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This page was generated on 2024-05-04 11:40:40 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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 1040/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
INSPEcT 1.34.0  (landing page)
Stefano de Pretis
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/INSPEcT
git_branch: RELEASE_3_19
git_last_commit: 455938d
git_last_commit_date: 2024-04-30 10:44:32 -0400 (Tue, 30 Apr 2024)
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  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for INSPEcT on kunpeng2


To the developers/maintainers of the INSPEcT package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/INSPEcT.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: INSPEcT
Version: 1.34.0
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:INSPEcT.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings INSPEcT_1.34.0.tar.gz
StartedAt: 2024-05-04 08:38:21 -0000 (Sat, 04 May 2024)
EndedAt: 2024-05-04 08:55:04 -0000 (Sat, 04 May 2024)
EllapsedTime: 1003.8 seconds
RetCode: 0
Status:   OK  
CheckDir: INSPEcT.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:INSPEcT.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings INSPEcT_1.34.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/INSPEcT.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    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 ‘INSPEcT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘INSPEcT’ version ‘1.34.0’
* 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 ‘INSPEcT’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    data   2.8Mb
* 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
output_pars: no visible global function definition for ‘plot.new’
plotSingleRNADynamic: no visible global function definition for ‘lines’
Undefined global functions or variables:
  lines plot.new
Consider adding
  importFrom("graphics", "lines", "plot.new")
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
makeSimDataset                  122.583  0.431 123.274
quantifyExpressionsFromBAMs      50.138  0.284  50.629
rocCurve                         42.233  0.116  42.427
INSPEcT_diffsteady-class         41.136  0.679  41.900
makeSimModel                     40.860  0.108  41.054
rocThresholds                    40.396  0.100  40.721
plotMA                           35.606  0.100  35.782
compareSteady                    35.082  0.199  35.356
modelRates                       24.581  0.068  24.700
quantifyExpressionsFromTrCounts  21.343  0.163  21.552
newINSPEcT                       20.829  0.044  20.919
processingDelay                  18.969  0.039  19.050
makeOscillatorySimModel           9.906  0.052   9.985
compareSteadyNoNascent            7.503  0.051   7.572
inspectFromPCR                    5.018  0.016   5.048
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/INSPEcT.Rcheck/00check.log’
for details.


Installation output

INSPEcT.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL INSPEcT
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’
* installing *source* package ‘INSPEcT’ ...
** 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 (INSPEcT)

Tests output


Example timings

INSPEcT.Rcheck/INSPEcT-Ex.timings

nameusersystemelapsed
AIC-INSPEcT-method0.2010.0040.207
Extract0.4640.0080.473
INSPEcT_diffsteady-class41.136 0.67941.900
calculateRatePvals0.2630.0000.264
chisqmodel0.2050.0000.205
chisqtest0.2000.0040.203
combine0.4610.0000.461
compareSteady35.082 0.19935.356
compareSteadyNoNascent7.5030.0517.572
convergence0.1930.0120.206
geneClass0.2570.0080.266
inHeatmap0.2430.0080.251
inspectFromPCR5.0180.0165.048
labeledSF0.2000.0040.205
logLik0.2050.0000.205
makeModelRates0.2660.0000.266
makeOscillatorySimModel9.9060.0529.985
makeSimDataset122.583 0.431123.274
makeSimModel40.860 0.10841.054
modelRates24.581 0.06824.700
modelRatesNF1.7690.0001.773
modelSelection0.1990.0000.200
modelingParams0.1970.0040.201
nGenes0.2000.0000.202
nTpts0.2010.0000.202
newINSPEcT20.829 0.04420.919
plotGene0.2580.0000.259
plotMA35.606 0.10035.782
processingDelay18.969 0.03919.050
quantifyExpressionsFromBAMs50.138 0.28450.629
quantifyExpressionsFromTrCounts21.343 0.16321.552
ratePvals0.1990.0040.203
ratesFirstGuess0.2010.0000.202
ratesFirstGuessVar0.1930.0080.201
removeModel0.3520.0000.353
rocCurve42.233 0.11642.427
rocThresholds40.396 0.10040.721
split0.3210.0000.321
tpts0.2010.0000.201
viewConfidenceIntervals0.1980.0040.202
viewModelRates0.2000.0010.201