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CHECK report for CONFESS on malbec2

This page was generated on 2019-10-16 12:08:44 -0400 (Wed, 16 Oct 2019).

Package 333/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CONFESS 1.12.0
Diana LOW
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/CONFESS
Branch: RELEASE_3_9
Last Commit: c2212da
Last Changed Date: 2019-05-02 11:54:01 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: CONFESS
Version: 1.12.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:CONFESS.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings CONFESS_1.12.0.tar.gz
StartedAt: 2019-10-16 00:45:31 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 00:50:12 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 280.8 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: CONFESS.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:CONFESS.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings CONFESS_1.12.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/CONFESS.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.12.0’
* 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-3.9-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 data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
Fluo_CV_prep    36.576  2.792  38.861
Fluo_adjustment 22.534  1.821  24.032
Fluo_modeling   11.569  0.235  11.769
* 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-3.9-bioc/meat/CONFESS.Rcheck/00check.log’
for details.



Installation output

CONFESS.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL CONFESS
###
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* installing to library ‘/home/biocbuild/bbs-3.9-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_byRun0.0150.0040.132
Fluo_CV_modeling0.0010.0000.000
Fluo_CV_prep36.576 2.79238.861
Fluo_adjustment22.534 1.82124.032
Fluo_inspection3.1650.9733.940
Fluo_modeling11.569 0.23511.769
Fluo_ordering1.0460.0611.088
LocationMatrix0.0070.0000.007
cluster2outlier0.0020.0000.002
createFluo0.0130.0000.013
defineLocClusters0.0560.0120.112
files0.0040.0000.003
getFluo0.0330.0080.041
getFluo_byRun0.0680.0120.076
pathEstimator0.0010.0000.001
readFiles0.0190.0000.018
simcells3.7730.1033.864
spotEstimator000