Back to Multiple platform build/check report for BioC 3.10 |
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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 | |