.cpp:42:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (m1m >= nused || m1m < 0) { throw std::runtime_error("first marker indices are out of range"); }
^
shuffle_scores.cpp:44:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (m2m >= nused || m2m < 0) { throw std::runtime_error("second marker indices are out of range"); }
^
shuffle_scores.cpp:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (usedex >= ngenes || usedex < 0) { throw std::runtime_error("used gene indices are out of range"); }
^
shuffle_scores.cpp: In instantiation of 'SEXPREC* shuffle_scores_internal(M, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; SEXP = SEXPREC*; Rcpp::IntegerVector = Rcpp::Vector<13>]':
shuffle_scores.cpp:99:130: required from here
shuffle_scores.cpp:28:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (npairs!=marker2.size()) { throw std::runtime_error("vectors of markers must be of the same length"); }
^
shuffle_scores.cpp:42:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (m1m >= nused || m1m < 0) { throw std::runtime_error("first marker indices are out of range"); }
^
shuffle_scores.cpp:44:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (m2m >= nused || m2m < 0) { throw std::runtime_error("second marker indices are out of range"); }
^
shuffle_scores.cpp:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (usedex >= ngenes || usedex < 0) { throw std::runtime_error("used gene indices are out of range"); }
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c sum_spikes.cpp -o sum_spikes.o
sum_spikes.cpp: In instantiation of 'SEXPREC* sum_spikes_internal(M, Rcpp::IntegerVector) [with V = Rcpp::Vector<13>; M = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; SEXP = SEXPREC*; Rcpp::IntegerVector = Rcpp::Vector<13>]':
sum_spikes.cpp:32:76: required from here
sum_spikes.cpp:9:49: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (curdex <= last || curdex<0 || curdex>=ngenes) {
^
sum_spikes.cpp: In instantiation of 'SEXPREC* sum_spikes_internal(M, Rcpp::IntegerVector) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; SEXP = SEXPREC*; Rcpp::IntegerVector = Rcpp::Vector<13>]':
sum_spikes.cpp:35:76: required from here
sum_spikes.cpp:9:49: 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˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c utils.cpp -o utils.o
utils.cpp: In function 'Rcpp::IntegerVector check_subset_vector(SEXP, size_t)':
utils.cpp:6:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (*sIt < 0 || *sIt>=len) {
^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o scran.dll tmp.def build_snn.o compute_CV2.o compute_rho.o find_mutual_nns.o fit_linear_model.o forge_system.o get_residuals.o get_scaled_ranks.o init.o overlap_exprs.o run_dormqr.o shuffle_scores.o sum_spikes.o utils.o -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/library/beachmat/lib/x64 -lbeachmat -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/library/Rhdf5lib/lib/x64 -lhdf5_cpp -lhdf5 -lszip -lz -lpsapi -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/scran.buildbin-libdir/scran/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'scran' as scran_1.6.9.zip
* DONE (scran)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.6-bioc/R/library'
package 'scran' successfully unpacked and MD5 sums checked
In R CMD INSTALL
