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

This page was generated on 20230412 11:05:18 0400 (Wed, 12 Apr 2023).
Hostname  OS  Arch (*)  R version  Installed pkgs 

nebbiolo2  Linux (Ubuntu 20.04.5 LTS)  x86_64  4.2.3 (20230315)  "Shortstop Beagle"  4502 
palomino4  Windows Server 2022 Datacenter  x64  4.2.3 (20230315 ucrt)  "Shortstop Beagle"  4282 
lconway  macOS 12.5.1 Monterey  x86_64  4.2.3 (20230315)  "Shortstop Beagle"  4310 
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To the developers/maintainers of the scran package:  Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scran.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 1816/2183  Hostname  OS / Arch  INSTALL  BUILD  CHECK  BUILD BIN  
scran 1.26.2 (landing page) Aaron Lun
 nebbiolo2  Linux (Ubuntu 20.04.5 LTS) / x86_64  OK  OK  WARNINGS  
palomino4  Windows Server 2022 Datacenter / x64  OK  OK  WARNINGS  OK  
lconway  macOS 12.5.1 Monterey / x86_64  OK  OK  WARNINGS  OK  
Package: scran 
Version: 1.26.2 
Command: /home/biocbuild/bbs3.16bioc/R/bin/R CMD check install=check:scran.installout.txt library=/home/biocbuild/bbs3.16bioc/R/sitelibrary timings scran_1.26.2.tar.gz 
StartedAt: 20230410 23:50:41 0400 (Mon, 10 Apr 2023) 
EndedAt: 20230411 00:04:58 0400 (Tue, 11 Apr 2023) 
EllapsedTime: 856.8 seconds 
RetCode: 0 
Status: WARNINGS 
CheckDir: scran.Rcheck 
Warnings: 1 
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs3.16bioc/R/bin/R CMD check install=check:scran.installout.txt library=/home/biocbuild/bbs3.16bioc/R/sitelibrary timings scran_1.26.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs3.16bioc/meat/scran.Rcheck’ * using R version 4.2.3 (20230315) * using platform: x86_64pclinuxgnu (64bit) * using session charset: UTF8 * checking for file ‘scran/DESCRIPTION’ ... OK * this is package ‘scran’ version ‘1.26.2’ * 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 ‘scran’ can be installed ... OK * checking installed package size ... NOTE installed size is 11.9Mb subdirectories of 1Mb or more: libs 10.9Mb * 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 ... WARNING Found the following significant warnings: Warning: 'combinePValues' is deprecated. Warning: 'combinePValues' is deprecated. Warning: 'combinePValues' is deprecated. Warning: 'combinePValues' is deprecated. Warning: 'correlateNull' is deprecated. Warning: 'correlateNull' is deprecated. Warning: 'correlateNull' is deprecated. Deprecated functions may be defunct as soon as of the next release of R. See ?Deprecated. Examples with CPU (user + system) or elapsed time > 5s user system elapsed cyclone 10.062 0.084 10.146 buildSNNGraph 6.125 0.044 6.170 pseudoBulkSpecific 5.061 0.039 5.101 * 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 ... ‘scran.Rmd’ using ‘UTF8’... OK NONE * checking rebuilding of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 2 NOTEs See ‘/home/biocbuild/bbs3.16bioc/meat/scran.Rcheck/00check.log’ for details.
scran.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs3.16bioc/R/bin/R CMD INSTALL scran ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs3.16bioc/R/sitelibrary’ * installing *source* package ‘scran’ ... ** using staged installation ** libs g++ std=gnu++11 I"/home/biocbuild/bbs3.16bioc/R/include" DNDEBUG I'/home/biocbuild/bbs3.16bioc/R/sitelibrary/Rcpp/include' I'/home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include' I'/home/biocbuild/bbs3.16bioc/R/sitelibrary/BH/include' I'/home/biocbuild/bbs3.16bioc/R/sitelibrary/dqrng/include' I'/home/biocbuild/bbs3.16bioc/R/sitelibrary/scuttle/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'/home/biocbuild/bbs3.16bioc/R/sitelibrary/Rcpp/include' I'/home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include' I'/home/biocbuild/bbs3.16bioc/R/sitelibrary/BH/include' I'/home/biocbuild/bbs3.16bioc/R/sitelibrary/dqrng/include' I'/home/biocbuild/bbs3.16bioc/R/sitelibrary/scuttle/include' I/usr/local/include fpic g O2 Wall c choose_effect_size.cpp o choose_effect_size.o choose_effect_size.cpp: In instantiation of ‘size_t instantiate_list(Rcpp::List, std::vector<T>&, std::string) [with V = Rcpp::Vector<13>; size_t = long unsigned int; Rcpp::List = Rcpp::Vector<19>; std::string = std::__cxx11::basic_string<char>]’: choose_effect_size.cpp:38:67: required from here choose_effect_size.cpp:13:23: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [Wsigncompare] 13  for (size_t c=0; c<input.size(); ++c) {  ~^~~~~~~~~~~~~ choose_effect_size.cpp: In instantiation of ‘size_t instantiate_list(Rcpp::List, std::vector<T>&, std::string) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; size_t = long unsigned int; Rcpp::List = Rcpp::Vector<19>; std::string = std::__cxx11::basic_string<char>]’: choose_effect_size.cpp:67:70: required from here choose_effect_size.cpp:13:23: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [Wsigncompare] g++ std=gnu++11 I"/home/biocbuild/bbs3.16bioc/R/include" DNDEBUG I'/home/biocbuild/bbs3.16bioc/R/sitelibrary/Rcpp/include' I'/home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include' I'/home/biocbuild/bbs3.16bioc/R/sitelibrary/BH/include' I'/home/biocbuild/bbs3.16bioc/R/sitelibrary/dqrng/include' I'/home/biocbuild/bbs3.16bioc/R/sitelibrary/scuttle/include' I/usr/local/include fpic g O2 Wall c combine_rho.cpp o combine_rho.o g++ std=gnu++11 I"/home/biocbuild/bbs3.16bioc/R/include" DNDEBUG I'/home/biocbuild/bbs3.16bioc/R/sitelibrary/Rcpp/include' I'/home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include' I'/home/biocbuild/bbs3.16bioc/R/sitelibrary/BH/include' I'/home/biocbuild/bbs3.16bioc/R/sitelibrary/dqrng/include' I'/home/biocbuild/bbs3.16bioc/R/sitelibrary/scuttle/include' I/usr/local/include fpic g O2 Wall c compute_blocked_stats.cpp o compute_blocked_stats.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 compute_blocked_stats.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'/home/biocbuild/bbs3.16bioc/R/sitelibrary/Rcpp/include' I'/home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include' I'/home/biocbuild/bbs3.16bioc/R/sitelibrary/BH/include' I'/home/biocbuild/bbs3.16bioc/R/sitelibrary/dqrng/include' I'/home/biocbuild/bbs3.16bioc/R/sitelibrary/scuttle/include' I/usr/local/include fpic g O2 Wall c compute_residual_stats.cpp o compute_residual_stats.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 compute_residual_stats.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'/home/biocbuild/bbs3.16bioc/R/sitelibrary/Rcpp/include' I'/home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include' I'/home/biocbuild/bbs3.16bioc/R/sitelibrary/BH/include' I'/home/biocbuild/bbs3.16bioc/R/sitelibrary/dqrng/include' I'/home/biocbuild/bbs3.16bioc/R/sitelibrary/scuttle/include' I/usr/local/include fpic g O2 Wall c compute_rho_null.cpp o compute_rho_null.o In file included from /home/biocbuild/bbs3.16bioc/R/sitelibrary/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/biocbuild/bbs3.16bioc/R/sitelibrary/BH/include/boost/mpl/arg.hpp:25, from /home/biocbuild/bbs3.16bioc/R/sitelibrary/BH/include/boost/mpl/placeholders.hpp:24, from /home/biocbuild/bbs3.16bioc/R/sitelibrary/BH/include/boost/iterator/iterator_categories.hpp:16, from /home/biocbuild/bbs3.16bioc/R/sitelibrary/BH/include/boost/iterator/iterator_concepts.hpp:10, from /home/biocbuild/bbs3.16bioc/R/sitelibrary/BH/include/boost/range/concepts.hpp:20, from /home/biocbuild/bbs3.16bioc/R/sitelibrary/BH/include/boost/range/size_type.hpp:20, from /home/biocbuild/bbs3.16bioc/R/sitelibrary/BH/include/boost/range/size.hpp:21, from /home/biocbuild/bbs3.16bioc/R/sitelibrary/BH/include/boost/random/hyperexponential_distribution.hpp:29, from /home/biocbuild/bbs3.16bioc/R/sitelibrary/BH/include/boost/random.hpp:70, from rand_custom.h:6, from compute_rho_null.cpp:3: /home/biocbuild/bbs3.16bioc/R/sitelibrary/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [Wparentheses] 194  failed ************ (Pred::************  ^ /home/biocbuild/bbs3.16bioc/R/sitelibrary/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [Wparentheses] 199  failed ************ (boost::mpl::not_<Pred>::************  ^ g++ std=gnu++11 I"/home/biocbuild/bbs3.16bioc/R/include" DNDEBUG I'/home/biocbuild/bbs3.16bioc/R/sitelibrary/Rcpp/include' I'/home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include' I'/home/biocbuild/bbs3.16bioc/R/sitelibrary/BH/include' I'/home/biocbuild/bbs3.16bioc/R/sitelibrary/dqrng/include' I'/home/biocbuild/bbs3.16bioc/R/sitelibrary/scuttle/include' I/usr/local/include fpic g O2 Wall c cyclone_scores.cpp o cyclone_scores.o In file included from /home/biocbuild/bbs3.16bioc/R/sitelibrary/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/biocbuild/bbs3.16bioc/R/sitelibrary/BH/include/boost/mpl/arg.hpp:25, from /home/biocbuild/bbs3.16bioc/R/sitelibrary/BH/include/boost/mpl/placeholders.hpp:24, from /home/biocbuild/bbs3.16bioc/R/sitelibrary/BH/include/boost/iterator/iterator_categories.hpp:16, from /home/biocbuild/bbs3.16bioc/R/sitelibrary/BH/include/boost/iterator/iterator_concepts.hpp:10, from /home/biocbuild/bbs3.16bioc/R/sitelibrary/BH/include/boost/range/concepts.hpp:20, from /home/biocbuild/bbs3.16bioc/R/sitelibrary/BH/include/boost/range/algorithm.hpp:29, from cyclone_scores.cpp:4: /home/biocbuild/bbs3.16bioc/R/sitelibrary/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [Wparentheses] 194  failed ************ (Pred::************  ^ /home/biocbuild/bbs3.16bioc/R/sitelibrary/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [Wparentheses] 199  failed ************ (boost::mpl::not_<Pred>::************  ^ 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 cyclone_scores.cpp:3: /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'/home/biocbuild/bbs3.16bioc/R/sitelibrary/Rcpp/include' I'/home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include' I'/home/biocbuild/bbs3.16bioc/R/sitelibrary/BH/include' I'/home/biocbuild/bbs3.16bioc/R/sitelibrary/dqrng/include' I'/home/biocbuild/bbs3.16bioc/R/sitelibrary/scuttle/include' I/usr/local/include fpic g O2 Wall c overlap_exprs.cpp o overlap_exprs.o overlap_exprs.cpp: In function ‘Rcpp::NumericMatrix overlap_exprs_paired(Rcpp::RObject, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::List, double)’: overlap_exprs.cpp:214:27: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [Wsigncompare] 214  for (size_t i=0; i<left.size(); ++i, ++oIt) {  ~^~~~~~~~~~~~ overlap_exprs.cpp:202:18: warning: unused variable ‘ngroups’ [Wunusedvariable] 202  const size_t ngroups=groups.size();  ^~~~~~~ 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 overlap_exprs.cpp:3: /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'/home/biocbuild/bbs3.16bioc/R/sitelibrary/Rcpp/include' I'/home/biocbuild/bbs3.16bioc/R/sitelibrary/beachmat/include' I'/home/biocbuild/bbs3.16bioc/R/sitelibrary/BH/include' I'/home/biocbuild/bbs3.16bioc/R/sitelibrary/dqrng/include' I'/home/biocbuild/bbs3.16bioc/R/sitelibrary/scuttle/include' I/usr/local/include fpic g O2 Wall c rand_custom.cpp o rand_custom.o In file included from /home/biocbuild/bbs3.16bioc/R/sitelibrary/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/biocbuild/bbs3.16bioc/R/sitelibrary/BH/include/boost/mpl/arg.hpp:25, from /home/biocbuild/bbs3.16bioc/R/sitelibrary/BH/include/boost/mpl/placeholders.hpp:24, from /home/biocbuild/bbs3.16bioc/R/sitelibrary/BH/include/boost/iterator/iterator_categories.hpp:16, from /home/biocbuild/bbs3.16bioc/R/sitelibrary/BH/include/boost/iterator/iterator_concepts.hpp:10, from /home/biocbuild/bbs3.16bioc/R/sitelibrary/BH/include/boost/range/concepts.hpp:20, from /home/biocbuild/bbs3.16bioc/R/sitelibrary/BH/include/boost/range/size_type.hpp:20, from /home/biocbuild/bbs3.16bioc/R/sitelibrary/BH/include/boost/range/size.hpp:21, from /home/biocbuild/bbs3.16bioc/R/sitelibrary/BH/include/boost/random/hyperexponential_distribution.hpp:29, from /home/biocbuild/bbs3.16bioc/R/sitelibrary/BH/include/boost/random.hpp:70, from rand_custom.h:6, from rand_custom.cpp:1: /home/biocbuild/bbs3.16bioc/R/sitelibrary/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [Wparentheses] 194  failed ************ (Pred::************  ^ /home/biocbuild/bbs3.16bioc/R/sitelibrary/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [Wparentheses] 199  failed ************ (boost::mpl::not_<Pred>::************  ^ g++ std=gnu++11 shared L/home/biocbuild/bbs3.16bioc/R/lib L/usr/local/lib o scran.so RcppExports.o choose_effect_size.o combine_rho.o compute_blocked_stats.o compute_residual_stats.o compute_rho_null.o cyclone_scores.o overlap_exprs.o rand_custom.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/00LOCKscran/00new/scran/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 (scran)
scran.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(scran) 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 Loading required package: scuttle > test_check("scran") 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 In file included from /home/biocbuild/bbs3.16bioc/R/sitelibrary/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/biocbuild/bbs3.16bioc/R/sitelibrary/BH/include/boost/mpl/arg.hpp:25, from /home/biocbuild/bbs3.16bioc/R/sitelibrary/BH/include/boost/mpl/placeholders.hpp:24, from /home/biocbuild/bbs3.16bioc/R/sitelibrary/BH/include/boost/iterator/iterator_categories.hpp:16, from /home/biocbuild/bbs3.16bioc/R/sitelibrary/BH/include/boost/iterator/iterator_concepts.hpp:10, from /home/biocbuild/bbs3.16bioc/R/sitelibrary/BH/include/boost/range/concepts.hpp:20, from /home/biocbuild/bbs3.16bioc/R/sitelibrary/BH/include/boost/range/algorithm.hpp:29, from filef8267c09c962.cpp:3: /home/biocbuild/bbs3.16bioc/R/sitelibrary/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [Wparentheses] 194  failed ************ (Pred::************  ^ /home/biocbuild/bbs3.16bioc/R/sitelibrary/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [Wparentheses] 199  failed ************ (boost::mpl::not_<Pred>::************  ^ [ FAIL 0  WARN 194  SKIP 1  PASS 4478 ] ══ Skipped tests ═══════════════════════════════════════════════════════════════ • monocle is a little broken because of clusterApply (1) [ FAIL 0  WARN 194  SKIP 1  PASS 4478 ] > > proc.time() user system elapsed 329.091 14.382 410.924
scran.Rcheck/scranEx.timings
name  user  system  elapsed  
DM  0.041  0.001  0.040  
buildSNNGraph  6.125  0.044  6.170  
clusterCells  2.180  0.004  2.184  
combineBlocks  1.043  0.032  1.076  
combineMarkers  1.569  0.004  1.574  
combinePValues  0.030  0.004  0.033  
combineVar  1.052  0.011  1.064  
computeMinRank  0.002  0.001  0.001  
convertTo  2.539  0.044  2.583  
correlateGenes  1.821  0.064  1.885  
correlateNull  0.222  0.000  0.222  
correlatePairs  1.847  0.020  1.867  
cyclone  10.062  0.084  10.146  
decideTestsPerLabel  3.050  0.120  3.171  
defunct  0.000  0.000  0.001  
denoisePCA  1.423  0.008  1.431  
findMarkers  2.152  0.004  2.156  
fitTrendCV2  0.601  0.000  0.601  
fitTrendPoisson  0.173  0.000  0.173  
fitTrendVar  1.165  0.020  1.185  
fixedPCA  1.150  0.012  1.162  
getClusteredPCs  3.218  0.008  3.226  
getMarkerEffects  1.049  0.012  1.061  
getTopHVGs  0.760  0.003  0.763  
getTopMarkers  1.714  0.013  1.727  
logBH  0.001  0.000  0.001  
modelGeneCV2  0.958  0.003  0.961  
modelGeneCV2WithSpikes  1.280  0.012  1.292  
modelGeneVar  1.261  0.001  1.260  
modelGeneVarByPoisson  0.950  0.007  0.959  
modelGeneVarWithSpikes  1.141  0.004  1.145  
multiMarkerStats  1.488  0.000  1.489  
pairwiseBinom  0.792  0.004  0.797  
pairwiseTTests  0.859  0.000  0.860  
pairwiseWilcox  0.710  0.007  0.718  
pseudoBulkDGE  2.857  0.048  2.906  
pseudoBulkSpecific  5.061  0.039  5.101  
quickCluster  1.828  0.004  1.832  
quickSubCluster  4.482  0.021  4.502  
rhoToPValue  0  0  0  
sandbag  0.631  0.003  0.635  
scaledColRanks  1.314  0.000  1.314  
scoreMarkers  1.125  0.001  1.124  
summaryMarkerStats  0.757  0.000  0.757  
testLinearModel  0.057  0.000  0.058  