Back to Multiple platform build/check report for BioC 3.16: simplified long 

This page was generated on 20230329 11:05:18 0400 (Wed, 29 Mar 2023).
Hostname  OS  Arch (*)  R version  Installed pkgs 

nebbiolo2  Linux (Ubuntu 20.04.5 LTS)  x86_64  4.2.3 (20230315)  "Shortstop Beagle"  4482 
palomino4  Windows Server 2022 Datacenter  x64  4.2.3 (20230315 ucrt)  "Shortstop Beagle"  4278 
lconway  macOS 12.5.1 Monterey  x86_64  4.2.3 (20230315)  "Shortstop Beagle"  4306 
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To the developers/maintainers of the scuttle package:  Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scuttle.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.  Make sure to use the following settings in order to reproduce any error or warning you see on this page. 
Package 1828/2183  Hostname  OS / Arch  INSTALL  BUILD  CHECK  BUILD BIN  
scuttle 1.8.4 (landing page) Aaron Lun
 nebbiolo2  Linux (Ubuntu 20.04.5 LTS) / x86_64  OK  OK  OK  
palomino4  Windows Server 2022 Datacenter / x64  OK  OK  OK  OK  
lconway  macOS 12.5.1 Monterey / x86_64  OK  OK  OK  OK  
Package: scuttle 
Version: 1.8.4 
Command: /home/biocbuild/bbs3.16bioc/R/bin/R CMD check install=check:scuttle.installout.txt library=/home/biocbuild/bbs3.16bioc/R/sitelibrary timings scuttle_1.8.4.tar.gz 
StartedAt: 20230328 00:00:55 0400 (Tue, 28 Mar 2023) 
EndedAt: 20230328 00:09:14 0400 (Tue, 28 Mar 2023) 
EllapsedTime: 499.6 seconds 
RetCode: 0 
Status: OK 
CheckDir: scuttle.Rcheck 
Warnings: 0 
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs3.16bioc/R/bin/R CMD check install=check:scuttle.installout.txt library=/home/biocbuild/bbs3.16bioc/R/sitelibrary timings scuttle_1.8.4.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs3.16bioc/meat/scuttle.Rcheck’ * using R version 4.2.3 (20230315) * using platform: x86_64pclinuxgnu (64bit) * using session charset: UTF8 * checking for file ‘scuttle/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘scuttle’ version ‘1.8.4’ * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘scuttle’ can be installed ... OK * checking installed package size ... NOTE installed size is 11.6Mb subdirectories of 1Mb or more: libs 11.1Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION metainformation ... OK * checking toplevel files ... OK * checking for leftover files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for nonASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd crossreferences ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed computePooledFactors 6.473 0.268 6.741 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘misc.Rmd’... OK ‘norm.Rmd’... OK ‘qc.Rmd’... OK NONE * checking rebuilding of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs3.16bioc/meat/scuttle.Rcheck/00check.log’ for details.
scuttle.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs3.16bioc/R/bin/R CMD INSTALL scuttle ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs3.16bioc/R/sitelibrary’ * installing *source* package ‘scuttle’ ... ** using staged installation ** libs g++ std=gnu++11 I"/home/biocbuild/bbs3.16bioc/R/include" DNDEBUG I../inst/include/ I'/home/biocbuild/bbs3.16bioc/R/sitelibrary/Rcpp/include' I'/home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include' I/usr/local/include fpic g O2 Wall c RcppExports.cpp o RcppExports.o g++ std=gnu++11 I"/home/biocbuild/bbs3.16bioc/R/include" DNDEBUG I../inst/include/ I'/home/biocbuild/bbs3.16bioc/R/sitelibrary/Rcpp/include' I'/home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include' I/usr/local/include fpic g O2 Wall c cumulative_prop.cpp o cumulative_prop.o In file included from /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/lin_matrix.h:12, from /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/read_lin_block.h:11, from /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/beachmat.h:24, from cumulative_prop.cpp:2: /home/biocbuild/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [Wsigncompare] 535  if (nnz != x.size()) { /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [Wsigncompare] 551  if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) {  ~~~~~~^~~~ /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [Wsigncompare] 551  if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) {  ~~~~~~^~~~ /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [Wsigncompare] 593  for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {  ~~^~~~~ /home/biocbuild/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [Wsigncompare] 535  if (nnz != x.size()) { /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [Wsigncompare] 551  if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) {  ~~~~~~^~~~ /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [Wsigncompare] 551  if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) {  ~~~~~~^~~~ /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [Wsigncompare] 593  for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {  ~~^~~~~ /home/biocbuild/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [Wsigncompare] 535  if (nnz != x.size()) { /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [Wsigncompare] 551  if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) {  ~~~~~~^~~~ /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [Wsigncompare] 551  if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) {  ~~~~~~^~~~ /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [Wsigncompare] 593  for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {  ~~^~~~~ /home/biocbuild/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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]’ /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [Wsigncompare] 250  if (idex != *pIt && static_cast<size_t>(i[idex]) == r) {  ~~~~~^~~~~~~ /home/biocbuild/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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]’ /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [Wsigncompare] /home/biocbuild/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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]’ /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [Wsigncompare] /home/biocbuild/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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]’ /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [Wsigncompare] g++ std=gnu++11 I"/home/biocbuild/bbs3.16bioc/R/include" DNDEBUG I../inst/include/ I'/home/biocbuild/bbs3.16bioc/R/sitelibrary/Rcpp/include' I'/home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include' I/usr/local/include fpic g O2 Wall c downsample_counts.cpp o downsample_counts.o In file included from /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/lin_matrix.h:12, from /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/read_lin_block.h:11, from /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/beachmat.h:24, from downsample_counts.cpp:2: /home/biocbuild/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [Wsigncompare] 535  if (nnz != x.size()) { /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [Wsigncompare] 551  if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) {  ~~~~~~^~~~ /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [Wsigncompare] 551  if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) {  ~~~~~~^~~~ /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [Wsigncompare] 593  for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {  ~~^~~~~ /home/biocbuild/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [Wsigncompare] 535  if (nnz != x.size()) { /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [Wsigncompare] 551  if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) {  ~~~~~~^~~~ /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [Wsigncompare] 551  if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) {  ~~~~~~^~~~ /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [Wsigncompare] 593  for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {  ~~^~~~~ /home/biocbuild/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [Wsigncompare] 535  if (nnz != x.size()) { /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [Wsigncompare] 551  if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) {  ~~~~~~^~~~ /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [Wsigncompare] 551  if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) {  ~~~~~~^~~~ /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [Wsigncompare] 593  for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {  ~~^~~~~ /home/biocbuild/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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]’ /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [Wsigncompare] 250  if (idex != *pIt && static_cast<size_t>(i[idex]) == r) {  ~~~~~^~~~~~~ /home/biocbuild/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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]’ /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [Wsigncompare] /home/biocbuild/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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]’ /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [Wsigncompare] /home/biocbuild/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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]’ /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [Wsigncompare] g++ std=gnu++11 I"/home/biocbuild/bbs3.16bioc/R/include" DNDEBUG I../inst/include/ I'/home/biocbuild/bbs3.16bioc/R/sitelibrary/Rcpp/include' I'/home/biocbuild/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/lin_matrix.h:12, from /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/read_lin_block.h:11, from /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/beachmat.h:24, from fit_linear_model.cpp:2: /home/biocbuild/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [Wsigncompare] 535  if (nnz != x.size()) { /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [Wsigncompare] 551  if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) {  ~~~~~~^~~~ /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [Wsigncompare] 551  if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) {  ~~~~~~^~~~ /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [Wsigncompare] 593  for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {  ~~^~~~~ /home/biocbuild/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [Wsigncompare] 535  if (nnz != x.size()) { /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [Wsigncompare] 551  if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) {  ~~~~~~^~~~ /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [Wsigncompare] 551  if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) {  ~~~~~~^~~~ /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [Wsigncompare] 593  for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {  ~~^~~~~ /home/biocbuild/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [Wsigncompare] 535  if (nnz != x.size()) { /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [Wsigncompare] 551  if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) {  ~~~~~~^~~~ /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [Wsigncompare] 551  if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) {  ~~~~~~^~~~ /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [Wsigncompare] 593  for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {  ~~^~~~~ /home/biocbuild/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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]’ /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [Wsigncompare] 250  if (idex != *pIt && static_cast<size_t>(i[idex]) == r) {  ~~~~~^~~~~~~ /home/biocbuild/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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]’ /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [Wsigncompare] /home/biocbuild/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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]’ /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [Wsigncompare] /home/biocbuild/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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]’ /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [Wsigncompare] g++ std=gnu++11 I"/home/biocbuild/bbs3.16bioc/R/include" DNDEBUG I../inst/include/ I'/home/biocbuild/bbs3.16bioc/R/sitelibrary/Rcpp/include' I'/home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include' I/usr/local/include fpic g O2 Wall c pool_size_factors.cpp o pool_size_factors.o pool_size_factors.cpp: In function ‘Rcpp::List pool_size_factors(Rcpp::RObject, Rcpp::NumericVector, Rcpp::IntegerVector, Rcpp::IntegerVector)’: pool_size_factors.cpp:56:15: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [Wsigncompare] 56  if (ngenes!=pseudo_cell.size()) {  ~~~~~~^~~~~~~~~~~~~~~~~~~~ pool_size_factors.cpp:61:22: warning: comparison of integer expressions of different signedness: ‘R_xlen_t’ {aka ‘long int’} and ‘long unsigned int’ [Wsigncompare] 61  if (order.size() < ncells*21) {  ~~~~~~~~~~~~~^~~~~~~~~~~~ pool_size_factors.cpp:170:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [Wsigncompare] 170  for (auto i=0; i<n; ++i, ++val, ++rows) {  ~^~ In file included from /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/lin_matrix.h:12, from /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/read_lin_block.h:11, from /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/beachmat.h:24, from pool_size_factors.cpp:2: /home/biocbuild/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [Wsigncompare] 535  if (nnz != x.size()) { /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [Wsigncompare] 551  if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) {  ~~~~~~^~~~ /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [Wsigncompare] 551  if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) {  ~~~~~~^~~~ /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [Wsigncompare] 593  for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {  ~~^~~~~ /home/biocbuild/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [Wsigncompare] 535  if (nnz != x.size()) { /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [Wsigncompare] 551  if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) {  ~~~~~~^~~~ /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [Wsigncompare] 551  if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) {  ~~~~~~^~~~ /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [Wsigncompare] 593  for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {  ~~^~~~~ /home/biocbuild/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [Wsigncompare] 535  if (nnz != x.size()) { /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [Wsigncompare] 551  if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) {  ~~~~~~^~~~ /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [Wsigncompare] 551  if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) {  ~~~~~~^~~~ /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [Wsigncompare] 593  for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {  ~~^~~~~ /home/biocbuild/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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]’ /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [Wsigncompare] 250  if (idex != *pIt && static_cast<size_t>(i[idex]) == r) {  ~~~~~^~~~~~~ /home/biocbuild/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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]’ /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [Wsigncompare] /home/biocbuild/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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]’ /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [Wsigncompare] /home/biocbuild/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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]’ /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [Wsigncompare] g++ std=gnu++11 I"/home/biocbuild/bbs3.16bioc/R/include" DNDEBUG I../inst/include/ I'/home/biocbuild/bbs3.16bioc/R/sitelibrary/Rcpp/include' I'/home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include' I/usr/local/include fpic g O2 Wall c sum_counts.cpp o sum_counts.o In file included from /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/lin_matrix.h:12, from /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/read_lin_block.h:11, from /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/beachmat.h:24, from sum_counts.cpp:2: /home/biocbuild/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [Wsigncompare] 535  if (nnz != x.size()) { /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [Wsigncompare] 551  if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) {  ~~~~~~^~~~ /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [Wsigncompare] 551  if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) {  ~~~~~~^~~~ /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [Wsigncompare] 593  for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {  ~~^~~~~ /home/biocbuild/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [Wsigncompare] 535  if (nnz != x.size()) { /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [Wsigncompare] 551  if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) {  ~~~~~~^~~~ /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [Wsigncompare] 551  if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) {  ~~~~~~^~~~ /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [Wsigncompare] 593  for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {  ~~^~~~~ /home/biocbuild/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [Wsigncompare] 535  if (nnz != x.size()) { /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [Wsigncompare] 551  if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) {  ~~~~~~^~~~ /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [Wsigncompare] 551  if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) {  ~~~~~~^~~~ /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [Wsigncompare] 593  for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {  ~~^~~~~ /home/biocbuild/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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]’ /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [Wsigncompare] 250  if (idex != *pIt && static_cast<size_t>(i[idex]) == r) {  ~~~~~^~~~~~~ /home/biocbuild/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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]’ /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [Wsigncompare] /home/biocbuild/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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]’ /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [Wsigncompare] /home/biocbuild/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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/bbs3.16bioc/R/sitelibrary/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]’ /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here /home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [Wsigncompare] g++ std=gnu++11 I"/home/biocbuild/bbs3.16bioc/R/include" DNDEBUG I../inst/include/ I'/home/biocbuild/bbs3.16bioc/R/sitelibrary/Rcpp/include' I'/home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include' I/usr/local/include fpic g O2 Wall c utils.cpp o utils.o g++ std=gnu++11 shared L/home/biocbuild/bbs3.16bioc/R/lib L/usr/local/lib o scuttle.so RcppExports.o cumulative_prop.o downsample_counts.o fit_linear_model.o pool_size_factors.o sum_counts.o utils.o L/home/biocbuild/bbs3.16bioc/R/lib lRlapack L/home/biocbuild/bbs3.16bioc/R/lib lRblas lgfortran lm lquadmath L/home/biocbuild/bbs3.16bioc/R/lib lR installing to /home/biocbuild/bbs3.16bioc/R/sitelibrary/00LOCKscuttle/00new/scuttle/libs ** R ** inst ** bytecompile 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)
scuttle.Rcheck/tests/testthat.Rout
R version 4.2.3 (20230315)  "Shortstop Beagle" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64pclinuxgnu (64bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for online help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(scuttle) Loading required package: SingleCellExperiment Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'MatrixGenerics' The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians > test_check("scuttle") Loading required package: Matrix Attaching package: 'Matrix' The following object is masked from 'package:S4Vectors': expand Attaching package: 'DelayedArray' The following objects are masked from 'package:base': apply, rowsum, scale, sweep [ FAIL 0  WARN 0  SKIP 0  PASS 1688 ] > > proc.time() user system elapsed 93.546 4.347 117.616
scuttle.Rcheck/scuttleEx.timings
name  user  system  elapsed  
addPerCellQCMetrics  1.569  0.032  1.601  
aggregateAcrossCells  1.836  0.088  1.924  
aggregateAcrossFeatures  0.538  0.012  0.549  
calculateAverage  0.422  0.004  0.426  
calculateCPM  0.507  0.012  0.519  
calculateFPKM  0.429  0.016  0.445  
calculateTPM  0.433  0.000  0.433  
cleanSizeFactors  0.023  0.000  0.022  
computePooledFactors  6.473  0.268  6.741  
computeSpikeFactors  0.540  0.016  0.556  
correctGroupSummary  0.056  0.004  0.060  
downsampleBatches  4.543  0.072  4.615  
downsampleMatrix  3.031  0.024  3.055  
fitLinearModel  0.087  0.008  0.095  
geometricSizeFactors  0.441  0.020  0.461  
isOutlier  0.781  0.032  0.812  
librarySizeFactors  0.42  0.00  0.42  
logNormCounts  1.322  0.024  1.346  
makePerCellDF  0.818  0.016  0.834  
makePerFeatureDF  0.660  0.008  0.668  
medianSizeFactors  0.419  0.008  0.426  
mockSCE  0.477  0.004  0.482  
normalizeCounts  1.543  0.036  1.579  
numDetectedAcrossCells  0.481  0.024  0.505  
numDetectedAcrossFeatures  1.318  0.080  1.399  
perCellQCFilters  0.725  0.000  0.725  
perCellQCMetrics  1.561  0.012  1.573  
perFeatureQCMetrics  0.52  0.00  0.52  
quickPerCellQC  1.260  0.032  1.292  
readSparseCounts  0.007  0.000  0.007  
sumCountsAcrossCells  0.493  0.000  0.493  
sumCountsAcrossFeatures  0.441  0.000  0.442  
summarizeAssayByGroup  0.515  0.004  0.520  
uniquifyFeatureNames  0.000  0.000  0.001  