Back to Multiple platform build/check report for BioC 3.16:   simplified   long
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This page was generated on 2023-04-12 11:05:29 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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 palomino4


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? 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 400/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CONFESS 1.26.0  (landing page)
Diana LOW
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/CONFESS
git_branch: RELEASE_3_16
git_last_commit: d1c2548
git_last_commit_date: 2022-11-01 11:13:27 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: CONFESS
Version: 1.26.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CONFESS.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings CONFESS_1.26.0.tar.gz
StartedAt: 2023-04-11 00:17:25 -0400 (Tue, 11 Apr 2023)
EndedAt: 2023-04-11 00:23:06 -0400 (Tue, 11 Apr 2023)
EllapsedTime: 341.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: CONFESS.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CONFESS.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings CONFESS_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/CONFESS.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (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 '1.26.0'
* 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 whether package 'CONFESS' can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'stats::BIC' by 'flowMerge::BIC' when loading 'CONFESS'
See 'F:/biocbuild/bbs-3.16-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    37.02   1.71   38.75
Fluo_adjustment 16.25   0.46   16.72
Fluo_modeling   12.86   0.66   13.52
* 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
  'F:/biocbuild/bbs-3.16-bioc/meat/CONFESS.Rcheck/00check.log'
for details.



Installation output

CONFESS.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL CONFESS
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/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'
** 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'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'stats::BIC' by 'flowMerge::BIC' when loading 'CONFESS'
** testing if installed package keeps a record of temporary installation path
* DONE (CONFESS)

Tests output


Example timings

CONFESS.Rcheck/CONFESS-Ex.timings

nameusersystemelapsed
FluoSelection_byRun0.020.000.01
Fluo_CV_modeling000
Fluo_CV_prep37.02 1.7138.75
Fluo_adjustment16.25 0.4616.72
Fluo_inspection1.540.031.57
Fluo_modeling12.86 0.6613.52
Fluo_ordering0.740.000.74
LocationMatrix000
cluster2outlier000
createFluo0.010.000.01
defineLocClusters0.050.000.07
files000
getFluo0.030.000.03
getFluo_byRun0.030.000.03
pathEstimator0.020.000.02
readFiles0.010.000.01
simcells0.990.031.02
spotEstimator000