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CHECK report for DropletUtils on malbec1

This page was generated on 2019-04-16 11:53:14 -0400 (Tue, 16 Apr 2019).

Package 436/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DropletUtils 1.2.2
Aaron Lun
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/DropletUtils
Branch: RELEASE_3_8
Last Commit: 1424ff5
Last Changed Date: 2019-01-04 13:09:29 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: DropletUtils
Version: 1.2.2
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:DropletUtils.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings DropletUtils_1.2.2.tar.gz
StartedAt: 2019-04-15 23:38:05 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 23:42:22 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 256.5 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: DropletUtils.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:DropletUtils.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings DropletUtils_1.2.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/DropletUtils.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.2.2’
* 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 ... 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 ... 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 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
* checking files in ‘vignettes’ ... OK
* checking examples ... WARNING
Found the following significant warnings:

  Warning: 'read10xMatrix' is deprecated.
  Warning: 'read10xMatrix' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
            user system elapsed
emptyDrops 5.308  0.032   5.346
* 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 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.8-bioc/meat/DropletUtils.Rcheck/00check.log’
for details.

Installation output

DropletUtils.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL DropletUtils
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘DropletUtils’ ...
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/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(MAT, SEXP, SEXP) [with V = Rcpp::Vector<13>; MAT = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; SEXP = SEXPREC*]’:
compute_multinom.cpp:45:85:   required from here
compute_multinom.cpp:11:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (ambient.size()!=NR) {
                       ^
compute_multinom.cpp: In instantiation of ‘SEXPREC* compute_multinom_internal(MAT, SEXP, SEXP) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; MAT = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; SEXP = SEXPREC*]’:
compute_multinom.cpp:48:85:   required from here
compute_multinom.cpp:11:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:238:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
                 from DropletUtils.h:5,
                 from compute_multinom.cpp:1:
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h: In instantiation of ‘beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<13>; beachmat::const_col_indexed_info<V> = std::tuple<long unsigned int, int*, int*>; typename V::iterator = int*; size_t = long unsigned int; typename V::iterator = int*]’:
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:77:33:   required from ‘beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator) [with T = int; V = Rcpp::Vector<13>; beachmat::const_col_indexed_info<V> = std::tuple<long unsigned int, int*, int*>; typename V::iterator = int*; size_t = long unsigned int; typename V::iterator = int*]’
compute_multinom.cpp:22:61:   required from ‘SEXPREC* compute_multinom_internal(MAT, SEXP, SEXP) [with V = Rcpp::Vector<13>; MAT = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; SEXP = SEXPREC*]’
compute_multinom.cpp:45:85:   required from here
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (indices.size()!=this->get_nrow()) {
                       ^
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h: In instantiation of ‘beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; beachmat::const_col_indexed_info<V> = std::tuple<long unsigned int, int*, double*>; typename V::iterator = double*; size_t = long unsigned int; typename V::iterator = double*]’:
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:77:33:   required from ‘beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; beachmat::const_col_indexed_info<V> = std::tuple<long unsigned int, int*, double*>; typename V::iterator = double*; size_t = long unsigned int; typename V::iterator = double*]’
compute_multinom.cpp:22:61:   required from ‘SEXPREC* compute_multinom_internal(MAT, SEXP, SEXP) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; MAT = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; SEXP = SEXPREC*]’
compute_multinom.cpp:48:85:   required from here
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/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:78:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (prop.size()!=ncells) {
                        ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:238:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
                 from DropletUtils.h:5,
                 from downsample_counts.cpp:1:
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h: In instantiation of ‘beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; beachmat::const_col_indexed_info<V> = std::tuple<long unsigned int, int*, double*>; typename V::iterator = double*; size_t = long unsigned int; typename V::iterator = double*]’:
downsample_counts.cpp:205:1:   required from here
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (indices.size()!=this->get_nrow()) {
                       ^
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h: In instantiation of ‘beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<13>; beachmat::const_col_indexed_info<V> = std::tuple<long unsigned int, int*, int*>; typename V::iterator = int*; size_t = long unsigned int; typename V::iterator = int*]’:
downsample_counts.cpp:205:1:   required from here
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/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:8:23: 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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/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:34:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (size_t i=1; i<output.size(); ++i) {
                           ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c init.cpp -o init.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c load_tenx_to_hdf5.cpp -o load_tenx_to_hdf5.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/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)’:
montecarlo_pval.cpp:76:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 if (chosen >= ngenes) {
                            ^
montecarlo_pval.cpp:92:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (higher<curlen) {
                       ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c utils.cpp -o utils.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.8-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 load_tenx_to_hdf5.o montecarlo_pval.o utils.o -L/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/lib -Wl,-rpath,/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/lib -lbeachmat -pthread -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/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
* DONE (DropletUtils)

Tests output

DropletUtils.Rcheck/tests/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
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: BiocParallel
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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, 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


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

> test_check("DropletUtils")
Error in H5Dread(h5dataset = h5dataset, h5spaceFile = h5spaceFile, h5spaceMem = h5spaceMem,  : 
  Not enough memory to read data! Try to read a subset of data by specifying the index or count parameter.
Error in H5Dread(h5dataset = h5dataset, h5spaceFile = h5spaceFile, h5spaceMem = h5spaceMem,  : 
  Not enough memory to read data! Try to read a subset of data by specifying the index or count parameter.
Error in H5Dread(h5dataset = h5dataset, h5spaceFile = h5spaceFile, h5spaceMem = h5spaceMem,  : 
  Not enough memory to read data! Try to read a subset of data by specifying the index or count parameter.
In addition: Warning message:
closing unused connection 3 (/tmp/RtmpHzxkB2/file776843e8738c/matrix.mtx) 
Error in H5Dread(h5dataset = h5dataset, h5spaceFile = h5spaceFile, h5spaceMem = h5spaceMem,  : 
  Not enough memory to read data! Try to read a subset of data by specifying the index or count parameter.
Error in H5Dread(h5dataset = h5dataset, h5spaceFile = h5spaceFile, h5spaceMem = h5spaceMem,  : 
  Not enough memory to read data! Try to read a subset of data by specifying the index or count parameter.
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 775 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 96.248   0.500  96.907

Example timings

DropletUtils.Rcheck/DropletUtils-Ex.timings

nameusersystemelapsed
barcodeRanks0.6440.0200.668
defaultDrops0.1720.0080.179
downsampleMatrix0.5920.0000.633
downsampleReads0.2520.0240.276
emptyDrops5.3080.0325.346
encodeSequences0.0000.0000.001
get10xMolInfoStats0.1800.0040.185
makeCountMatrix0.0080.0000.010
read10xCounts0.1680.0000.170
read10xMatrix0.0840.0040.103
read10xMolInfo0.2280.0000.229
swappedDrops0.5800.0040.588
write10xCounts0.0160.0040.023