Astrid Deschênes
| Snapshot Date: 2024-11-27 13:40 -0500 (Wed, 27 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/CNVMetrics |
| git_branch: devel |
| git_last_commit: 961ad8c |
| git_last_commit_date: 2024-10-29 11:07:10 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-11-28 12:16 -0500 (Thu, 28 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4748 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4459 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4398 |
| 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 | ||||
| Package 390/2272 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CNVMetrics 1.11.0 (landing page) Astrid Deschênes
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the CNVMetrics package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: CNVMetrics |
| Version: 1.11.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CNVMetrics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CNVMetrics_1.11.0.tar.gz |
| StartedAt: 2024-11-27 20:43:24 -0500 (Wed, 27 Nov 2024) |
| EndedAt: 2024-11-27 20:48:43 -0500 (Wed, 27 Nov 2024) |
| EllapsedTime: 318.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CNVMetrics.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CNVMetrics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CNVMetrics_1.11.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/CNVMetrics.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CNVMetrics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CNVMetrics’ version ‘1.11.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 code 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 ... NOTE
checkRd: (-1) CNVMetrics-package.Rd:23-24: Lost braces
23 | \item \code{\link{calculateOverlapMetric}} {for calculating metric
| ^
checkRd: (-1) CNVMetrics-package.Rd:25-26: Lost braces
25 | \item \code{\link{calculateLog2ratioMetric}} {for calculating metric
| ^
checkRd: (-1) CNVMetrics-package.Rd:27: Lost braces; missing escapes or markup?
27 | \item \code{\link{processSim}} {for generating simulations}
| ^
checkRd: (-1) CNVMetrics-package.Rd:28: Lost braces; missing escapes or markup?
28 | \item \code{\link{plotMetric}} {for plotting metrics}
| ^
checkRd: (-1) calculateLog2ratioMetric.Rd:42-47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calculateLog2ratioMetric.Rd:52-53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calculateLog2ratioMetric.Rd:54-56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calculateOneLog2valueMetricT.Rd:37: Lost braces
37 | that have to be excluded for the metric calculation or code{NULL}.}
| ^
checkRd: (-1) calculateOneLog2valueMetricT.Rd:42-49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calculateOneOverlapMetricT.Rd:33-40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calculateOverlapMetric.Rd:39-44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calculateOverlapMetric.Rd:50-51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calculateOverlapMetric.Rd:52-54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) processSim.Rd:27-28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) processSim.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) processSim.Rd:30-31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) processSim.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) processSim.Rd:33-34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) processSim.Rd:35-36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simChr.Rd:26: Lost braces
26 | a code{list} containing one entry per simulation. Each entry is
| ^
checkRd: (-1) simChr.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simChr.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simChr.Rd:31-33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simChr.Rd:34-36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simChr.Rd:37-38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simChr.Rd:39-40: Lost braces in \itemize; \value handles \item{}{} directly
* 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 ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/Users/biocbuild/bbs-3.21-bioc/meat/CNVMetrics.Rcheck/00check.log’
for details.
CNVMetrics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CNVMetrics ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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)
CNVMetrics.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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 77 ]
>
> proc.time()
user system elapsed
23.648 0.356 24.062
CNVMetrics.Rcheck/CNVMetrics-Ex.timings
| name | user | system | elapsed | |
| calculateJaccard | 0.318 | 0.030 | 0.349 | |
| calculateLog2ratioMetric | 0.670 | 0.009 | 0.681 | |
| calculateOneLog2valueMetricT | 0.256 | 0.008 | 0.264 | |
| calculateOneOverlapMetricT | 0.832 | 0.009 | 0.841 | |
| calculateOverlapMetric | 1.340 | 0.009 | 1.351 | |
| calculateSorensen | 0.164 | 0.007 | 0.171 | |
| calculateSzymkiewicz | 0.162 | 0.006 | 0.168 | |
| calculateWeightedEuclideanDistanceFor2Samples | 0.184 | 0.007 | 0.192 | |
| createDisjoinSegmentsForTwoSamples | 0.183 | 0.007 | 0.190 | |
| plotMetric | 0.905 | 0.010 | 0.920 | |
| plotOneMetric | 0.853 | 0.008 | 0.865 | |
| processChr | 0.068 | 0.007 | 0.076 | |
| processSim | 0.187 | 0.008 | 0.195 | |
| simChr | 0.087 | 0.009 | 0.097 | |
| validateCalculateOverlapMetricParameters | 0 | 0 | 0 | |
| validatecalculateLog2ratioMetricParameters | 0 | 0 | 0 | |