Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:22:46 -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 coseq on merida1


To the developers/maintainers of the coseq package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/coseq.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 417/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
coseq 1.20.0  (landing page)
Andrea Rau
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/coseq
git_branch: RELEASE_3_15
git_last_commit: 2952e7d
git_last_commit_date: 2022-04-26 11:38:25 -0400 (Tue, 26 Apr 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: coseq
Version: 1.20.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:coseq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings coseq_1.20.0.tar.gz
StartedAt: 2022-10-19 01:03:22 -0400 (Wed, 19 Oct 2022)
EndedAt: 2022-10-19 01:10:33 -0400 (Wed, 19 Oct 2022)
EllapsedTime: 430.8 seconds
RetCode: 0
Status:   OK  
CheckDir: coseq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:coseq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings coseq_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/coseq.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 ‘coseq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘coseq’ 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 ‘coseq’ 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
compareARI    6.655  0.196   6.870
summary       6.227  0.028   6.320
plot          6.194  0.036   6.246
compareICL    6.084  0.040   6.146
coseq         6.058  0.039   6.115
coseqHelpers  6.060  0.036   6.119
coseq-package 6.015  0.040   6.079
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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

coseq.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘coseq’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘plot’ in package ‘coseq’
** 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 (coseq)

Tests output

coseq.Rcheck/tests/testthat.Rout


R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library("testthat")
> library("coseq")
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians


Attaching package: 'coseq'

The following object is masked from 'package:stats4':

    plot

The following object is masked from 'package:graphics':

    plot

The following object is masked from 'package:base':

    plot

> test_check("coseq")
****************************************
coseq analysis: kmeans approach & logclr transformation
K = 0 to 3 
Use seed argument in coseq for reproducible results.
****************************************
****************************************
coseq analysis: Gamma approach & logclr transformation
K = 2 to 4 
Use seed argument in coseq for reproducible results.
****************************************
****************************************
coseq analysis: kmeans approach & other transformation
K = 2 to 4 
Use seed argument in coseq for reproducible results.
****************************************
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 7 ]
> 
> proc.time()
   user  system elapsed 
 18.839   0.765  19.637 

Example timings

coseq.Rcheck/coseq-Ex.timings

nameusersystemelapsed
NormMixClus2.9540.3043.242
NormMixClusK0.9530.2921.226
NormMixParam0.6200.2560.854
clusterEntropy0.0010.0010.002
clusterInertia0.8620.0860.950
compareARI6.6550.1966.870
compareICL6.0840.0406.146
coseq-package6.0150.0406.079
coseq6.0580.0396.115
coseqHelpers6.0600.0366.119
coseqRun2.3210.0182.348
kmeansProbaPost0.0080.0010.010
matchContTable0.0060.0000.007
plot6.1940.0366.246
summary6.2270.0286.320
transformRNAseq0.0150.0010.016