Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-03-27 11:38:56 -0400 (Wed, 27 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4698
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4436
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4461
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4376
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 38/2264HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
airpart 1.11.0  (landing page)
Wancen Mu
Snapshot Date: 2024-03-26 14:00:18 -0400 (Tue, 26 Mar 2024)
git_url: https://git.bioconductor.org/packages/airpart
git_branch: devel
git_last_commit: 3983727
git_last_commit_date: 2023-10-24 11:31:27 -0400 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 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
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 airpart on lconway


To the developers/maintainers of the airpart package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/airpart.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: airpart
Version: 1.11.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:airpart.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings airpart_1.11.0.tar.gz
StartedAt: 2024-03-26 18:47:38 -0400 (Tue, 26 Mar 2024)
EndedAt: 2024-03-26 18:53:19 -0400 (Tue, 26 Mar 2024)
EllapsedTime: 341.2 seconds
RetCode: 0
Status:   OK  
CheckDir: airpart.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:airpart.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings airpart_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/airpart.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* 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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘airpart/DESCRIPTION’ ... OK
* this is package ‘airpart’ version ‘1.11.0’
* 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 ‘airpart’ 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) cellQC.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) cellQC.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) cellQC.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) cellQC.Rd:47-49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) cellQC.Rd:50-52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) cellQC.Rd:53-55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) featureQC.Rd:29-30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) featureQC.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) featureQC.Rd:32-33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) featureQC.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) makeSimulatedData.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) makeSimulatedData.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) makeSimulatedData.Rd:45-46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summaryAllelicRatio.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summaryAllelicRatio.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summaryAllelicRatio.Rd:21: 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
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
consensusPart 7.401  1.574   6.018
fusedLasso    7.641  0.543   8.301
makeStep      7.906  0.202   8.197
allelicRatio  7.226  0.278   7.571
makeHeatmap   5.936  0.158   6.180
makeForest    5.299  0.203   5.573
* 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-3.19-bioc/meat/airpart.Rcheck/00check.log’
for details.


Installation output

airpart.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘airpart’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** 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 (airpart)

Tests output

airpart.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-03-18 r86148) -- "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(airpart)
> 
> test_check("airpart")
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, aperm, 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, table, tapply,
    union, unique, unsplit, which.max, which.min


Attaching package: 'S4Vectors'

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

    findMatches

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

    I, expand.grid, unname

model-based optimal number of clusters: 3 
model-based optimal number of clusters: 3 
model-based optimal number of clusters: 3 
model-based optimal number of clusters: 3 
[ FAIL 0 | WARN 29 | SKIP 0 | PASS 13 ]

[ FAIL 0 | WARN 29 | SKIP 0 | PASS 13 ]
> 
> proc.time()
   user  system elapsed 
 24.992   1.417  26.772 

Example timings

airpart.Rcheck/airpart-Ex.timings

nameusersystemelapsed
allelicRatio7.2260.2787.571
cellQC0.6580.0310.697
consensusPart7.4011.5746.018
estDisp1.9760.1372.132
extractResult4.2850.1474.483
featureQC1.8420.0661.931
fusedLasso7.6410.5438.301
geneCluster0.6290.0120.651
makeForest5.2990.2035.573
makeHeatmap5.9360.1586.180
makeOffByOneAdjMat0.1460.0030.151
makeSimulatedData0.3850.0220.413
makeStep7.9060.2028.197
makeViolin4.7580.1534.976
preprocess0.5060.0210.531
summaryAllelicRatio0.9020.0230.940
wilcoxExt1.7630.0401.825