Package: DropletUtils

Version: 1.6.1

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:DropletUtils.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings DropletUtils_1.6.1.tar.gz

StartedAt: 2020-04-15 05:23:20 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 05:28:21 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 301.4 seconds

RetCode: 0

Status:  OK

CheckDir: DropletUtils.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:DropletUtils.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings DropletUtils_1.6.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/DropletUtils.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DropletUtils/DESCRIPTION’ ... OK
* this is package ‘DropletUtils’ version ‘1.6.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘DropletUtils’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 27.3Mb
  sub-directories of 1Mb or more:
    libs  27.1Mb
* 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 compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.10-bioc/R/library/DropletUtils/libs/DropletUtils.so’:
  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
  Found ‘__printf_chk’, possibly from ‘printf’ (C)
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand_r’, possibly from ‘rand_r’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (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
Examples with CPU or elapsed time > 5s
            user system elapsed
emptyDrops 5.244  0.036   5.291
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.10-bioc/meat/DropletUtils.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL DropletUtils
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘DropletUtils’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rhdf5lib/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/dqrng/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c compute_multinom.cpp -o compute_multinom.o
compute_multinom.cpp: In instantiation of ‘SEXPREC* compute_multinom_internal(SEXP, SEXP, SEXP) [with V = Rcpp::Vector<13>; MAT = beachmat::lin_matrix<int, Rcpp::Vector<13> >; SEXP = SEXPREC*]’:
compute_multinom.cpp:73:105:   required from here
compute_multinom.cpp:41:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (ambient.size()!=NR) {
         ~~~~~~~~~~~~~~^~~~
compute_multinom.cpp: In instantiation of ‘SEXPREC* compute_multinom_internal(SEXP, SEXP, SEXP) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; MAT = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; SEXP = SEXPREC*]’:
compute_multinom.cpp:75:105:   required from here
compute_multinom.cpp:41:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
In file included from compute_multinom.cpp:5:0:
/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include/beachmat/utils/const_column.h: In instantiation of ‘Rcpp::traits::storage_type<13>::type* beachmat::const_column<M>::get_indices() [with M = beachmat::lin_matrix<int, Rcpp::Vector<13> >; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]’:
compute_multinom.cpp:54:18:   required from ‘SEXPREC* compute_multinom_internal(SEXP, SEXP, SEXP) [with V = Rcpp::Vector<13>; MAT = beachmat::lin_matrix<int, Rcpp::Vector<13> >; SEXP = SEXPREC*]’
compute_multinom.cpp:73:105:   required from here
/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include/beachmat/utils/const_column.h:66:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (ref->get_nrow() > indices.size()) {
/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include/beachmat/utils/const_column.h: In instantiation of ‘Rcpp::traits::storage_type<13>::type* beachmat::const_column<M>::get_indices() [with M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]’:
compute_multinom.cpp:54:18:   required from ‘SEXPREC* compute_multinom_internal(SEXP, SEXP, SEXP) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; MAT = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; SEXP = SEXPREC*]’
compute_multinom.cpp:75:105:   required from here
/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include/beachmat/utils/const_column.h:66:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rhdf5lib/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/dqrng/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c downsample_counts.cpp -o downsample_counts.o
downsample_counts.cpp: In function ‘bool check_downsampling_mode(size_t, Rcpp::NumericVector, Rcpp::LogicalVector)’:
downsample_counts.cpp:99:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (prop.size()!=ncells) {
             ~~~~~~~~~~~^~~~~~~~
downsample_counts.cpp: In function ‘SEXPREC* downsample_runs(SEXP, SEXP, SEXP, SEXP)’:
downsample_counts.cpp:209:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (nmolecules!=read_vec.size()) {
         ~~~~~~~~~~^~~~~~~~~~~~~~~~~
In file included from downsample_counts.cpp:5:0:
/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include/beachmat/utils/const_column.h: In instantiation of ‘Rcpp::traits::storage_type<13>::type* beachmat::const_column<M>::get_indices() [with M = beachmat::lin_matrix<int, Rcpp::Vector<13> >; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]’:
downsample_counts.cpp:171:17:   required from ‘Rcpp::RObject downsample_matrix_internal(Rcpp::RObject, Rcpp::NumericVector, Rcpp::LogicalVector) [with V = Rcpp::Vector<13>; M = beachmat::lin_matrix<int, Rcpp::Vector<13> >; O = beachmat::lin_output<int, Rcpp::Vector<13> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::LogicalVector = Rcpp::Vector<10, Rcpp::PreserveStorage>]’
downsample_counts.cpp:189:55:   required from here
/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include/beachmat/utils/const_column.h:66:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (ref->get_nrow() > indices.size()) {
/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include/beachmat/utils/const_column.h: In instantiation of ‘Rcpp::traits::storage_type<13>::type* beachmat::const_column<M>::get_indices() [with M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]’:
downsample_counts.cpp:171:17:   required from ‘Rcpp::RObject downsample_matrix_internal(Rcpp::RObject, Rcpp::NumericVector, Rcpp::LogicalVector) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; O = beachmat::lin_output<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::LogicalVector = Rcpp::Vector<10, Rcpp::PreserveStorage>]’
downsample_counts.cpp:193:55:   required from here
/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include/beachmat/utils/const_column.h:66:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rhdf5lib/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/dqrng/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c encode_sequences.cpp -o encode_sequences.o
encode_sequences.cpp: In function ‘SEXPREC* encode_sequences(SEXP)’:
encode_sequences.cpp:11:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t i=0; i<output.size(); ++i) {
                      ~^~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rhdf5lib/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/dqrng/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c find_swapped.cpp -o find_swapped.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rhdf5lib/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/dqrng/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c get_cell_barcodes.cpp -o get_cell_barcodes.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rhdf5lib/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/dqrng/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c group_cells.cpp -o group_cells.o
group_cells.cpp: In function ‘SEXPREC* group_cells(SEXP, SEXP)’:
group_cells.cpp:12:10: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (N!=Gems.size()) {
         ~^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rhdf5lib/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/dqrng/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c init.cpp -o init.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rhdf5lib/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/dqrng/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c montecarlo_pval.cpp -o montecarlo_pval.o
montecarlo_pval.cpp: In function ‘SEXPREC* montecarlo_pval(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
montecarlo_pval.cpp:105:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (higher<curlen) {
                 ~~~~~~^~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rhdf5lib/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/dqrng/include" -I/usr/local/include  -fpic  -g -O2  -Wall -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 between signed and unsigned integer expressions [-Wsign-compare]
     if (seeds.size()!=N) {
         ~~~~~~~~~~~~^~~
rand_custom.cpp:14:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (streams.size()!=N) {
         ~~~~~~~~~~~~~~^~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rhdf5lib/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/dqrng/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c utils.cpp -o utils.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.10-bioc/R/lib -L/usr/local/lib -o DropletUtils.so compute_multinom.o downsample_counts.o encode_sequences.o find_swapped.o get_cell_barcodes.o group_cells.o init.o montecarlo_pval.o rand_custom.o utils.o /home/biocbuild/bbs-3.10-bioc/R/library/Rhdf5lib/lib/libhdf5_cpp.a /home/biocbuild/bbs-3.10-bioc/R/library/Rhdf5lib/lib/libhdf5.a /home/biocbuild/bbs-3.10-bioc/R/library/Rhdf5lib/lib/libsz.a -lz -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.10-bioc/R/library/00LOCK-DropletUtils/00new/DropletUtils/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 (DropletUtils)

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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(testthat)
> library(DropletUtils)
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
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, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    aperm, apply, rowsum

> test_check("DropletUtils")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 828 | SKIPPED: 0 | WARNINGS: 7 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
127.856   1.324 125.944 

name	user	system	elapsed
barcodeRanks	0.784	0.012	0.796
defaultDrops	0.100	0.012	0.111
downsampleBatches	0.524	0.000	0.540
downsampleMatrix	0.140	0.004	0.141
downsampleReads	0.148	0.008	0.194
emptyDrops	5.244	0.036	5.291
encodeSequences	0.000	0.000	0.001
get10xMolInfoStats	0.120	0.000	0.119
makeCountMatrix	0.004	0.000	0.004
read10xCounts	0.1	0.0	0.1
read10xMolInfo	0.112	0.000	0.114
swappedDrops	0.440	0.008	0.449
write10xCounts	0.008	0.000	0.011