Back to Multiple platform build/check report for BioC 3.18:   simplified   long
ABCDEFGHIJKLMNOPQ[R]STUVWXYZ

This page was generated on 2024-04-17 11:38:10 -0400 (Wed, 17 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4676
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4414
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4437
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 1778/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rnaseqcomp 1.32.0  (landing page)
Mingxiang Teng
Snapshot Date: 2024-04-15 14:05:01 -0400 (Mon, 15 Apr 2024)
git_url: https://git.bioconductor.org/packages/rnaseqcomp
git_branch: RELEASE_3_18
git_last_commit: 05f2020
git_last_commit_date: 2023-10-24 10:44:11 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for rnaseqcomp on merida1


To the developers/maintainers of the rnaseqcomp package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/rnaseqcomp.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: rnaseqcomp
Version: 1.32.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:rnaseqcomp.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings rnaseqcomp_1.32.0.tar.gz
StartedAt: 2024-04-16 07:59:08 -0400 (Tue, 16 Apr 2024)
EndedAt: 2024-04-16 08:00:19 -0400 (Tue, 16 Apr 2024)
EllapsedTime: 70.7 seconds
RetCode: 0
Status:   OK  
CheckDir: rnaseqcomp.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:rnaseqcomp.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings rnaseqcomp_1.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/rnaseqcomp.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* 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 ‘rnaseqcomp/DESCRIPTION’ ... OK
* this is package ‘rnaseqcomp’ version ‘1.32.0’
* 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 ‘rnaseqcomp’ 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 ... NOTE
plot2TX: no visible global function definition for ‘lines’
plot2TX: no visible global function definition for ‘box’
plot2TX: no visible global function definition for ‘legend’
plot2TX : <anonymous>: no visible binding for global variable ‘sd’
plot2TX : <anonymous>: no visible global function definition for ‘sd’
plotFC: no visible global function definition for ‘loess.smooth’
plotFC: no visible global function definition for ‘lines’
plotFC: no visible global function definition for ‘legend’
plotFC : <anonymous>: no visible global function definition for
  ‘median’
plotFC : <anonymous>: no visible global function definition for ‘sd’
plotNE: no visible global function definition for ‘lines’
plotNE: no visible global function definition for ‘points’
plotNE: no visible global function definition for ‘box’
plotNE: no visible global function definition for ‘legend’
plotROC: no visible global function definition for ‘median’
plotROC: no visible global function definition for ‘sd’
plotROC: no visible global function definition for ‘lines’
plotROC: no visible global function definition for ‘arrows’
plotROC: no visible global function definition for ‘abline’
plotROC: no visible global function definition for ‘legend’
plotSD : <anonymous>: no visible binding for global variable ‘sd’
plotSD: no visible global function definition for ‘loess.smooth’
plotSD: no visible global function definition for ‘lines’
plotSD: no visible global function definition for ‘box’
plotSD: no visible global function definition for ‘legend’
plotSD : <anonymous> : <anonymous>: no visible global function
  definition for ‘median’
plotSD : <anonymous> : <anonymous>: no visible global function
  definition for ‘mad’
signalCalibrate : <anonymous>: no visible binding for global variable
  ‘median’
signalCalibrate: no visible global function definition for ‘median’
Undefined global functions or variables:
  abline arrows box legend lines loess.smooth mad median points sd
Consider adding
  importFrom("graphics", "abline", "arrows", "box", "legend", "lines",
             "points")
  importFrom("stats", "loess.smooth", "mad", "median", "sd")
to your NAMESPACE file.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... 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
plotROC 10.869  1.323  13.380
plotNE   4.698  0.657   5.883
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.18-bioc/meat/rnaseqcomp.Rcheck/00check.log’
for details.



Installation output

rnaseqcomp.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘rnaseqcomp’ ...
** using staged installation
** R
** data
** 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 (rnaseqcomp)

Tests output


Example timings

rnaseqcomp.Rcheck/rnaseqcomp-Ex.timings

nameusersystemelapsed
plot2TX0.8840.0901.058
plotFC0.3880.0350.460
plotNE4.6980.6575.883
plotROC10.869 1.32313.380
plotSD3.0590.0493.485
signalCalibrate0.2890.0100.341