SingleR 1.2.4
Aaron Lun
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/SingleR |
| Branch: RELEASE_3_11 |
| Last Commit: 4653a3c |
| Last Changed Date: 2020-05-24 18:13:10 -0400 (Sun, 24 May 2020) |
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | WARNINGS | NA | |
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | ERROR | skipped | skipped | |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/SingleR_1.2.4.tar.gz && rm -rf SingleR.buildbin-libdir && mkdir SingleR.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SingleR.buildbin-libdir SingleR_1.2.4.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL SingleR_1.2.4.zip && rm SingleR_1.2.4.tar.gz SingleR_1.2.4.zip
###
##############################################################################
##############################################################################
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 123k 100 123k 0 0 1868k 0 --:--:-- --:--:-- --:--:-- 2089k
install for i386
* installing *source* package 'SingleR' ...
** 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:/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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fine_tune_de.cpp -o fine_tune_de.o
fine_tune_de.cpp: In constructor 'de_markers::de_markers(Rcpp::List)':
fine_tune_de.cpp:6:27: 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<marker_genes.size(); ++i) {
~^~~~~~~~~~~~~~~~~~~~
fine_tune_de.cpp:9:31: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
for (size_t j=0; j<internals.size(); ++j) {
~^~~~~~~~~~~~~~~~~
fine_tune_de.cpp: In function 'Rcpp::List fine_tune_label_de(SEXP, Rcpp::NumericMatrix, Rcpp::List, double, double, Rcpp::List)':
fine_tune_de.cpp:41:23: 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<References.size(); ++i) {
~^~~~~~~~~~~~~~~~~~
In file included from fine_tune_de.cpp:2:
fine_tuner.h: In instantiation of 'tuned_stats fine_tuner::assign(int, beachmat::numeric_matrix*, Rcpp::NumericMatrix, const matrix_list&, double, double, const PICKER&) [with PICKER = de_markers; tuned_stats = std::tuple<int, double, double>; beachmat::numeric_matrix = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::NumericMatrix = Rcpp::Matrix<14>; matrix_list = std::vector<std::unique_ptr<beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> > > >]':
fine_tune_de.cpp:54:95: required from here
fine_tuner.h:40:27: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'int' [-Wsign-compare]
for (size_t i=0; i<cur_scores.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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fine_tune_sd.cpp -o fine_tune_sd.o
fine_tune_sd.cpp: In function 'Rcpp::List fine_tune_label_sd(SEXP, Rcpp::NumericMatrix, Rcpp::List, double, double, Rcpp::NumericMatrix, double)':
fine_tune_sd.cpp:46:23: 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<References.size(); ++i) {
~^~~~~~~~~~~~~~~~~~
In file included from fine_tune_sd.cpp:2:
fine_tuner.h: In instantiation of 'tuned_stats fine_tuner::assign(int, beachmat::numeric_matrix*, Rcpp::NumericMatrix, const matrix_list&, double, double, const PICKER&) [with PICKER = sd_markers; tuned_stats = std::tuple<int, double, double>; beachmat::numeric_matrix = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::NumericMatrix = Rcpp::Matrix<14>; matrix_list = std::vector<std::unique_ptr<beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> > > >]':
fine_tune_sd.cpp:59:95: required from here
fine_tuner.h:40:27: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'int' [-Wsign-compare]
for (size_t i=0; i<cur_scores.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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c recompute_scores.cpp -o recompute_scores.o
recompute_scores.cpp: In function 'Rcpp::RObject recompute_scores(Rcpp::List, Rcpp::RObject, Rcpp::IntegerMatrix, Rcpp::List, Rcpp::List, double)':
recompute_scores.cpp:38:22: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const unsigned int'} [-Wsign-compare]
if (Labels.nrow()!=nref) {
~~~~~~~~~~~~~^~~~~~
recompute_scores.cpp:41:22: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const unsigned int'} [-Wsign-compare]
if (Labels.ncol()!=ncells) {
~~~~~~~~~~~~~^~~~~~~~
recompute_scores.cpp:45:21: warning: comparison of integer expressions of different signedness: 'R_xlen_t' {aka 'int'} and 'const size_t' {aka 'const unsigned int'} [-Wsign-compare]
if (Genes.size()!=nref) {
~~~~~~~~~~~~^~~~~~
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o SingleR.dll tmp.def RcppExports.o fine_tune_de.o fine_tune_sd.o recompute_scores.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/SingleR.buildbin-libdir/00LOCK-SingleR/00new/SingleR/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'SingleR'
finding HTML links ... done
BlueprintEncodeData html
finding level-2 HTML links ... done
DatabaseImmuneCellExpressionData html
HumanPrimaryCellAtlasData html
ImmGenData html
MonacoImmuneData html
MouseRNAseqData html
NovershternHematopoieticData html
SingleR html
aggregateReference html
classifySingleR html
combine-predictions html
combineCommonResults html
combineRecomputedResults html
getDeltaFromMedian html
matchReferences html
mockData html
plotScoreDistribution html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpgB2bOC/R.INSTALL18206353720c/SingleR/man/plotScoreDistribution.Rd:67: file link 'grid.arrange' in package 'gridExtra' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpgB2bOC/R.INSTALL18206353720c/SingleR/man/plotScoreDistribution.Rd:197: file link 'grid.arrange' in package 'gridExtra' does not exist and so has been treated as a topic
plotScoreHeatmap html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpgB2bOC/R.INSTALL18206353720c/SingleR/man/plotScoreHeatmap.Rd:75: file link 'grid.arrange' in package 'gridExtra' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpgB2bOC/R.INSTALL18206353720c/SingleR/man/plotScoreHeatmap.Rd:208: file link 'grid.arrange' in package 'gridExtra' does not exist and so has been treated as a topic
pruneScores html
trainSingleR 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 'SingleR' ...
** 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:/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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fine_tune_de.cpp -o fine_tune_de.o
fine_tune_de.cpp: In constructor 'de_markers::de_markers(Rcpp::List)':
fine_tune_de.cpp:6:27: 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<marker_genes.size(); ++i) {
~^~~~~~~~~~~~~~~~~~~~
fine_tune_de.cpp:9:31: 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 j=0; j<internals.size(); ++j) {
~^~~~~~~~~~~~~~~~~
fine_tune_de.cpp: In function 'Rcpp::List fine_tune_label_de(SEXP, Rcpp::NumericMatrix, Rcpp::List, double, double, Rcpp::List)':
fine_tune_de.cpp:41:23: 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<References.size(); ++i) {
~^~~~~~~~~~~~~~~~~~
In file included from fine_tune_de.cpp:2:
fine_tuner.h: In instantiation of 'tuned_stats fine_tuner::assign(int, beachmat::numeric_matrix*, Rcpp::NumericMatrix, const matrix_list&, double, double, const PICKER&) [with PICKER = de_markers; tuned_stats = std::tuple<int, double, double>; beachmat::numeric_matrix = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::NumericMatrix = Rcpp::Matrix<14>; matrix_list = std::vector<std::unique_ptr<beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> > > >]':
fine_tune_de.cpp:54:95: required from here
fine_tuner.h:40:27: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
for (size_t i=0; i<cur_scores.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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fine_tune_sd.cpp -o fine_tune_sd.o
fine_tune_sd.cpp: In function 'Rcpp::List fine_tune_label_sd(SEXP, Rcpp::NumericMatrix, Rcpp::List, double, double, Rcpp::NumericMatrix, double)':
fine_tune_sd.cpp:46:23: 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<References.size(); ++i) {
~^~~~~~~~~~~~~~~~~~
In file included from fine_tune_sd.cpp:2:
fine_tuner.h: In instantiation of 'tuned_stats fine_tuner::assign(int, beachmat::numeric_matrix*, Rcpp::NumericMatrix, const matrix_list&, double, double, const PICKER&) [with PICKER = sd_markers; tuned_stats = std::tuple<int, double, double>; beachmat::numeric_matrix = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::NumericMatrix = Rcpp::Matrix<14>; matrix_list = std::vector<std::unique_ptr<beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> > > >]':
fine_tune_sd.cpp:59:95: required from here
fine_tuner.h:40:27: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
for (size_t i=0; i<cur_scores.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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c recompute_scores.cpp -o recompute_scores.o
recompute_scores.cpp: In function 'Rcpp::RObject recompute_scores(Rcpp::List, Rcpp::RObject, Rcpp::IntegerMatrix, Rcpp::List, Rcpp::List, double)':
recompute_scores.cpp:38:22: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
if (Labels.nrow()!=nref) {
~~~~~~~~~~~~~^~~~~~
recompute_scores.cpp:41:22: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
if (Labels.ncol()!=ncells) {
~~~~~~~~~~~~~^~~~~~~~
recompute_scores.cpp:45:21: 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 (Genes.size()!=nref) {
~~~~~~~~~~~~^~~~~~
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o SingleR.dll tmp.def RcppExports.o fine_tune_de.o fine_tune_sd.o recompute_scores.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/SingleR.buildbin-libdir/SingleR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SingleR' as SingleR_1.2.4.zip
* DONE (SingleR)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'SingleR' successfully unpacked and MD5 sums checked