Back to Multiple platform build/check report for BioC 3.10
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

CHECK report for SingleR on malbec1

This page was generated on 2020-04-15 12:16:08 -0400 (Wed, 15 Apr 2020).

Package 1606/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SingleR 1.0.6
Aaron Lun
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/SingleR
Branch: RELEASE_3_10
Last Commit: 5803a1f
Last Changed Date: 2020-04-08 12:05:48 -0400 (Wed, 08 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK 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: SingleR
Version: 1.0.6
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:SingleR.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings SingleR_1.0.6.tar.gz
StartedAt: 2020-04-15 06:51:01 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 07:00:25 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 564.6 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: SingleR.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:SingleR.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings SingleR_1.0.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/SingleR.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 ‘SingleR/DESCRIPTION’ ... OK
* this is package ‘SingleR’ version ‘1.0.6’
* package encoding: UTF-8
* 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 ‘SingleR’ 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 ... WARNING
Codoc mismatches from documentation object 'plotScoreHeatmap':
plotScoreHeatmap
  Code: function(results, cells.use = NULL, labels.use = NULL, clusters
                 = NULL, show.labels = TRUE, show.pruned = FALSE,
                 max.labels = 40, normalize = TRUE, cells.order = NULL,
                 order.by.clusters = FALSE, annotation_col = NULL,
                 show_colnames = FALSE, color = NULL, ...)
  Docs: function(results, cells.use = NULL, labels.use = NULL, clusters
                 = NULL, show.labels = TRUE, show.pruned = FALSE,
                 max.labels = 40, normalize = TRUE, cells.order = NULL,
                 order.by.clusters = FALSE, annotation_col = NULL,
                 show_colnames = FALSE, ...)
  Argument names in code not in docs:
    color
  Mismatches in argument names:
    Position: 13 Code: color Docs: ...

* 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
Examples with CPU or elapsed time > 5s
                                   user system elapsed
DatabaseImmuneCellExpressionData 10.100  0.428  11.041
BlueprintEncodeData               8.840  0.276   9.832
plotScoreDistribution             7.540  0.012   7.698
HumanPrimaryCellAtlasData         6.308  0.152   6.869
MouseRNAseqData                   5.728  0.096   6.089
ImmGenData                        5.576  0.124   6.323
MonacoImmuneData                  5.576  0.064   5.889
NovershternHematopoieticData      4.792  0.052   5.724
* 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-3.10-bioc/meat/SingleR.Rcheck/00check.log’
for details.



Installation output

SingleR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL SingleR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘SingleR’ ...
** 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/usr/local/include  -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.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/usr/local/include  -fpic  -g -O2  -Wall -c fine_tune_de.cpp -o fine_tune_de.o
fine_tune_de.cpp: In constructor ‘de_markers::de_markers(Rcpp::List)’:
fine_tune_de.cpp:6:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (size_t i=0; i<marker_genes.size(); ++i) {
                          ~^~~~~~~~~~~~~~~~~~~~
fine_tune_de.cpp:9:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (size_t j=0; j<internals.size(); ++j) {
                              ~^~~~~~~~~~~~~~~~~
fine_tune_de.cpp: In function ‘Rcpp::List fine_tune_label_de(SEXP, Rcpp::NumericMatrix, Rcpp::List, double, double, Rcpp::List)’:
fine_tune_de.cpp:38:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t i=0; i<References.size(); ++i) {
                      ~^~~~~~~~~~~~~~~~~~
In file included from fine_tune_de.cpp:2:0:
fine_tuner.h: In instantiation of ‘tuned_stats fine_tuner::assign(int, beachmat::numeric_matrix*, Rcpp::NumericMatrix, const matrix_list&, double, double, const PICKER&) [with PICKER = de_markers; tuned_stats = std::tuple<int, double, double>; beachmat::numeric_matrix = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::NumericMatrix = Rcpp::Matrix<14>; matrix_list = std::vector<std::unique_ptr<beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> > > >]’:
fine_tune_de.cpp:51:95:   required from here
fine_tuner.h:42:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (size_t i=0; i<cur_scores.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/usr/local/include  -fpic  -g -O2  -Wall -c fine_tune_sd.cpp -o fine_tune_sd.o
fine_tune_sd.cpp: In function ‘Rcpp::List fine_tune_label_sd(SEXP, Rcpp::NumericMatrix, Rcpp::List, double, double, Rcpp::NumericMatrix, double)’:
fine_tune_sd.cpp:46:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t i=0; i<References.size(); ++i) {
                      ~^~~~~~~~~~~~~~~~~~
In file included from fine_tune_sd.cpp:2:0:
fine_tuner.h: In instantiation of ‘tuned_stats fine_tuner::assign(int, beachmat::numeric_matrix*, Rcpp::NumericMatrix, const matrix_list&, double, double, const PICKER&) [with PICKER = sd_markers; tuned_stats = std::tuple<int, double, double>; beachmat::numeric_matrix = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::NumericMatrix = Rcpp::Matrix<14>; matrix_list = std::vector<std::unique_ptr<beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> > > >]’:
fine_tune_sd.cpp:59:95:   required from here
fine_tuner.h:42:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (size_t i=0; i<cur_scores.size(); ++i) {
                          ~^~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.10-bioc/R/lib -L/usr/local/lib -o SingleR.so RcppExports.o fine_tune_de.o fine_tune_sd.o -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.10-bioc/R/library/00LOCK-SingleR/00new/SingleR/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 (SingleR)

Tests output

SingleR.Rcheck/tests/testthat.Rout


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(SingleR)
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("SingleR")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 362 | SKIPPED: 0 | WARNINGS: 6 | FAILED: 0 ]
Warning message:
call dbDisconnect() when finished working with a connection 
> 
> proc.time()
   user  system elapsed 
217.580   4.988 302.953 

Example timings

SingleR.Rcheck/SingleR-Ex.timings

nameusersystemelapsed
BlueprintEncodeData8.8400.2769.832
DatabaseImmuneCellExpressionData10.100 0.42811.041
HumanPrimaryCellAtlasData6.3080.1526.869
ImmGenData5.5760.1246.323
MonacoImmuneData5.5760.0645.889
MouseRNAseqData5.7280.0966.089
NovershternHematopoieticData4.7920.0525.724
SingleR1.4440.0121.463
aggregateReference1.2120.0281.240
classifySingleR0.3160.0080.326
combineResults1.1440.0001.142
getDeltaFromMedian0.6840.0000.705
matchReferences0.8920.0040.897
plotScoreDistribution7.5400.0127.698
plotScoreHeatmap1.7680.0081.779
pruneScores0.6960.0000.698
trainSingleR1.5800.0041.619