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CHECK report for BiocSingular on malbec2

This page was generated on 2019-10-16 12:17:26 -0400 (Wed, 16 Oct 2019).

Package 152/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocSingular 1.0.0
Aaron Lun
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/BiocSingular
Branch: RELEASE_3_9
Last Commit: d2b091c
Last Changed Date: 2019-05-02 11:54:14 -0400 (Thu, 02 May 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: BiocSingular
Version: 1.0.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:BiocSingular.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings BiocSingular_1.0.0.tar.gz
StartedAt: 2019-10-16 00:06:02 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 00:09:03 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 180.8 seconds
RetCode: 0
Status:  OK 
CheckDir: BiocSingular.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:BiocSingular.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings BiocSingular_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/BiocSingular.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 ‘BiocSingular/DESCRIPTION’ ... OK
* this is package ‘BiocSingular’ version ‘1.0.0’
* 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-3.9-bioc/meat/BiocSingular.Rcheck/00check.log’
for details.



Installation output

BiocSingular.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL BiocSingular
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘BiocSingular’ ...
** 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/usr/local/include  -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
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/usr/local/include  -fpic  -g -O2  -Wall -c compute_scale.cpp -o compute_scale.o
compute_scale.cpp: In instantiation of ‘Rcpp::NumericVector compute_scale_internal(Rcpp::RObject, Rcpp::RObject) [with M = beachmat::lin_matrix >; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl]’:
compute_scale.cpp:60:79:   required from here
compute_scale.cpp:21:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (numeric_centers.size()!=ncols) {
             ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~
compute_scale.cpp: In instantiation of ‘Rcpp::NumericVector compute_scale_internal(Rcpp::RObject, Rcpp::RObject) [with M = beachmat::lin_matrix >; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl]’:
compute_scale.cpp:62:79:   required from here
compute_scale.cpp:21:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o BiocSingular.so RcppExports.o compute_scale.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-BiocSingular/00new/BiocSingular/libs
** R
** 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)

Tests output

BiocSingular.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(BiocSingular)
> library(testthat)
> test_check("BiocSingular")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 6278 | SKIPPED: 0 | WARNINGS: 10 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 79.691   5.549  84.403 

Example timings

BiocSingular.Rcheck/BiocSingular-Ex.timings

nameusersystemelapsed
BiocSingularParam0.0130.0000.013
DeferredMatrix0.1140.0040.118
LowRankMatrix0.8800.1721.115
runExactSVD0.0270.0000.028
runIrlbaSVD0.0290.0000.029
runPCA0.0540.0000.054
runRandomSVD0.1870.0080.196
runSVD0.2040.0000.204