Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-19 13:07:51 -0500 (Wed, 19 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
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 CONFESS on machv2


To the developers/maintainers of the CONFESS package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CONFESS.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here 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 384/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CONFESS 1.22.0  (landing page)
Diana LOW
Snapshot Date: 2022-01-18 01:55:07 -0500 (Tue, 18 Jan 2022)
git_url: https://git.bioconductor.org/packages/CONFESS
git_branch: RELEASE_3_14
git_last_commit: f55571a
git_last_commit_date: 2021-10-26 12:26:56 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: CONFESS
Version: 1.22.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CONFESS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CONFESS_1.22.0.tar.gz
StartedAt: 2022-01-18 11:37:43 -0500 (Tue, 18 Jan 2022)
EndedAt: 2022-01-18 11:47:36 -0500 (Tue, 18 Jan 2022)
EllapsedTime: 592.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: CONFESS.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CONFESS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CONFESS_1.22.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/CONFESS.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CONFESS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CONFESS’ version ‘1.22.0’
* 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 ‘CONFESS’ can be installed ... WARNING
Found the following significant warnings:
  Warning: multiple methods tables found for ‘direction’
  Warning: multiple methods tables found for ‘gridDistance’
  Warning: replacing previous import ‘stats::BIC’ by ‘flowMerge::BIC’ when loading ‘CONFESS’
See ‘/Users/biocbuild/bbs-3.14-bioc/meat/CONFESS.Rcheck/00install.out’ for details.
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
Fluo_CV_prep    53.779  7.458  60.557
Fluo_adjustment 31.552  4.096  35.232
Fluo_modeling   16.336  1.008  17.317
Fluo_inspection  3.760  2.494   5.961
* 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 WARNING
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/CONFESS.Rcheck/00check.log’
for details.



Installation output

CONFESS.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CONFESS
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘CONFESS’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘stats::BIC’ by ‘flowMerge::BIC’ when loading ‘CONFESS’
Warning: multiple methods tables found for ‘direction’
Warning: multiple methods tables found for ‘gridDistance’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘stats::BIC’ by ‘flowMerge::BIC’ when loading ‘CONFESS’
Warning: multiple methods tables found for ‘direction’
Warning: multiple methods tables found for ‘gridDistance’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘stats::BIC’ by ‘flowMerge::BIC’ when loading ‘CONFESS’
Warning: multiple methods tables found for ‘direction’
Warning: multiple methods tables found for ‘gridDistance’
** testing if installed package keeps a record of temporary installation path
* DONE (CONFESS)

Tests output


Example timings

CONFESS.Rcheck/CONFESS-Ex.timings

nameusersystemelapsed
FluoSelection_byRun0.0440.0030.048
Fluo_CV_modeling000
Fluo_CV_prep53.779 7.45860.557
Fluo_adjustment31.552 4.09635.232
Fluo_inspection3.7602.4945.961
Fluo_modeling16.336 1.00817.317
Fluo_ordering1.2300.1511.366
LocationMatrix0.0070.0010.007
cluster2outlier0.0020.0010.002
createFluo0.0120.0020.014
defineLocClusters0.1040.0250.129
files0.0040.0010.006
getFluo0.0400.0120.051
getFluo_byRun0.0620.0260.085
pathEstimator0.0010.0000.002
readFiles0.0240.0030.025
simcells1.4700.1451.605
spotEstimator0.0000.0010.001