DropletUtils 1.8.0
Aaron Lun
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/DropletUtils |
| Branch: RELEASE_3_11 |
| Last Commit: b08edb4 |
| Last Changed Date: 2020-04-27 15:13:00 -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 | OK | 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/DropletUtils_1.8.0.tar.gz && rm -rf DropletUtils.buildbin-libdir && mkdir DropletUtils.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DropletUtils.buildbin-libdir DropletUtils_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL DropletUtils_1.8.0.zip && rm DropletUtils_1.8.0.tar.gz DropletUtils_1.8.0.zip
###
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install for i386
* installing *source* package 'DropletUtils' ...
** 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:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/dqrng/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:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/dqrng/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c compute_multinom.cpp -o compute_multinom.o
compute_multinom.cpp: In instantiation of 'Rcpp::NumericVector compute_multinom_internal(Rcpp::RObject, Rcpp::NumericVector, double) [with V = Rcpp::Vector<13>; MAT = beachmat::lin_matrix<int, Rcpp::Vector<13> >; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
compute_multinom.cpp:72:105: required from here
compute_multinom.cpp:40:23: warning: comparison of integer expressions of different signedness: 'R_xlen_t' {aka 'int'} and 'const size_t' {aka 'const unsigned int'} [-Wsign-compare]
if (ambient.size()!=NR) {
~~~~~~~~~~~~~~^~~~
compute_multinom.cpp: In instantiation of 'Rcpp::NumericVector compute_multinom_internal(Rcpp::RObject, Rcpp::NumericVector, double) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; MAT = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
compute_multinom.cpp:74:105: required from here
compute_multinom.cpp:40:23: warning: comparison of integer expressions of different signedness: 'R_xlen_t' {aka 'int'} and 'const size_t' {aka 'const unsigned int'} [-Wsign-compare]
In file included from compute_multinom.cpp:5:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include/beachmat/utils/const_column.h: In instantiation of 'Rcpp::traits::storage_type<13>::type* beachmat::const_column<M>::get_indices() [with M = beachmat::lin_matrix<int, Rcpp::Vector<13> >; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]':
compute_multinom.cpp:53:18: required from 'Rcpp::NumericVector compute_multinom_internal(Rcpp::RObject, Rcpp::NumericVector, double) [with V = Rcpp::Vector<13>; MAT = beachmat::lin_matrix<int, Rcpp::Vector<13> >; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
compute_multinom.cpp:72:105: required from here
C:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include/beachmat/utils/const_column.h:66:29: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
if (ref->get_nrow() > indices.size()) {
C:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include/beachmat/utils/const_column.h: In instantiation of 'Rcpp::traits::storage_type<13>::type* beachmat::const_column<M>::get_indices() [with M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]':
compute_multinom.cpp:53:18: required from 'Rcpp::NumericVector compute_multinom_internal(Rcpp::RObject, Rcpp::NumericVector, double) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; MAT = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
compute_multinom.cpp:74:105: required from here
C:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include/beachmat/utils/const_column.h:66:29: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
"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:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/dqrng/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c downsample_counts.cpp -o downsample_counts.o
downsample_counts.cpp: In function 'void check_downsampling_mode(size_t, Rcpp::NumericVector, bool)':
downsample_counts.cpp:99:24: warning: comparison of integer expressions of different signedness: 'R_xlen_t' {aka 'int'} and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
if (prop.size()!=ncells) {
~~~~~~~~~~~^~~~~~~~
downsample_counts.cpp: In function 'Rcpp::IntegerVector downsample_runs(Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::NumericVector, bool)':
downsample_counts.cpp:210:19: warning: comparison of integer expressions of different signedness: 'const bigint_t' {aka 'const long long unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
if (nmolecules!=reads.size()) {
~~~~~~~~~~^~~~~~~~~~~~~~
In file included from downsample_counts.cpp:5:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include/beachmat/utils/const_column.h: In instantiation of 'Rcpp::traits::storage_type<13>::type* beachmat::const_column<M>::get_indices() [with M = beachmat::lin_matrix<int, Rcpp::Vector<13> >; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]':
downsample_counts.cpp:174:17: required from 'Rcpp::RObject downsample_matrix_internal(Rcpp::RObject, Rcpp::NumericVector, bool) [with V = Rcpp::Vector<13>; M = beachmat::lin_matrix<int, Rcpp::Vector<13> >; O = beachmat::lin_output<int, Rcpp::Vector<13> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>]'
downsample_counts.cpp:192:55: required from here
C:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include/beachmat/utils/const_column.h:66:29: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
if (ref->get_nrow() > indices.size()) {
C:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include/beachmat/utils/const_column.h: In instantiation of 'Rcpp::traits::storage_type<13>::type* beachmat::const_column<M>::get_indices() [with M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]':
downsample_counts.cpp:174:17: required from 'Rcpp::RObject downsample_matrix_internal(Rcpp::RObject, Rcpp::NumericVector, bool) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; O = beachmat::lin_output<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>]'
downsample_counts.cpp:196:55: required from here
C:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include/beachmat/utils/const_column.h:66:29: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
"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:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/dqrng/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c encode_sequences.cpp -o encode_sequences.o
encode_sequences.cpp: In function 'Rcpp::IntegerVector encode_sequences(Rcpp::StringVector)':
encode_sequences.cpp:8:23: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
for (size_t i=0; i<output.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:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/dqrng/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c find_chimeric.cpp -o find_chimeric.o
find_chimeric.cpp: In function 'Rcpp::List find_chimeric(Rcpp::StringVector, Rcpp::IntegerVector, Rcpp::IntegerVector, double, bool)':
find_chimeric.cpp:28:23: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'int' [-Wsign-compare]
for (size_t i=0; i<nmolecules; ++i, ++uIt) {
~^~~~~~~~~~~
"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:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/dqrng/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c find_swapped.cpp -o find_swapped.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:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/dqrng/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c get_cell_barcodes.cpp -o get_cell_barcodes.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:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/dqrng/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c group_cells.cpp -o group_cells.o
group_cells.cpp: In function 'Rcpp::List group_cells(Rcpp::StringVector, Rcpp::IntegerVector)':
group_cells.cpp:10:10: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
if (N!=gems.size()) {
~^~~~~~~~~~~~~
"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:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/dqrng/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c hashed_deltas.cpp -o hashed_deltas.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:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/dqrng/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c montecarlo_pval.cpp -o montecarlo_pval.o
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/apply.hpp:24,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/aux_/iter_apply.hpp:17,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/aux_/find_if_pred.hpp:14,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/find_if.hpp:17,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/find.hpp:17,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/aux_/contains_impl.hpp:20,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/contains.hpp:20,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/math/policies/policy.hpp:10,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/math/special_functions/math_fwd.hpp:29,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/math/special_functions/fpclassify.hpp:19,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/random/hyperexponential_distribution.hpp:22,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/random.hpp:69,
from montecarlo_pval.cpp:3:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::************
^
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
failed ************ (boost::mpl::not_<Pred>::************
^
montecarlo_pval.cpp: In function 'Rcpp::IntegerVector montecarlo_pval(Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::NumericVector, Rcpp::NumericVector, int, double, Rcpp::List, Rcpp::IntegerVector)':
montecarlo_pval.cpp:99:23: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'const int' [-Wsign-compare]
if (higher<curlen) {
~~~~~~^~~~~~~
"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:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/dqrng/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rand_custom.cpp -o rand_custom.o
rand_custom.cpp: In function 'void check_pcg_vectors(Rcpp::List, Rcpp::IntegerVector, size_t, const char*)':
rand_custom.cpp:8:21: warning: comparison of integer expressions of different signedness: 'R_xlen_t' {aka 'int'} and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
if (seeds.size()!=N) {
~~~~~~~~~~~~^~~
rand_custom.cpp:14:23: warning: comparison of integer expressions of different signedness: 'R_xlen_t' {aka 'int'} and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
if (streams.size()!=N) {
~~~~~~~~~~~~~~^~~
"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:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/dqrng/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c utils.cpp -o utils.o
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o DropletUtils.dll tmp.def RcppExports.o compute_multinom.o downsample_counts.o encode_sequences.o find_chimeric.o find_swapped.o get_cell_barcodes.o group_cells.o hashed_deltas.o montecarlo_pval.o rand_custom.o utils.o -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/library/Rhdf5lib/lib/i386 -lhdf5_cpp -lhdf5 -lszip -lz -lpsapi -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/DropletUtils.buildbin-libdir/00LOCK-DropletUtils/00new/DropletUtils/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'DropletUtils'
finding HTML links ... done
barcodeRanks html
finding level-2 HTML links ... done
chimericDrops html
defaultDrops html
downsampleBatches html
downsampleMatrix html
downsampleReads html
emptyDrops html
encodeSequences html
estimateAmbience html
get10xMolInfoStats html
hashedDrops html
makeCountMatrix html
maximumAmbience html
read10xCounts html
read10xMolInfo html
swappedDrops html
write10xCounts 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 'DropletUtils' ...
** 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:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/dqrng/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:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/dqrng/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c compute_multinom.cpp -o compute_multinom.o
compute_multinom.cpp: In instantiation of 'Rcpp::NumericVector compute_multinom_internal(Rcpp::RObject, Rcpp::NumericVector, double) [with V = Rcpp::Vector<13>; MAT = beachmat::lin_matrix<int, Rcpp::Vector<13> >; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
compute_multinom.cpp:72:105: required from here
compute_multinom.cpp:40:23: warning: comparison of integer expressions of different signedness: 'R_xlen_t' {aka 'long long int'} and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
if (ambient.size()!=NR) {
~~~~~~~~~~~~~~^~~~
compute_multinom.cpp: In instantiation of 'Rcpp::NumericVector compute_multinom_internal(Rcpp::RObject, Rcpp::NumericVector, double) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; MAT = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
compute_multinom.cpp:74:105: required from here
compute_multinom.cpp:40:23: warning: comparison of integer expressions of different signedness: 'R_xlen_t' {aka 'long long int'} and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
In file included from compute_multinom.cpp:5:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include/beachmat/utils/const_column.h: In instantiation of 'Rcpp::traits::storage_type<13>::type* beachmat::const_column<M>::get_indices() [with M = beachmat::lin_matrix<int, Rcpp::Vector<13> >; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]':
compute_multinom.cpp:53:18: required from 'Rcpp::NumericVector compute_multinom_internal(Rcpp::RObject, Rcpp::NumericVector, double) [with V = Rcpp::Vector<13>; MAT = beachmat::lin_matrix<int, Rcpp::Vector<13> >; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
compute_multinom.cpp:72:105: required from here
C:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include/beachmat/utils/const_column.h:66:29: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
if (ref->get_nrow() > indices.size()) {
C:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include/beachmat/utils/const_column.h: In instantiation of 'Rcpp::traits::storage_type<13>::type* beachmat::const_column<M>::get_indices() [with M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]':
compute_multinom.cpp:53:18: required from 'Rcpp::NumericVector compute_multinom_internal(Rcpp::RObject, Rcpp::NumericVector, double) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; MAT = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
compute_multinom.cpp:74:105: required from here
C:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include/beachmat/utils/const_column.h:66:29: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
"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:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/dqrng/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c downsample_counts.cpp -o downsample_counts.o
downsample_counts.cpp: In function 'void check_downsampling_mode(size_t, Rcpp::NumericVector, bool)':
downsample_counts.cpp:99:24: warning: comparison of integer expressions of different signedness: 'R_xlen_t' {aka 'long long int'} and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
if (prop.size()!=ncells) {
~~~~~~~~~~~^~~~~~~~
downsample_counts.cpp: In function 'Rcpp::IntegerVector downsample_runs(Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::NumericVector, bool)':
downsample_counts.cpp:210:19: warning: comparison of integer expressions of different signedness: 'const bigint_t' {aka 'const long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
if (nmolecules!=reads.size()) {
~~~~~~~~~~^~~~~~~~~~~~~~
In file included from downsample_counts.cpp:5:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include/beachmat/utils/const_column.h: In instantiation of 'Rcpp::traits::storage_type<13>::type* beachmat::const_column<M>::get_indices() [with M = beachmat::lin_matrix<int, Rcpp::Vector<13> >; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]':
downsample_counts.cpp:174:17: required from 'Rcpp::RObject downsample_matrix_internal(Rcpp::RObject, Rcpp::NumericVector, bool) [with V = Rcpp::Vector<13>; M = beachmat::lin_matrix<int, Rcpp::Vector<13> >; O = beachmat::lin_output<int, Rcpp::Vector<13> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>]'
downsample_counts.cpp:192:55: required from here
C:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include/beachmat/utils/const_column.h:66:29: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
if (ref->get_nrow() > indices.size()) {
C:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include/beachmat/utils/const_column.h: In instantiation of 'Rcpp::traits::storage_type<13>::type* beachmat::const_column<M>::get_indices() [with M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]':
downsample_counts.cpp:174:17: required from 'Rcpp::RObject downsample_matrix_internal(Rcpp::RObject, Rcpp::NumericVector, bool) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; O = beachmat::lin_output<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>]'
downsample_counts.cpp:196:55: required from here
C:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include/beachmat/utils/const_column.h:66:29: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
"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:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/dqrng/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c encode_sequences.cpp -o encode_sequences.o
encode_sequences.cpp: In function 'Rcpp::IntegerVector encode_sequences(Rcpp::StringVector)':
encode_sequences.cpp:8:23: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
for (size_t i=0; i<output.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:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/dqrng/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c find_chimeric.cpp -o find_chimeric.o
find_chimeric.cpp: In function 'Rcpp::List find_chimeric(Rcpp::StringVector, Rcpp::IntegerVector, Rcpp::IntegerVector, double, bool)':
find_chimeric.cpp:28:23: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'long long int' [-Wsign-compare]
for (size_t i=0; i<nmolecules; ++i, ++uIt) {
~^~~~~~~~~~~
"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:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/dqrng/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c find_swapped.cpp -o find_swapped.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:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/dqrng/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c get_cell_barcodes.cpp -o get_cell_barcodes.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:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/dqrng/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c group_cells.cpp -o group_cells.o
group_cells.cpp: In function 'Rcpp::List group_cells(Rcpp::StringVector, Rcpp::IntegerVector)':
group_cells.cpp:10:10: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
if (N!=gems.size()) {
~^~~~~~~~~~~~~
"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:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/dqrng/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c hashed_deltas.cpp -o hashed_deltas.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:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/dqrng/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c montecarlo_pval.cpp -o montecarlo_pval.o
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/apply.hpp:24,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/aux_/iter_apply.hpp:17,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/aux_/find_if_pred.hpp:14,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/find_if.hpp:17,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/find.hpp:17,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/aux_/contains_impl.hpp:20,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/contains.hpp:20,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/math/policies/policy.hpp:10,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/math/special_functions/math_fwd.hpp:29,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/math/special_functions/fpclassify.hpp:19,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/random/hyperexponential_distribution.hpp:22,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/random.hpp:69,
from montecarlo_pval.cpp:3:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::************
^
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
failed ************ (boost::mpl::not_<Pred>::************
^
montecarlo_pval.cpp: In function 'Rcpp::IntegerVector montecarlo_pval(Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::NumericVector, Rcpp::NumericVector, int, double, Rcpp::List, Rcpp::IntegerVector)':
montecarlo_pval.cpp:99:23: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'const int' [-Wsign-compare]
if (higher<curlen) {
~~~~~~^~~~~~~
"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:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/dqrng/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rand_custom.cpp -o rand_custom.o
rand_custom.cpp: In function 'void check_pcg_vectors(Rcpp::List, Rcpp::IntegerVector, size_t, const char*)':
rand_custom.cpp:8:21: warning: comparison of integer expressions of different signedness: 'R_xlen_t' {aka 'long long int'} and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
if (seeds.size()!=N) {
~~~~~~~~~~~~^~~
rand_custom.cpp:14:23: warning: comparison of integer expressions of different signedness: 'R_xlen_t' {aka 'long long int'} and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
if (streams.size()!=N) {
~~~~~~~~~~~~~~^~~
"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:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/dqrng/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c utils.cpp -o utils.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o DropletUtils.dll tmp.def RcppExports.o compute_multinom.o downsample_counts.o encode_sequences.o find_chimeric.o find_swapped.o get_cell_barcodes.o group_cells.o hashed_deltas.o montecarlo_pval.o rand_custom.o utils.o -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/library/Rhdf5lib/lib/x64 -lhdf5_cpp -lhdf5 -lszip -lz -lpsapi -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/DropletUtils.buildbin-libdir/DropletUtils/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DropletUtils' as DropletUtils_1.8.0.zip
* DONE (DropletUtils)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'DropletUtils' successfully unpacked and MD5 sums checked