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INSTALL report for scuttle on malbec1

This page was generated on 2021-05-06 12:29:03 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the scuttle package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1666/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scuttle 1.0.4  (landing page)
Aaron Lun
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/scuttle
Branch: RELEASE_3_12
Last Commit: a827e27
Last Changed Date: 2020-12-17 02:50:00 -0400 (Thu, 17 Dec 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: scuttle
Version: 1.0.4
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL scuttle
StartedAt: 2021-05-05 16:30:43 -0400 (Wed, 05 May 2021)
EndedAt: 2021-05-05 16:31:51 -0400 (Wed, 05 May 2021)
EllapsedTime: 67.8 seconds
RetCode: 0
Status:   OK  

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL scuttle
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘scuttle’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c cumulative_prop.cpp -o cumulative_prop.o
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:12:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:11,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/beachmat.h:24,
                 from cumulative_prop.cpp:2:
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56:   required from ‘beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:36:39:   required from ‘std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (nnz != x.size()) {
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                       ~~~~~~^~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                                                   ~~~~~~^~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
                                 ~~^~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56:   required from ‘beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:38:39:   required from ‘std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (nnz != x.size()) {
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                       ~~~~~~^~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                                                   ~~~~~~^~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
                                 ~~^~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56:   required from ‘beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:40:39:   required from ‘std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (nnz != x.size()) {
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                       ~~~~~~^~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                                                   ~~~~~~^~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
                                 ~~^~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const double*; I = int; P = long unsigned int; size_t = long unsigned int]’:
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from ‘beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const int*; ALT = int*; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82:   required from ‘beachmat::sparse_index<const int*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’
cumulative_prop.cpp:66:1:   required from here
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (idex != *pIt && static_cast<size_t>(i[idex]) == r) {
                 ~~~~~^~~~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const double*; I = int; P = long unsigned int; size_t = long unsigned int]’:
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from ‘beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const double*; ALT = double*; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85:   required from ‘beachmat::sparse_index<const double*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’
cumulative_prop.cpp:66:1:   required from here
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const int*; I = int; P = long unsigned int; size_t = long unsigned int]’:
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from ‘beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const int*; ALT = int*; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82:   required from ‘beachmat::sparse_index<const int*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’
cumulative_prop.cpp:66:1:   required from here
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const int*; I = int; P = long unsigned int; size_t = long unsigned int]’:
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from ‘beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const double*; ALT = double*; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85:   required from ‘beachmat::sparse_index<const double*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’
cumulative_prop.cpp:66:1:   required from here
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c downsample_counts.cpp -o downsample_counts.o
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:12:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:11,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/beachmat.h:24,
                 from downsample_counts.cpp:2:
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56:   required from ‘beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:36:39:   required from ‘std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (nnz != x.size()) {
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                       ~~~~~~^~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                                                   ~~~~~~^~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
                                 ~~^~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56:   required from ‘beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:38:39:   required from ‘std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (nnz != x.size()) {
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                       ~~~~~~^~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                                                   ~~~~~~^~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
                                 ~~^~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56:   required from ‘beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:40:39:   required from ‘std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (nnz != x.size()) {
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                       ~~~~~~^~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                                                   ~~~~~~^~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
                                 ~~^~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const double*; I = int; P = long unsigned int; size_t = long unsigned int]’:
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from ‘beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const int*; ALT = int*; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82:   required from ‘beachmat::sparse_index<const int*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’
downsample_counts.cpp:112:1:   required from here
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (idex != *pIt && static_cast<size_t>(i[idex]) == r) {
                 ~~~~~^~~~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const double*; I = int; P = long unsigned int; size_t = long unsigned int]’:
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from ‘beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const double*; ALT = double*; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85:   required from ‘beachmat::sparse_index<const double*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’
downsample_counts.cpp:112:1:   required from here
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const int*; I = int; P = long unsigned int; size_t = long unsigned int]’:
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from ‘beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const int*; ALT = int*; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82:   required from ‘beachmat::sparse_index<const int*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’
downsample_counts.cpp:112:1:   required from here
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const int*; I = int; P = long unsigned int; size_t = long unsigned int]’:
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from ‘beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const double*; ALT = double*; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85:   required from ‘beachmat::sparse_index<const double*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’
downsample_counts.cpp:112:1:   required from here
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c fit_linear_model.cpp -o fit_linear_model.o
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:12:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:11,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/beachmat.h:24,
                 from fit_linear_model.cpp:2:
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56:   required from ‘beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:36:39:   required from ‘std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (nnz != x.size()) {
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                       ~~~~~~^~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                                                   ~~~~~~^~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
                                 ~~^~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56:   required from ‘beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:38:39:   required from ‘std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (nnz != x.size()) {
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                       ~~~~~~^~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                                                   ~~~~~~^~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
                                 ~~^~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56:   required from ‘beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:40:39:   required from ‘std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (nnz != x.size()) {
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                       ~~~~~~^~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                                                   ~~~~~~^~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
                                 ~~^~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const double*; I = int; P = long unsigned int; size_t = long unsigned int]’:
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from ‘beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const int*; ALT = int*; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82:   required from ‘beachmat::sparse_index<const int*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’
fit_linear_model.cpp:60:1:   required from here
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (idex != *pIt && static_cast<size_t>(i[idex]) == r) {
                 ~~~~~^~~~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const double*; I = int; P = long unsigned int; size_t = long unsigned int]’:
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from ‘beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const double*; ALT = double*; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85:   required from ‘beachmat::sparse_index<const double*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’
fit_linear_model.cpp:60:1:   required from here
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const int*; I = int; P = long unsigned int; size_t = long unsigned int]’:
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from ‘beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const int*; ALT = int*; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82:   required from ‘beachmat::sparse_index<const int*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’
fit_linear_model.cpp:60:1:   required from here
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const int*; I = int; P = long unsigned int; size_t = long unsigned int]’:
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from ‘beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const double*; ALT = double*; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85:   required from ‘beachmat::sparse_index<const double*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’
fit_linear_model.cpp:60:1:   required from here
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c sum_counts.cpp -o sum_counts.o
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:12:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:11,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/beachmat.h:24,
                 from sum_counts.cpp:2:
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56:   required from ‘beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:36:39:   required from ‘std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (nnz != x.size()) {
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                       ~~~~~~^~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                                                   ~~~~~~^~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
                                 ~~^~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56:   required from ‘beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:38:39:   required from ‘std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (nnz != x.size()) {
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                       ~~~~~~^~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                                                   ~~~~~~^~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
                                 ~~^~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56:   required from ‘beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:40:39:   required from ‘std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (nnz != x.size()) {
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                       ~~~~~~^~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                                                   ~~~~~~^~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
                                 ~~^~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const double*; I = int; P = long unsigned int; size_t = long unsigned int]’:
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from ‘beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const int*; ALT = int*; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82:   required from ‘beachmat::sparse_index<const int*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’
sum_counts.cpp:31:1:   required from here
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (idex != *pIt && static_cast<size_t>(i[idex]) == r) {
                 ~~~~~^~~~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const double*; I = int; P = long unsigned int; size_t = long unsigned int]’:
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from ‘beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const double*; ALT = double*; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85:   required from ‘beachmat::sparse_index<const double*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’
sum_counts.cpp:31:1:   required from here
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const int*; I = int; P = long unsigned int; size_t = long unsigned int]’:
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from ‘beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const int*; ALT = int*; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82:   required from ‘beachmat::sparse_index<const int*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’
sum_counts.cpp:31:1:   required from here
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const int*; I = int; P = long unsigned int; size_t = long unsigned int]’:
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from ‘beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const double*; ALT = double*; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85:   required from ‘beachmat::sparse_index<const double*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’
sum_counts.cpp:31:1:   required from here
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c utils.cpp -o utils.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.12-bioc/R/lib -L/usr/local/lib -o scuttle.so RcppExports.o cumulative_prop.o downsample_counts.o fit_linear_model.o sum_counts.o utils.o -L/home/biocbuild/bbs-3.12-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.12-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-bioc/R/library/00LOCK-scuttle/00new/scuttle/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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (scuttle)