Back to Multiple platform build/check report for BioC 3.9
ABC[D]EFGHIJKLMNOPQRSTUVWXYZ

CHECK report for DropletUtils on malbec2

This page was generated on 2019-10-16 12:13:00 -0400 (Wed, 16 Oct 2019).

Package 465/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DropletUtils 1.4.3
Aaron Lun
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/DropletUtils
Branch: RELEASE_3_9
Last Commit: c74dbae
Last Changed Date: 2019-08-06 22:55:31 -0400 (Tue, 06 Aug 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: DropletUtils
Version: 1.4.3
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:DropletUtils.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings DropletUtils_1.4.3.tar.gz
StartedAt: 2019-10-16 01:20:31 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 01:25:16 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 285.1 seconds
RetCode: 0
Status:  OK 
CheckDir: DropletUtils.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:DropletUtils.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings DropletUtils_1.4.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/DropletUtils.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.4.3’
* 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 26.5Mb
  sub-directories of 1Mb or more:
    libs  26.3Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.9-bioc/R/library/DropletUtils/libs/DropletUtils.so’:
  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (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
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/DropletUtils.Rcheck/00check.log’
for details.

Installation output

DropletUtils.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL DropletUtils
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘DropletUtils’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.9-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 >; 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 >; 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-3.9-bioc/R/library/beachmat/include/beachmat/utils/const_column.h: In instantiation of ‘Rcpp::traits::storage_type<13>::type* beachmat::const_column::get_indices() [with M = beachmat::lin_matrix >; 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 >; SEXP = SEXPREC*]’
compute_multinom.cpp:73:105:   required from here
/home/biocbuild/bbs-3.9-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-3.9-bioc/R/library/beachmat/include/beachmat/utils/const_column.h: In instantiation of ‘Rcpp::traits::storage_type<13>::type* beachmat::const_column::get_indices() [with M = beachmat::lin_matrix >; 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 >; SEXP = SEXPREC*]’
compute_multinom.cpp:75:105:   required from here
/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/library/beachmat/include/beachmat/utils/const_column.h: In instantiation of ‘Rcpp::traits::storage_type<13>::type* beachmat::const_column::get_indices() [with M = beachmat::lin_matrix >; 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 >; O = beachmat::lin_output >; Rcpp::RObject = Rcpp::RObject_Impl; 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-3.9-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-3.9-bioc/R/library/beachmat/include/beachmat/utils/const_column.h: In instantiation of ‘Rcpp::traits::storage_type<13>::type* beachmat::const_column::get_indices() [with M = beachmat::lin_matrix >; 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 >; O = beachmat::lin_output >; Rcpp::RObject = Rcpp::RObject_Impl; 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-3.9-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-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.9-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 instead.
 BOOST_HEADER_DEPRECATED("");
                                                           ^
montecarlo_pval.cpp: In function ‘SEXPREC* montecarlo_pval(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
montecarlo_pval.cpp:95:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 if (chosen >= ngenes) {
                     ~~~~~~~^~~~~~~~~
montecarlo_pval.cpp:111:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (higher

Tests output

DropletUtils.Rcheck/tests/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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: 817 | SKIPPED: 0 | WARNINGS: 7 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
113.873   1.550 111.156

Example timings

DropletUtils.Rcheck/DropletUtils-Ex.timings

nameusersystemelapsed
barcodeRanks0.7470.0240.771
defaultDrops0.1020.0120.114
downsampleMatrix0.3640.0000.372
downsampleReads0.2140.0160.252
emptyDrops4.8580.0404.898
encodeSequences000
get10xMolInfoStats0.1230.0040.127
makeCountMatrix0.0050.0000.005
read10xCounts0.1050.0000.105
read10xMolInfo0.1000.0040.104
swappedDrops0.3350.0040.338
write10xCounts0.0130.0000.013