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INSTALL report for DropletUtils on malbec1

This page was generated on 2019-04-16 11:53:14 -0400 (Tue, 16 Apr 2019).

Package 436/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DropletUtils 1.2.2
Aaron Lun
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/DropletUtils
Branch: RELEASE_3_8
Last Commit: 1424ff5
Last Changed Date: 2019-01-04 13:09:29 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64 [ OK ] OK  WARNINGS UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: DropletUtils
Version: 1.2.2
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL DropletUtils
StartedAt: 2019-04-15 18:16:07 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 18:17:27 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 79.7 seconds
RetCode: 0
Status:  OK 

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL DropletUtils
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘DropletUtils’ ...
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c compute_multinom.cpp -o compute_multinom.o
compute_multinom.cpp: In instantiation of ‘SEXPREC* compute_multinom_internal(MAT, SEXP, SEXP) [with V = Rcpp::Vector<13>; MAT = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; SEXP = SEXPREC*]’:
compute_multinom.cpp:45:85:   required from here
compute_multinom.cpp:11:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (ambient.size()!=NR) {
                       ^
compute_multinom.cpp: In instantiation of ‘SEXPREC* compute_multinom_internal(MAT, SEXP, SEXP) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; MAT = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; SEXP = SEXPREC*]’:
compute_multinom.cpp:48:85:   required from here
compute_multinom.cpp:11:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:238:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
                 from DropletUtils.h:5,
                 from compute_multinom.cpp:1:
/home/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 unsigned int, int*, int*>; typename V::iterator = int*; size_t = long unsigned int; typename V::iterator = int*]’:
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:77:33:   required from ‘beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator) [with T = int; V = Rcpp::Vector<13>; beachmat::const_col_indexed_info<V> = std::tuple<long unsigned int, int*, int*>; typename V::iterator = int*; size_t = long unsigned int; typename V::iterator = int*]’
compute_multinom.cpp:22:61:   required from ‘SEXPREC* compute_multinom_internal(MAT, SEXP, SEXP) [with V = Rcpp::Vector<13>; MAT = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; SEXP = SEXPREC*]’
compute_multinom.cpp:45:85:   required from here
/home/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()) {
                       ^
/home/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 unsigned int, int*, double*>; typename V::iterator = double*; size_t = long unsigned int; typename V::iterator = double*]’:
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:77:33:   required from ‘beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; beachmat::const_col_indexed_info<V> = std::tuple<long unsigned int, int*, double*>; typename V::iterator = double*; size_t = long unsigned int; typename V::iterator = double*]’
compute_multinom.cpp:22:61:   required from ‘SEXPREC* compute_multinom_internal(MAT, SEXP, SEXP) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; MAT = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; SEXP = SEXPREC*]’
compute_multinom.cpp:48:85:   required from here
/home/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]
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c downsample_counts.cpp -o downsample_counts.o
downsample_counts.cpp: In function ‘bool check_downsampling_mode(size_t, Rcpp::NumericVector, Rcpp::LogicalVector)’:
downsample_counts.cpp:78:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (prop.size()!=ncells) {
                        ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:238:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
                 from DropletUtils.h:5,
                 from downsample_counts.cpp:1:
/home/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 unsigned int, int*, double*>; typename V::iterator = double*; size_t = long unsigned int; typename V::iterator = double*]’:
downsample_counts.cpp:205:1:   required from here
/home/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()) {
                       ^
/home/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 unsigned int, int*, int*>; typename V::iterator = int*; size_t = long unsigned int; typename V::iterator = int*]’:
downsample_counts.cpp:205:1:   required from here
/home/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]
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c encode_sequences.cpp -o encode_sequences.o
encode_sequences.cpp: In function ‘SEXPREC* encode_sequences(SEXP)’:
encode_sequences.cpp:8:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t i=0; i<output.size(); ++i) {
                       ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c find_swapped.cpp -o find_swapped.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c get_cell_barcodes.cpp -o get_cell_barcodes.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c group_cells.cpp -o group_cells.o
group_cells.cpp: In function ‘SEXPREC* group_cells(SEXP, SEXP)’:
group_cells.cpp:34:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (size_t i=1; i<output.size(); ++i) {
                           ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c init.cpp -o init.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c load_tenx_to_hdf5.cpp -o load_tenx_to_hdf5.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c montecarlo_pval.cpp -o montecarlo_pval.o
montecarlo_pval.cpp: In function ‘SEXPREC* montecarlo_pval(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
montecarlo_pval.cpp:76:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 if (chosen >= ngenes) {
                            ^
montecarlo_pval.cpp:92:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (higher<curlen) {
                       ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c utils.cpp -o utils.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o DropletUtils.so compute_multinom.o downsample_counts.o encode_sequences.o find_swapped.o get_cell_barcodes.o group_cells.o init.o load_tenx_to_hdf5.o montecarlo_pval.o utils.o -L/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/lib -Wl,-rpath,/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/lib -lbeachmat -pthread -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/DropletUtils/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DropletUtils)