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This page was generated on 2021-10-15 15:05:38 -0400 (Fri, 15 Oct 2021).

CHECK results for CONFESS on nebbiolo1

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 376/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CONFESS 1.20.0  (landing page)
Diana LOW
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/CONFESS
git_branch: RELEASE_3_13
git_last_commit: 5f6120a
git_last_commit_date: 2021-05-19 12:19:35 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 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: 1.20.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:CONFESS.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings CONFESS_1.20.0.tar.gz
StartedAt: 2021-10-14 09:22:17 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 09:27:23 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 306.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: CONFESS.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:CONFESS.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings CONFESS_1.20.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/CONFESS.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (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 ‘1.20.0’
* 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: replacing previous import ‘stats::BIC’ by ‘flowMerge::BIC’ when loading ‘CONFESS’
See ‘/home/biocbuild/bbs-3.13-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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
Fluo_CV_prep    38.237  2.803  40.312
Fluo_adjustment 15.101  1.318  16.001
Fluo_modeling   14.083  0.331  14.374
* 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
  ‘/home/biocbuild/bbs-3.13-bioc/meat/CONFESS.Rcheck/00check.log’
for details.



Installation output

CONFESS.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL CONFESS
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-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_byRun0.0120.0000.013
Fluo_CV_modeling000
Fluo_CV_prep38.237 2.80340.312
Fluo_adjustment15.101 1.31816.001
Fluo_inspection2.1570.7282.643
Fluo_modeling14.083 0.33114.374
Fluo_ordering0.5990.0500.632
LocationMatrix0.0000.0030.004
cluster2outlier0.0000.0010.001
createFluo0.0060.0020.007
defineLocClusters0.0660.0040.070
files0.0010.0020.002
getFluo0.0210.0040.024
getFluo_byRun0.0330.0080.038
pathEstimator0.0010.0000.001
readFiles0.0160.0000.015
simcells0.8320.0400.863
spotEstimator0.0000.0010.000