Aaron Lun
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/BiocSingular |
| Branch: RELEASE_3_10 |
| Last Commit: 1dd1697 |
| Last Changed Date: 2020-02-14 03:19:44 -0400 (Fri, 14 Feb 2020) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:15:15 -0400 (Wed, 15 Apr 2020).
| Package 159/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| BiocSingular 1.2.2 Aaron Lun
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: BiocSingular |
| Version: 1.2.2 |
| Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:BiocSingular.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings BiocSingular_1.2.2.tar.gz |
| StartedAt: 2020-04-15 06:17:56 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 06:27:08 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 551.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BiocSingular.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:BiocSingular.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings BiocSingular_1.2.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/BiocSingular.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 ‘BiocSingular/DESCRIPTION’ ... OK * this is package ‘BiocSingular’ 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 ‘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-3.10-bioc/meat/BiocSingular.Rcheck/00check.log’ for details.
BiocSingular.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL BiocSingular
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘BiocSingular’ ...
** 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 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<int, Rcpp::Vector<13> >; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
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<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
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-3.10-bioc/R/lib -L/usr/local/lib -o BiocSingular.so RcppExports.o compute_scale.o -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.10-bioc/R/library/00LOCK-BiocSingular/00new/BiocSingular/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 (BiocSingular)
BiocSingular.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(BiocSingular)
> library(testthat)
> test_check("BiocSingular")
Loading required package: stats4
Loading required package: matrixStats
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
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
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 22377 | SKIPPED: 0 | WARNINGS: 10 | FAILED: 0 ]
>
> proc.time()
user system elapsed
375.692 73.864 436.044
BiocSingular.Rcheck/BiocSingular-Ex.timings
| name | user | system | elapsed | |
| BiocSingularParam | 0.024 | 0.000 | 0.026 | |
| DeferredMatrix | 0.18 | 0.00 | 0.18 | |
| LowRankMatrix | 0.116 | 0.000 | 0.116 | |
| ResidualMatrix | 1.452 | 0.004 | 1.634 | |
| runExactSVD | 0.044 | 0.000 | 0.042 | |
| runIrlbaSVD | 0.036 | 0.000 | 0.038 | |
| runPCA | 0.052 | 0.012 | 0.065 | |
| runRandomSVD | 0.308 | 0.000 | 0.312 | |
| runSVD | 0.332 | 0.000 | 0.477 | |