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This page was generated on 2024-11-20 12:08 -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 1783/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rnits 1.40.0  (landing page)
Dipen P. Sangurdekar
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/Rnits
git_branch: RELEASE_3_20
git_last_commit: b91bcc9
git_last_commit_date: 2024-10-29 09:54:24 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  


CHECK results for Rnits on kunpeng2

To the developers/maintainers of the Rnits package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rnits.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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: Rnits
Version: 1.40.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:Rnits.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Rnits_1.40.0.tar.gz
StartedAt: 2024-11-20 11:48:44 -0000 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 11:50:00 -0000 (Wed, 20 Nov 2024)
EllapsedTime: 76.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: Rnits.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:Rnits.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Rnits_1.40.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/Rnits.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rnits/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rnits’ version ‘1.40.0’
* 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 ‘Rnits’ 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 ... NOTE
build.Rnits: no visible global function definition for ‘median’
build.Rnits: no visible global function definition for ‘sd’
finds0: no visible global function definition for ‘rnorm’
finds0: no visible global function definition for ‘quantile’
finds0: no visible global function definition for ‘mad’
finds0 : <anonymous>: no visible global function definition for ‘sd’
modelfit: no visible global function definition for ‘hat’
ranknormalization: no visible binding for global variable ‘median’
ranknormalization: no visible global function definition for
  ‘smooth.spline’
ranknormalization: no visible global function definition for ‘predict’
ranknormalization: no visible global function definition for ‘par’
solvemat: no visible global function definition for ‘hat’
tsFit: no visible global function definition for ‘txtProgressBar’
tsFit: no visible global function definition for ‘setTxtProgressBar’
calculateGCV,Rnits: no visible global function definition for ‘glm’
calculateGCV,Rnits: no visible binding for global variable ‘gaussian’
fit,Rnits: no visible global function definition for ‘kmeans’
fit,Rnits : <anonymous>: no visible global function definition for
  ‘p.adjust’
fit,Rnits: no visible global function definition for ‘par’
fit,Rnits: no visible global function definition for ‘hist’
getCID,Rnits: no visible global function definition for ‘setNames’
getPval,Rnits: no visible global function definition for ‘setNames’
getStat,Rnits: no visible global function definition for ‘setNames’
plotResults,Rnits: no visible global function definition for ‘aes’
plotResults,Rnits: no visible binding for global variable ‘Time’
plotResults,Rnits: no visible binding for global variable ‘value’
plotResults,Rnits: no visible global function definition for
  ‘geom_point’
plotResults,Rnits: no visible binding for global variable ‘Sample’
plotResults,Rnits: no visible global function definition for
  ‘geom_smooth’
plotResults,Rnits: no visible global function definition for ‘ylab’
plotResults,Rnits: no visible global function definition for ‘theme_bw’
plotResults,Rnits: no visible global function definition for ‘theme’
plotResults,Rnits: no visible global function definition for
  ‘scale_color_brewer’
plotResults,Rnits: no visible global function definition for
  ‘facet_wrap’
plotResults,Rnits: no visible global function definition for ‘dev.off’
summary,Rnits: no visible global function definition for ‘hist’
timeAlign,Rnits: no visible global function definition for ‘quantile’
timeAlign,Rnits: no visible global function definition for ‘mvfft’
timeAlign,Rnits: no visible global function definition for ‘abline’
Undefined global functions or variables:
  Sample Time abline aes dev.off facet_wrap gaussian geom_point
  geom_smooth glm hat hist kmeans mad median mvfft p.adjust par predict
  quantile rnorm scale_color_brewer sd setNames setTxtProgressBar
  smooth.spline theme theme_bw txtProgressBar value ylab
Consider adding
  importFrom("grDevices", "dev.off")
  importFrom("graphics", "abline", "hist", "par")
  importFrom("stats", "gaussian", "glm", "hat", "kmeans", "mad",
             "median", "mvfft", "p.adjust", "predict", "quantile",
             "rnorm", "sd", "setNames", "smooth.spline")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... NOTE
Invalid package aliases in Rd file 'rnits.Rd':
  ‘rnits-package’
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in Rd file 'plotResults-methods.Rd':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 LazyData ... 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
calculateGCV-methods 6.516   0.06   6.417
* 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 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/Rnits.Rcheck/00check.log’
for details.


Installation output

Rnits.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL Rnits
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’
* installing *source* package ‘Rnits’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (Rnits)

Tests output


Example timings

Rnits.Rcheck/Rnits-Ex.timings

nameusersystemelapsed
build.Rnits0.6450.0200.667
calculateGCV-methods6.5160.0606.417
fit-methods0.3310.0080.340
getCID-methods0.3410.0040.345
getFitModel-methods0.3460.0000.346
getLR-methods0.4930.0080.502
getPval-methods0.3370.0000.339
getStat-methods0.3500.0040.354
plotResults-methods0.3650.0240.390
summarizeProbes-methods0.3480.0000.348
summary-methods0.3570.0000.358
timeAlign-methods1.7680.0121.783
topData-methods0.3530.0000.354