Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:23:52 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for TOAST on merida1


To the developers/maintainers of the TOAST package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TOAST.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 2021/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TOAST 1.10.1  (landing page)
Ziyi Li
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/TOAST
git_branch: RELEASE_3_15
git_last_commit: acbb0d2
git_last_commit_date: 2022-08-24 15:38:38 -0400 (Wed, 24 Aug 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: TOAST
Version: 1.10.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TOAST.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TOAST_1.10.1.tar.gz
StartedAt: 2022-10-19 08:59:22 -0400 (Wed, 19 Oct 2022)
EndedAt: 2022-10-19 09:06:12 -0400 (Wed, 19 Oct 2022)
EllapsedTime: 409.5 seconds
RetCode: 0
Status:   OK  
CheckDir: TOAST.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TOAST.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TOAST_1.10.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/TOAST.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.10.1’
* 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 94.310  1.983  96.408
Tsisal   11.771  0.563  12.345
cedar     2.654  0.094  40.401
* 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

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL TOAST
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/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_array0.0190.0040.023
ChooseMarker0.0540.0060.060
DEVarSelect0.0810.0110.092
GetPrior0.0020.0010.003
MDeconv0.0650.0030.068
RA_100samples0.2160.0090.227
Tsisal11.771 0.56312.345
assignCellType0.0010.0000.002
beta_emp0.0250.0030.028
cedar 2.654 0.09440.401
csDeconv94.310 1.98396.408
csTest0.1710.0030.173
findRefinx0.0110.0000.012
fitModel0.1090.0070.116
makeDesign0.0070.0000.006
plotCorr2.0050.0102.017