##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:BiocSingular.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings BiocSingular_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/BiocSingular.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiocSingular/DESCRIPTION’ ... OK
* this is package ‘BiocSingular’ version ‘1.6.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BiocSingular’ 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 compiled code ... NOTE
Note: information on .o files is not available
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/BiocSingular.Rcheck/00check.log’
for details.

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##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL BiocSingular
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘BiocSingular’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include' -I/usr/local/include   -fpic  -g -O2  -Wall -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 between signed and unsigned integer expressions [-Wsign-compare]
         if (numeric_centers.size()!=ncols) {
             ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:12:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:11,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/beachmat.h:24,
                 from compute_scale.cpp:2:
/home/biocbuild/bbs-3.12-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>]’:
/home/biocbuild/bbs-3.12-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>]’
/home/biocbuild/bbs-3.12-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>]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (nnz != x.size()) {
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                       ~~~~~~^~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                                                   ~~~~~~^~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
                                 ~~^~~~~
/home/biocbuild/bbs-3.12-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>]’:
/home/biocbuild/bbs-3.12-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>]’
/home/biocbuild/bbs-3.12-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>]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (nnz != x.size()) {
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                       ~~~~~~^~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                                                   ~~~~~~^~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
                                 ~~^~~~~
/home/biocbuild/bbs-3.12-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>]’:
/home/biocbuild/bbs-3.12-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>]’
/home/biocbuild/bbs-3.12-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>]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (nnz != x.size()) {
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                       ~~~~~~^~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                                                   ~~~~~~^~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
                                 ~~^~~~~
/home/biocbuild/bbs-3.12-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 unsigned int; size_t = long unsigned int]’:
/home/biocbuild/bbs-3.12-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 unsigned int]’
/home/biocbuild/bbs-3.12-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 unsigned int]’
compute_scale.cpp:73:1:   required from here
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (idex != *pIt && static_cast<size_t>(i[idex]) == r) {
                 ~~~~~^~~~~~~
/home/biocbuild/bbs-3.12-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 unsigned int; size_t = long unsigned int]’:
/home/biocbuild/bbs-3.12-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 unsigned int]’
/home/biocbuild/bbs-3.12-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 unsigned int]’
compute_scale.cpp:73:1:   required from here
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
/home/biocbuild/bbs-3.12-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 unsigned int; size_t = long unsigned int]’:
/home/biocbuild/bbs-3.12-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 unsigned int]’
/home/biocbuild/bbs-3.12-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 unsigned int]’
compute_scale.cpp:73:1:   required from here
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
/home/biocbuild/bbs-3.12-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 unsigned int; size_t = long unsigned int]’:
/home/biocbuild/bbs-3.12-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 unsigned int]’
/home/biocbuild/bbs-3.12-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 unsigned int]’
compute_scale.cpp:73:1:   required from here
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.12-bioc/R/lib -L/usr/local/lib -o BiocSingular.so RcppExports.o compute_scale.o -L/home/biocbuild/bbs-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-bioc/R/library/00LOCK-BiocSingular/00new/BiocSingular/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BiocSingular)

R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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(BiocSingular)
> library(testthat)
> test_check("BiocSingular")
Loading required package: stats4
Loading required package: Matrix
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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: 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: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:Matrix':

    expand

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges

Attaching package: 'DelayedArray'

The following objects are masked from 'package:base':

    aperm, apply, rowsum

[ FAIL 0 | WARN 6 | SKIP 0 | PASS 10405 ]
> 
> proc.time()
   user  system elapsed 
142.908  60.412 165.146