Jonathan Griffiths
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/DropletUtils |
| git_branch: master |
| git_last_commit: b5fd73b |
| git_last_commit_date: 2021-11-11 13:22:23 -0400 (Thu, 11 Nov 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:25 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 DropletUtils package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DropletUtils.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 549/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| DropletUtils 1.15.2 (landing page) Jonathan Griffiths
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: DropletUtils |
| Version: 1.15.2 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DropletUtils.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings DropletUtils_1.15.2.tar.gz |
| StartedAt: 2022-03-17 18:58:54 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:05:17 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 383.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DropletUtils.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DropletUtils.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings DropletUtils_1.15.2.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/DropletUtils.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DropletUtils/DESCRIPTION' ... OK
* this is package 'DropletUtils' version '1.15.2'
* 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 ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'DropletUtils' can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.6Mb
sub-directories of 1Mb or more:
libs 5.0Mb
* 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 ... NOTE
GNU make is a SystemRequirements.
* 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 'D:/biocbuild/bbs-3.15-bioc/R/library/DropletUtils/libs/x64/DropletUtils.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
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 ... OK
* 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: 4 NOTEs
See
'D:/biocbuild/bbs-3.15-bioc/meat/DropletUtils.Rcheck/00check.log'
for details.
DropletUtils.Rcheck/00install.out
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##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL DropletUtils
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'DropletUtils' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/dqrng/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/scuttle/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/dqrng/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/scuttle/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c downsample_run.cpp -o downsample_run.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/dqrng/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/scuttle/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c encode_sequences.cpp -o encode_sequences.o
encode_sequences.cpp: In function 'Rcpp::IntegerVector encode_sequences(Rcpp::StringVector)':
encode_sequences.cpp:8:23: 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]
for (size_t i=0; i<output.size(); ++i) {
~^~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/dqrng/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/scuttle/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c find_chimeric.cpp -o find_chimeric.o
find_chimeric.cpp: In function 'Rcpp::List find_chimeric(Rcpp::StringVector, Rcpp::IntegerVector, Rcpp::IntegerVector, double, bool)':
find_chimeric.cpp:28:23: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'long long int' [-Wsign-compare]
for (size_t i=0; i<nmolecules; ++i, ++uIt) {
~^~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/dqrng/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/scuttle/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c find_swapped.cpp -o find_swapped.o
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:12,
from D:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:11,
from D:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/beachmat.h:24,
from find_swapped.cpp:2:
D:/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>]':
D:/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>]'
D:/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>]'
D:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here
D:/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]
if (nnz != x.size()) {
D:/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]
if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
~~~~~~^~~~
D:/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]
if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
~~~~~~^~~~
D:/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]
for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
~~^~~~~
D:/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>]':
D:/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>]'
D:/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>]'
D:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here
D:/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]
if (nnz != x.size()) {
D:/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]
if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
~~~~~~^~~~
D:/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]
if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
~~~~~~^~~~
D:/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]
for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
~~^~~~~
D:/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>]':
D:/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>]'
D:/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>]'
D:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here
D:/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]
if (nnz != x.size()) {
D:/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]
if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
~~~~~~^~~~
D:/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]
if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
~~~~~~^~~~
D:/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]
for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
~~^~~~~
D:/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]':
D:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73: required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const int*; ALT = int*; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long long unsigned int]'
D:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82: required from 'beachmat::sparse_index<const int*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long long unsigned int]'
D:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here
D:/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]
if (idex != *pIt && static_cast<size_t>(i[idex]) == r) {
~~~~~^~~~~~~
D:/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]':
D:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73: required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const double*; ALT = double*; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long long unsigned int]'
D:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85: required from 'beachmat::sparse_index<const double*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long long unsigned int]'
D:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here
D:/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]
D:/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]':
D:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73: required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const int*; ALT = int*; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long long unsigned int]'
D:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82: required from 'beachmat::sparse_index<const int*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long long unsigned int]'
D:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here
D:/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]
D:/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]':
D:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73: required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const double*; ALT = double*; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long long unsigned int]'
D:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85: required from 'beachmat::sparse_index<const double*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long long unsigned int]'
D:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here
D:/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]
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/dqrng/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/scuttle/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c get_cell_barcodes.cpp -o get_cell_barcodes.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/dqrng/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/scuttle/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c group_cells.cpp -o group_cells.o
group_cells.cpp: In function 'Rcpp::List group_cells(Rcpp::StringVector, Rcpp::IntegerVector)':
group_cells.cpp:10:10: 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]
if (N!=gems.size()) {
~^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/dqrng/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/scuttle/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c hashed_deltas.cpp -o hashed_deltas.o
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:12,
from D:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:11,
from D:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/beachmat.h:24,
from hashed_deltas.cpp:2:
D:/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>]':
D:/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>]'
D:/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>]'
D:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here
D:/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]
if (nnz != x.size()) {
D:/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]
if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
~~~~~~^~~~
D:/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]
if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
~~~~~~^~~~
D:/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]
for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
~~^~~~~
D:/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>]':
D:/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>]'
D:/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>]'
D:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here
D:/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]
if (nnz != x.size()) {
D:/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]
if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
~~~~~~^~~~
D:/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]
if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
~~~~~~^~~~
D:/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]
for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
~~^~~~~
D:/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>]':
D:/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>]'
D:/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>]'
D:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here
D:/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]
if (nnz != x.size()) {
D:/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]
if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
~~~~~~^~~~
D:/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]
if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
~~~~~~^~~~
D:/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]
for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
~~^~~~~
D:/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]':
D:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73: required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const int*; ALT = int*; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long long unsigned int]'
D:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82: required from 'beachmat::sparse_index<const int*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long long unsigned int]'
D:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here
D:/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]
if (idex != *pIt && static_cast<size_t>(i[idex]) == r) {
~~~~~^~~~~~~
D:/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]':
D:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73: required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const double*; ALT = double*; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long long unsigned int]'
D:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85: required from 'beachmat::sparse_index<const double*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long long unsigned int]'
D:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here
D:/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]
D:/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]':
D:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73: required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const int*; ALT = int*; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long long unsigned int]'
D:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82: required from 'beachmat::sparse_index<const int*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long long unsigned int]'
D:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here
D:/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]
D:/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]':
D:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73: required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const double*; ALT = double*; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long long unsigned int]'
D:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85: required from 'beachmat::sparse_index<const double*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long long unsigned int]'
D:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here
D:/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]
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/dqrng/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/scuttle/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c montecarlo_pval.cpp -o montecarlo_pval.o
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/iterator/iterator_concepts.hpp:10,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/range/concepts.hpp:20,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/range/size_type.hpp:20,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/range/size.hpp:21,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/random/hyperexponential_distribution.hpp:29,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/random.hpp:70,
from montecarlo_pval.cpp:3:
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::************
^
D:/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]
failed ************ (boost::mpl::not_<Pred>::************
^
montecarlo_pval.cpp: In function 'Rcpp::IntegerVector montecarlo_pval(Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::NumericVector, Rcpp::NumericVector, int, double, Rcpp::List, Rcpp::IntegerVector)':
montecarlo_pval.cpp:99:23: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'const int' [-Wsign-compare]
if (higher<curlen) {
~~~~~~^~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/dqrng/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/scuttle/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c rand_custom.cpp -o rand_custom.o
rand_custom.cpp: In function 'void check_pcg_vectors(Rcpp::List, Rcpp::IntegerVector, size_t, const char*)':
rand_custom.cpp:8:21: warning: comparison of integer expressions of different signedness: 'R_xlen_t' {aka 'long long int'} and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
if (seeds.size()!=N) {
~~~~~~~~~~~~^~~
rand_custom.cpp:14:23: warning: comparison of integer expressions of different signedness: 'R_xlen_t' {aka 'long long int'} and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
if (streams.size()!=N) {
~~~~~~~~~~~~~~^~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/beachmat/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/dqrng/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/scuttle/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c utils.cpp -o utils.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o DropletUtils.dll tmp.def RcppExports.o downsample_run.o encode_sequences.o find_chimeric.o find_swapped.o get_cell_barcodes.o group_cells.o hashed_deltas.o montecarlo_pval.o rand_custom.o utils.o -LD:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/lib/x64 -lhdf5_cpp -lhdf5 -lcurl -lssh2 -lssl -lcrypto -lwldap32 -lws2_32 -lcrypt32 -lszip -lz -lpsapi -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-DropletUtils/00new/DropletUtils/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'DropletUtils'
finding HTML links ... done
ambientContribMaximum html
finding level-2 HTML links ... done
ambientContribNegative html
ambientContribSparse html
ambientProfileBimodal html
ambientProfileEmpty html
barcodeRanks html
chimericDrops html
cleanTagCounts html
defaultDrops html
downsampleReads html
emptyDrops html
emptyDropsCellRanger html
encodeSequences html
get10xMolInfoStats html
hashedDrops html
makeCountMatrix html
read10xCounts html
read10xMolInfo html
reexports html
removeAmbience html
swappedDrops html
write10xCounts html
** 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 (DropletUtils)
Making 'packages.html' ... done
DropletUtils.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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(DropletUtils)
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
> test_check("DropletUtils")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 993 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 993 ]
>
> proc.time()
user system elapsed
191.31 4.68 207.73
DropletUtils.Rcheck/DropletUtils-Ex.timings
| name | user | system | elapsed | |
| ambientContribMaximum | 0.41 | 0.00 | 0.40 | |
| ambientContribNegative | 0.03 | 0.00 | 0.03 | |
| ambientContribSparse | 0.03 | 0.00 | 0.04 | |
| ambientProfileBimodal | 0 | 0 | 0 | |
| ambientProfileEmpty | 0.62 | 0.03 | 0.65 | |
| barcodeRanks | 0.27 | 0.03 | 0.30 | |
| chimericDrops | 0.16 | 0.00 | 0.25 | |
| cleanTagCounts | 0.04 | 0.00 | 0.05 | |
| defaultDrops | 0.13 | 0.02 | 0.14 | |
| downsampleReads | 0.14 | 0.03 | 0.17 | |
| emptyDrops | 3.25 | 0.18 | 3.44 | |
| emptyDropsCellRanger | 2.61 | 0.22 | 2.82 | |
| encodeSequences | 0.01 | 0.00 | 0.02 | |
| get10xMolInfoStats | 0.61 | 0.05 | 0.67 | |
| hashedDrops | 0.10 | 0.02 | 0.11 | |
| makeCountMatrix | 0 | 0 | 0 | |
| read10xCounts | 0.39 | 0.06 | 0.61 | |
| read10xMolInfo | 0.11 | 0.03 | 0.25 | |
| removeAmbience | 0.36 | 0.06 | 0.42 | |
| swappedDrops | 0.40 | 0.10 | 0.66 | |
| write10xCounts | 0.13 | 0.04 | 0.44 | |