Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-11-20 12:02 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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 397/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNVMetrics 1.10.0  (landing page)
Astrid Deschênes
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/CNVMetrics
git_branch: RELEASE_3_20
git_last_commit: c4dee6a
git_last_commit_date: 2024-10-29 11:07:10 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for CNVMetrics on teran2

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.

raw results


Summary

Package: CNVMetrics
Version: 1.10.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:CNVMetrics.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings CNVMetrics_1.10.0.tar.gz
StartedAt: 2024-11-20 00:38:08 -0500 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 00:40:27 -0500 (Wed, 20 Nov 2024)
EllapsedTime: 138.6 seconds
RetCode: 0
Status:   OK  
CheckDir: CNVMetrics.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:CNVMetrics.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings CNVMetrics_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/CNVMetrics.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘CNVMetrics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CNVMetrics’ version ‘1.10.0’
* 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 ‘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 loading without being on the library search path ... 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/CNVMetrics.Rcheck/00check.log’
for details.


Installation output

CNVMetrics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL CNVMetrics
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-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 version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 
 25.137   0.378  26.816 

Example timings

CNVMetrics.Rcheck/CNVMetrics-Ex.timings

nameusersystemelapsed
calculateJaccard0.2670.0650.342
calculateLog2ratioMetric0.5960.0030.602
calculateOneLog2valueMetricT0.2070.0040.211
calculateOneOverlapMetricT0.7680.0030.776
calculateOverlapMetric1.2180.0041.234
calculateSorensen0.1380.0010.139
calculateSzymkiewicz0.1340.0010.135
calculateWeightedEuclideanDistanceFor2Samples0.1560.0040.160
createDisjoinSegmentsForTwoSamples0.1540.0020.168
plotMetric0.8200.0010.829
plotOneMetric0.7740.0010.775
processChr0.0490.0030.052
processSim0.1640.0020.166
simChr0.0660.0010.066
validateCalculateOverlapMetricParameters0.0010.0000.000
validatecalculateLog2ratioMetricParameters000