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This page was generated on 2024-03-28 11:36:09 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4708
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4446
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4471
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4426
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 31/2270HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AffyRNADegradation 1.49.0  (landing page)
Mario Fasold
Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/AffyRNADegradation
git_branch: devel
git_last_commit: 64e63e3
git_last_commit_date: 2023-10-24 09:49:00 -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 AffyRNADegradation on nebbiolo1


To the developers/maintainers of the AffyRNADegradation package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/AffyRNADegradation.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: AffyRNADegradation
Version: 1.49.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:AffyRNADegradation.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings AffyRNADegradation_1.49.0.tar.gz
StartedAt: 2024-03-27 20:07:59 -0400 (Wed, 27 Mar 2024)
EndedAt: 2024-03-27 20:10:49 -0400 (Wed, 27 Mar 2024)
EllapsedTime: 170.1 seconds
RetCode: 0
Status:   OK  
CheckDir: AffyRNADegradation.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:AffyRNADegradation.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings AffyRNADegradation_1.49.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/AffyRNADegradation.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘AffyRNADegradation/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AffyRNADegradation’ version ‘1.49.0’
* 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 ‘AffyRNADegradation’ 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 ... NOTE
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ComputeTongs: no visible global function definition for ‘filter’
ComputeTongs: no visible global function definition for ‘na.omit’
EstimateHookParams: no visible global function definition for ‘loess’
EstimateHookParams: no visible global function definition for
  ‘quantile’
GetTongs: no visible global function definition for ‘ave’
PlotDegradationHooks: no visible global function definition for
  ‘rainbow’
PlotDegradationHooks: no visible global function definition for ‘lines’
PlotDegradationHooks: no visible global function definition for
  ‘legend’
PlotDx: no visible global function definition for ‘grid’
PlotDx: no visible global function definition for ‘points’
PlotDx: no visible global function definition for ‘lines’
PlotTongs: no visible global function definition for ‘grid’
PlotTongs: no visible global function definition for ‘lines’
PlotTongs: no visible global function definition for ‘legend’
RNADegradation: no visible global function definition for ‘ave’
RNADegradation: no visible global function definition for ‘loess’
RNADegradation: no visible global function definition for ‘approx’
RNADegradation: no visible global function definition for ‘new’
TryToFitDecayFunction: no visible global function definition for ‘nls’
TryToFitDecayFunction: no visible global function definition for ‘coef’
getProbeInfo.index: no visible global function definition for ‘ave’
Undefined global functions or variables:
  approx ave coef filter grid legend lines loess na.omit new nls points
  quantile rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "grid", "legend", "lines", "points")
  importFrom("methods", "new")
  importFrom("stats", "approx", "ave", "coef", "filter", "loess",
             "na.omit", "nls", "quantile")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                             user system elapsed
AffyDegradationBatch-class 18.130  0.555  18.689
AffyRNADegradation         14.125  0.226  14.352
AffyRNADegradation-package 13.932  0.164  14.097
GetTongs                    7.390  0.068   7.458
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/AffyRNADegradation.Rcheck/00check.log’
for details.


Installation output

AffyRNADegradation.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL AffyRNADegradation
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘AffyRNADegradation’ ...
** 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 (AffyRNADegradation)

Tests output


Example timings

AffyRNADegradation.Rcheck/AffyRNADegradation-Ex.timings

nameusersystemelapsed
AffyDegradationBatch-class18.130 0.55518.689
AffyRNADegradation-package13.932 0.16414.097
AffyRNADegradation14.125 0.22614.352
GetTongs7.3900.0687.458