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This page was generated on 2022-03-18 11:07:02 -0400 (Fri, 18 Mar 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" 4334
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4097
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" 4083
merida1macOS 10.14.6 Mojavex86_64R 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

INSTALL results for BiocSingular on riesling1


To the developers/maintainers of the BiocSingular package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BiocSingular.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.

raw results

Package 166/2090HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocSingular 1.11.0  (landing page)
Aaron Lun
Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022)
git_url: https://git.bioconductor.org/packages/BiocSingular
git_branch: master
git_last_commit: 706a908
git_last_commit_date: 2021-10-26 12:49:33 -0400 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: BiocSingular
Version: 1.11.0
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL BiocSingular
StartedAt: 2022-03-17 15:40:38 -0400 (Thu, 17 Mar 2022)
EndedAt: 2022-03-17 15:42:10 -0400 (Thu, 17 Mar 2022)
EllapsedTime: 91.2 seconds
RetCode: 0
Status:   OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL BiocSingular
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'BiocSingular' ...
** 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"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"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c compute_scale.cpp -o compute_scale.o
compute_scale.cpp: In function 'Rcpp::NumericVector compute_scale(Rcpp::RObject, Rcpp::RObject)':
compute_scale.cpp:21:35: 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 (numeric_centers.size()!=ncols) {
             ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~
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 compute_scale.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++ -shared -s -static-libgcc -o BiocSingular.dll tmp.def RcppExports.o compute_scale.o -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-BiocSingular/00new/BiocSingular/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BiocSingular'
    finding HTML links ... done
    BiocSingularParam                       html  
    finding level-2 HTML links ... done

    DeferredMatrix                          html  
    LowRankMatrix                           html  
    ResidualMatrix                          html  
    options                                 html  
    runExactSVD                             html  
    runIrlbaSVD                             html  
    runPCA                                  html  
    runRandomSVD                            html  
    runSVD                                  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 (BiocSingular)
Making 'packages.html' ... done