Back to Multiple platform build/check report for BioC 3.11
ABCDEFGHIJKLMNOPQRS[T]UVWXYZ

CHECK report for TOAST on malbec2

This page was generated on 2020-10-17 11:55:56 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE TOAST PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1811/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TOAST 1.2.0
Ziyi Li
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/TOAST
Branch: RELEASE_3_11
Last Commit: b069f38
Last Changed Date: 2020-04-27 15:28:03 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  NA 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: TOAST
Version: 1.2.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:TOAST.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings TOAST_1.2.0.tar.gz
StartedAt: 2020-10-17 06:07:52 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 06:11:07 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 195.6 seconds
RetCode: 0
Status:  OK 
CheckDir: TOAST.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:TOAST.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings TOAST_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/TOAST.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TOAST/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TOAST’ version ‘1.2.0’
* 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 ‘TOAST’ 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
csDeconv 51.146  0.196  51.352
* 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: OK


Installation output

TOAST.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL TOAST
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘TOAST’ ...
** using staged installation
** R
** data
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (TOAST)

Tests output


Example timings

TOAST.Rcheck/TOAST-Ex.timings

nameusersystemelapsed
CBS_PBMC_array0.0380.0000.038
ChooseMarker0.0470.0000.047
DEVarSelect0.5940.0000.594
GetPrior0.0020.0000.002
MDeconv0.0510.0000.051
RA_100samples0.2120.0040.216
assignCellType0.0020.0000.002
csDeconv51.146 0.19651.352
csTest0.1060.0040.110
findRefinx0.010.000.01
fitModel0.0530.0000.053
makeDesign0.0030.0000.003