Aaron Lun
| Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022) |
| git_url: https://git.bioconductor.org/packages/scran |
| git_branch: RELEASE_3_15 |
| git_last_commit: 1a83eb7 |
| git_last_commit_date: 2022-09-08 20:09:29 -0400 (Thu, 08 Sep 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-10-19 13:22:15 -0400 (Wed, 19 Oct 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4386 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" | 4138 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4205 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
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 1787/2140 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| scran 1.24.1 (landing page) Aaron Lun
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: scran |
| Version: 1.24.1 |
| Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:scran.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings scran_1.24.1.tar.gz |
| StartedAt: 2022-10-19 04:00:00 -0400 (Wed, 19 Oct 2022) |
| EndedAt: 2022-10-19 04:13:59 -0400 (Wed, 19 Oct 2022) |
| EllapsedTime: 839.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: scran.Rcheck |
| Warnings: 1 |
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### Running command:
###
### F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:scran.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings scran_1.24.1.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/scran.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'scran/DESCRIPTION' ... OK
* this is package 'scran' version '1.24.1'
* 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 whether package 'scran' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII 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 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 cross-references ... 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 for x64 is not available
File 'F:/biocbuild/bbs-3.15-bioc/R/library/scran/libs/x64/scran.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* 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 10.42 2.14 12.58
pseudoBulkSpecific 7.36 0.12 7.48
buildSNNGraph 5.77 0.14 5.90
quickSubCluster 5.44 0.10 5.53
decideTestsPerLabel 5.30 0.05 5.36
pseudoBulkDGE 5.07 0.03 5.10
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 1 NOTE
See
'F:/biocbuild/bbs-3.15-bioc/meat/scran.Rcheck/00check.log'
for details.
scran.Rcheck/00install.out
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###
### Running command:
###
### F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL scran
###
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* installing to library 'F:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'scran' ...
** using staged installation
** libs
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/dqrng/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/scuttle/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/dqrng/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/scuttle/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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 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 long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
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 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 long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/dqrng/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/scuttle/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c combine_rho.cpp -o combine_rho.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/dqrng/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/scuttle/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c compute_blocked_stats.cpp -o compute_blocked_stats.o
In file included from F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:12,
from F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:11,
from F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/beachmat.h:24,
from compute_blocked_stats.cpp:2:
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56: required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:36:39: required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
535 | if (nnz != x.size()) {
| ~~~~^~~~~~~~~~~
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
| ~~~~~~^~~~
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
| ~~~~~~^~~~
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
593 | for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
| ~~^~~~~
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56: required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:38:39: required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
535 | if (nnz != x.size()) {
| ~~~~^~~~~~~~~~~
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
| ~~~~~~^~~~
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
| ~~~~~~^~~~
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
593 | for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
| ~~^~~~~
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56: required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:40:39: required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
535 | if (nnz != x.size()) {
| ~~~~^~~~~~~~~~~
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
| ~~~~~~^~~~
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
| ~~~~~~^~~~
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
593 | for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
| ~~^~~~~
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const double*; I = int; P = long long unsigned int; size_t = long long unsigned int]':
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:42: 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 long unsigned int]'
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:51: 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 long unsigned int]'
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const long long unsigned int' [-Wsign-compare]
250 | if (idex != *pIt && static_cast<size_t>(i[idex]) == r) {
| ~~~~~^~~~~~~
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const double*; I = int; P = long long unsigned int; size_t = long long unsigned int]':
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:42: 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 long unsigned int]'
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:54: 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 long unsigned int]'
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const long long unsigned int' [-Wsign-compare]
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const int*; I = int; P = long long unsigned int; size_t = long long unsigned int]':
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:42: 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 long unsigned int]'
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:51: 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 long unsigned int]'
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const long long unsigned int' [-Wsign-compare]
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const int*; I = int; P = long long unsigned int; size_t = long long unsigned int]':
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:42: 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 long unsigned int]'
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:54: 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 long unsigned int]'
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const long long unsigned int' [-Wsign-compare]
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/dqrng/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/scuttle/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c compute_residual_stats.cpp -o compute_residual_stats.o
In file included from F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:12,
from F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:11,
from F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/beachmat.h:24,
from compute_residual_stats.cpp:2:
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56: required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:36:39: required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
535 | if (nnz != x.size()) {
| ~~~~^~~~~~~~~~~
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
| ~~~~~~^~~~
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
| ~~~~~~^~~~
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
593 | for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
| ~~^~~~~
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56: required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:38:39: required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
535 | if (nnz != x.size()) {
| ~~~~^~~~~~~~~~~
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
| ~~~~~~^~~~
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
| ~~~~~~^~~~
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
593 | for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
| ~~^~~~~
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56: required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:40:39: required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
535 | if (nnz != x.size()) {
| ~~~~^~~~~~~~~~~
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
| ~~~~~~^~~~
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
| ~~~~~~^~~~
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
593 | for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
| ~~^~~~~
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const double*; I = int; P = long long unsigned int; size_t = long long unsigned int]':
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:42: 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 long unsigned int]'
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:51: 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 long unsigned int]'
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const long long unsigned int' [-Wsign-compare]
250 | if (idex != *pIt && static_cast<size_t>(i[idex]) == r) {
| ~~~~~^~~~~~~
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const double*; I = int; P = long long unsigned int; size_t = long long unsigned int]':
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:42: 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 long unsigned int]'
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:54: 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 long unsigned int]'
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const long long unsigned int' [-Wsign-compare]
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const int*; I = int; P = long long unsigned int; size_t = long long unsigned int]':
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:42: 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 long unsigned int]'
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:51: 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 long unsigned int]'
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const long long unsigned int' [-Wsign-compare]
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const int*; I = int; P = long long unsigned int; size_t = long long unsigned int]':
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:42: 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 long unsigned int]'
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:54: 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 long unsigned int]'
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const long long unsigned int' [-Wsign-compare]
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/dqrng/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/scuttle/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c compute_rho_null.cpp -o compute_rho_null.o
In file included from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/iterator/iterator_concepts.hpp:10,
from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/range/concepts.hpp:20,
from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/range/size_type.hpp:20,
from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/range/size.hpp:21,
from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/random/hyperexponential_distribution.hpp:29,
from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/random.hpp:70,
from rand_custom.h:6,
from compute_rho_null.cpp:3:
F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
194 | failed ************ (Pred::************
| ^
F:/biocbuild/bbs-3.15-bioc/R/library/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"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/dqrng/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/scuttle/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cyclone_scores.cpp -o cyclone_scores.o
In file included from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/iterator/iterator_concepts.hpp:10,
from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/range/concepts.hpp:20,
from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/range/algorithm.hpp:29,
from cyclone_scores.cpp:4:
F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
194 | failed ************ (Pred::************
| ^
F:/biocbuild/bbs-3.15-bioc/R/library/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 F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:12,
from F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:11,
from F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/beachmat.h:24,
from cyclone_scores.cpp:3:
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56: required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:36:39: required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
535 | if (nnz != x.size()) {
| ~~~~^~~~~~~~~~~
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
| ~~~~~~^~~~
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
| ~~~~~~^~~~
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
593 | for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
| ~~^~~~~
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56: required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:38:39: required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
535 | if (nnz != x.size()) {
| ~~~~^~~~~~~~~~~
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
| ~~~~~~^~~~
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
| ~~~~~~^~~~
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
593 | for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
| ~~^~~~~
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56: required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:40:39: required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
535 | if (nnz != x.size()) {
| ~~~~^~~~~~~~~~~
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
| ~~~~~~^~~~
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
| ~~~~~~^~~~
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
593 | for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
| ~~^~~~~
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const double*; I = int; P = long long unsigned int; size_t = long long unsigned int]':
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:42: 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 long unsigned int]'
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:51: 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 long unsigned int]'
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const long long unsigned int' [-Wsign-compare]
250 | if (idex != *pIt && static_cast<size_t>(i[idex]) == r) {
| ~~~~~^~~~~~~
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const double*; I = int; P = long long unsigned int; size_t = long long unsigned int]':
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:42: 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 long unsigned int]'
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:54: 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 long unsigned int]'
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const long long unsigned int' [-Wsign-compare]
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const int*; I = int; P = long long unsigned int; size_t = long long unsigned int]':
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:42: 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 long unsigned int]'
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:51: 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 long unsigned int]'
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const long long unsigned int' [-Wsign-compare]
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const int*; I = int; P = long long unsigned int; size_t = long long unsigned int]':
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:42: 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 long unsigned int]'
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:54: 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 long unsigned int]'
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const long long unsigned int' [-Wsign-compare]
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/dqrng/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/scuttle/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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 long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
214 | for (size_t i=0; i<left.size(); ++i, ++oIt) {
| ~^~~~~~~~~~~~
overlap_exprs.cpp:202:18: warning: unused variable 'ngroups' [-Wunused-variable]
202 | const size_t ngroups=groups.size();
| ^~~~~~~
In file included from F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:12,
from F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:11,
from F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/beachmat.h:24,
from overlap_exprs.cpp:3:
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56: required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:36:39: required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
535 | if (nnz != x.size()) {
| ~~~~^~~~~~~~~~~
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
| ~~~~~~^~~~
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
| ~~~~~~^~~~
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
593 | for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
| ~~^~~~~
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56: required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:38:39: required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
535 | if (nnz != x.size()) {
| ~~~~^~~~~~~~~~~
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
| ~~~~~~^~~~
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
| ~~~~~~^~~~
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
593 | for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
| ~~^~~~~
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56: required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:40:39: required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
535 | if (nnz != x.size()) {
| ~~~~^~~~~~~~~~~
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
| ~~~~~~^~~~
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
| ~~~~~~^~~~
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
593 | for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
| ~~^~~~~
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const double*; I = int; P = long long unsigned int; size_t = long long unsigned int]':
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:42: 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 long unsigned int]'
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:51: 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 long unsigned int]'
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const long long unsigned int' [-Wsign-compare]
250 | if (idex != *pIt && static_cast<size_t>(i[idex]) == r) {
| ~~~~~^~~~~~~
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const double*; I = int; P = long long unsigned int; size_t = long long unsigned int]':
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:42: 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 long unsigned int]'
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:54: 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 long unsigned int]'
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const long long unsigned int' [-Wsign-compare]
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const int*; I = int; P = long long unsigned int; size_t = long long unsigned int]':
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:42: 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 long unsigned int]'
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:51: 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 long unsigned int]'
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const long long unsigned int' [-Wsign-compare]
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const int*; I = int; P = long long unsigned int; size_t = long long unsigned int]':
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:42: 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 long unsigned int]'
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:54: 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 long unsigned int]'
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here
F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const long long unsigned int' [-Wsign-compare]
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/dqrng/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/scuttle/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rand_custom.cpp -o rand_custom.o
In file included from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/iterator/iterator_concepts.hpp:10,
from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/range/concepts.hpp:20,
from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/range/size_type.hpp:20,
from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/range/size.hpp:21,
from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/random/hyperexponential_distribution.hpp:29,
from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/random.hpp:70,
from rand_custom.h:6,
from rand_custom.cpp:1:
F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
194 | failed ************ (Pred::************
| ^
F:/biocbuild/bbs-3.15-bioc/R/library/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++ -shared -s -static-libgcc -o scran.dll tmp.def 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 -LF:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lRlapack -LF:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-scran/00new/scran/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** 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 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
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 on-line 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, 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
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
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':
aperm, apply, rowsum, scale, sweep
[ FAIL 0 | WARN 183 | SKIP 3 | PASS 4447 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• On Windows (2)
• monocle is a little broken because of clusterApply (1)
[ FAIL 0 | WARN 183 | SKIP 3 | PASS 4447 ]
>
> proc.time()
user system elapsed
410.87 4.81 519.96
scran.Rcheck/scran-Ex.timings
| name | user | system | elapsed | |
| DM | 0.06 | 0.00 | 0.07 | |
| buildSNNGraph | 5.77 | 0.14 | 5.90 | |
| clusterCells | 1.91 | 0.02 | 1.92 | |
| combineBlocks | 1.48 | 0.07 | 1.56 | |
| combineMarkers | 1.81 | 0.02 | 2.25 | |
| combinePValues | 0.04 | 0.00 | 0.03 | |
| combineVar | 1.18 | 0.05 | 1.24 | |
| computeMinRank | 0 | 0 | 0 | |
| convertTo | 3.13 | 0.11 | 3.23 | |
| correlateGenes | 1.54 | 0.04 | 1.60 | |
| correlateNull | 0.22 | 0.02 | 0.23 | |
| correlatePairs | 1.60 | 0.01 | 1.61 | |
| cyclone | 10.42 | 2.14 | 12.58 | |
| decideTestsPerLabel | 5.30 | 0.05 | 5.36 | |
| defunct | 0 | 0 | 0 | |
| denoisePCA | 2.28 | 0.03 | 2.31 | |
| findMarkers | 2.48 | 0.03 | 2.51 | |
| fitTrendCV2 | 0.74 | 0.00 | 0.74 | |
| fitTrendPoisson | 0.31 | 0.00 | 0.32 | |
| fitTrendVar | 1.05 | 0.00 | 1.04 | |
| fixedPCA | 1.28 | 0.00 | 1.28 | |
| getClusteredPCs | 2.94 | 0.03 | 2.97 | |
| getMarkerEffects | 1.07 | 0.02 | 1.09 | |
| getTopHVGs | 1.23 | 0.02 | 1.25 | |
| getTopMarkers | 2.39 | 0.00 | 2.40 | |
| logBH | 0 | 0 | 0 | |
| modelGeneCV2 | 1.25 | 0.00 | 1.25 | |
| modelGeneCV2WithSpikes | 1.33 | 0.01 | 1.34 | |
| modelGeneVar | 1.53 | 0.00 | 1.53 | |
| modelGeneVarByPoisson | 1.22 | 0.02 | 1.23 | |
| modelGeneVarWithSpikes | 1.63 | 0.00 | 1.63 | |
| multiMarkerStats | 2.03 | 0.00 | 2.03 | |
| pairwiseBinom | 0.93 | 0.04 | 0.97 | |
| pairwiseTTests | 1.12 | 0.00 | 1.12 | |
| pairwiseWilcox | 1.04 | 0.04 | 1.07 | |
| pseudoBulkDGE | 5.07 | 0.03 | 5.10 | |
| pseudoBulkSpecific | 7.36 | 0.12 | 7.48 | |
| quickCluster | 2.07 | 0.03 | 2.11 | |
| quickSubCluster | 5.44 | 0.10 | 5.53 | |
| rhoToPValue | 0 | 0 | 0 | |
| sandbag | 0.59 | 0.01 | 0.69 | |
| scaledColRanks | 1.67 | 0.08 | 1.75 | |
| scoreMarkers | 1.16 | 0.02 | 1.17 | |
| summaryMarkerStats | 1.17 | 0.03 | 1.20 | |
| testLinearModel | 0.08 | 0.00 | 0.08 | |