Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-01-22 11:05:37 -0500 (Sat, 22 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4163
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4058
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4000
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4117
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 CNVMetrics on nebbiolo1


To the developers/maintainers of the CNVMetrics package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CNVMetrics.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 357/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNVMetrics 0.99.3  (landing page)
Astrid Deschênes
Snapshot Date: 2022-01-21 13:55:18 -0500 (Fri, 21 Jan 2022)
git_url: https://git.bioconductor.org/packages/CNVMetrics
git_branch: master
git_last_commit: 02e3123
git_last_commit_date: 2021-12-06 00:10:08 -0500 (Mon, 06 Dec 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    NA    NA  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'GenomicRanges' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: CNVMetrics
Version: 0.99.3
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:CNVMetrics.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings CNVMetrics_0.99.3.tar.gz
StartedAt: 2022-01-21 18:41:48 -0500 (Fri, 21 Jan 2022)
EndedAt: 2022-01-21 18:43:33 -0500 (Fri, 21 Jan 2022)
EllapsedTime: 104.7 seconds
RetCode: 0
Status:   OK  
CheckDir: CNVMetrics.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:CNVMetrics.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings CNVMetrics_0.99.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/CNVMetrics.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CNVMetrics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CNVMetrics’ version ‘0.99.3’
* 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 ‘CNVMetrics’ 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* 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

CNVMetrics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL CNVMetrics
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘CNVMetrics’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (CNVMetrics)

Tests output

CNVMetrics.Rcheck/tests/testthat.Rout


R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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(CNVMetrics)
> 
> ## Run all unit tests
> test_check("CNVMetrics")
CNV Metrics
Metric:
sorensen

AMPLIFICATION:
           sample01 sample02 sample03
sample01         NA       NA       NA
sample02 0.04647582       NA       NA
sample03 0.05465532        0       NA


DELETION:
          sample01 sample02 sample03
sample01        NA       NA       NA
sample02 0.0541291       NA       NA
sample03 0.0000000        0       NA

CNV Metrics
Metric:
sorensen

AMPLIFICATION:
           sample01  sample02  sample03 sample04 sample05
sample01         NA        NA        NA       NA       NA
sample02 0.04647582        NA        NA       NA       NA
sample03 0.05465532 0.0000000        NA       NA       NA
sample04 0.05820635 0.0000000 0.9676239       NA       NA
sample05 0.14207052 0.3293641 0.0000000        0       NA
[ -- omitted 1 row/column ]

DELETION:
          sample01 sample02  sample03  sample04 sample05
sample01        NA       NA        NA        NA       NA
sample02 0.0541291       NA        NA        NA       NA
sample03 0.0000000        0        NA        NA       NA
sample04 0.0000000        0 0.9791909        NA       NA
sample05 0.0000000        0 0.9363260 0.9570782       NA
[ -- omitted 1 row/column ]
CNV Metrics
Metric:
szymkiewicz

AMPLIFICATION:
           sample01  sample02 sample03 sample04 sample05
sample01         NA        NA       NA       NA       NA
sample02 0.07796751        NA       NA       NA       NA
sample03 1.00000000 0.0000000       NA       NA       NA
sample04 1.00000000 0.0000000        1       NA       NA
sample05 0.64222246 0.7269269        0        0       NA
[ -- omitted 2 rows/columns ]

DELETION:
          sample01 sample02 sample03 sample04 sample05
sample01        NA       NA       NA       NA       NA
sample02 0.6477475       NA       NA       NA       NA
sample03 0.0000000        0       NA       NA       NA
sample04 0.0000000        0        1       NA       NA
sample05 0.0000000        0        1        1       NA
[ -- omitted 2 rows/columns ]
CNV Metrics
Metric:
weightedEuclideanDistance

LOG2RATIO:
           sample01 sample02 sample03
sample01         NA       NA       NA
sample02 0.06352523       NA       NA
sample03 0.11004168       NA       NA

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 68 ]
> 
> proc.time()
   user  system elapsed 
 29.520   0.388  29.893 

Example timings

CNVMetrics.Rcheck/CNVMetrics-Ex.timings

nameusersystemelapsed
calculateJaccard0.3440.0040.349
calculateLog2ratioMetric0.9310.0080.939
calculateOneLog2valueMetricT0.3300.0040.333
calculateOneOverlapMetricT1.1420.0041.149
calculateOverlapMetric1.7980.0111.808
calculateSorensen0.2350.0000.235
calculateSzymkiewicz0.2540.0000.254
calculateWeightedEuclideanDistanceFor2Samples0.2820.0000.281
createDisjoinSegmentsForTwoSamples0.2580.0000.258
plotMetric1.3580.0161.374
plotOneMetric1.2100.0121.222
validateCalculateOverlapMetricParameters0.0010.0000.001
validatecalculateLog2ratioMetricParameters0.0010.0010.001