Back to Multiple platform build/check report for BioC 3.19:   simplified   long
ABCDEFGH[I]JKLMNOPQRSTUVWXYZ

This page was generated on 2024-05-04 11:36:42 -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 nebbiolo1


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.

raw results


Summary

Package: INSPEcT
Version: 1.34.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:INSPEcT.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings INSPEcT_1.34.0.tar.gz
StartedAt: 2024-05-04 00:17:32 -0400 (Sat, 04 May 2024)
EndedAt: 2024-05-04 00:36:12 -0400 (Sat, 04 May 2024)
EllapsedTime: 1120.4 seconds
RetCode: 0
Status:   OK  
CheckDir: INSPEcT.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:INSPEcT.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings INSPEcT_1.34.0.tar.gz
###
##############################################################################
##############################################################################


* 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: 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 ‘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  6.9Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    data   2.9Mb
* 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                  72.252  0.536  72.788
modelRates                      36.773  0.167  36.942
quantifyExpressionsFromBAMs     32.370  1.109  33.569
INSPEcT_diffsteady-class        28.507  1.171  29.680
rocCurve                        24.450  0.352  24.803
makeSimModel                    24.116  0.112  24.229
rocThresholds                   23.905  0.140  24.045
plotMA                          22.575  0.028  22.604
compareSteady                   21.740  0.296  22.036
quantifyExpressionsFromTrCounts 16.600  0.328  16.929
newINSPEcT                      13.737  0.080  13.818
processingDelay                 12.784  0.056  12.839
inspectFromPCR                   6.229  0.059   6.289
makeOscillatorySimModel          5.655  0.034   5.691
compareSteadyNoNascent           5.092  0.032   5.124
* 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/INSPEcT.Rcheck/00check.log’
for details.


Installation output

INSPEcT.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/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-method0.2280.0080.237
Extract0.3730.0120.385
INSPEcT_diffsteady-class28.507 1.17129.680
calculateRatePvals0.2360.0080.243
chisqmodel0.1890.0000.189
chisqtest0.1850.0040.188
combine0.3870.0200.408
compareSteady21.740 0.29622.036
compareSteadyNoNascent5.0920.0325.124
convergence0.1860.0040.190
geneClass0.2230.0000.223
inHeatmap0.2370.0000.237
inspectFromPCR6.2290.0596.289
labeledSF0.1910.0000.192
logLik0.1850.0040.189
makeModelRates0.2210.0060.225
makeOscillatorySimModel5.6550.0345.691
makeSimDataset72.252 0.53672.788
makeSimModel24.116 0.11224.229
modelRates36.773 0.16736.942
modelRatesNF3.7460.0163.762
modelSelection0.1890.0000.190
modelingParams0.1840.0040.188
nGenes0.1870.0000.188
nTpts0.1880.0000.188
newINSPEcT13.737 0.08013.818
plotGene0.2210.0070.229
plotMA22.575 0.02822.604
processingDelay12.784 0.05612.839
quantifyExpressionsFromBAMs32.370 1.10933.569
quantifyExpressionsFromTrCounts16.600 0.32816.929
ratePvals0.1860.0040.190
ratesFirstGuess0.1890.0000.189
ratesFirstGuessVar0.1860.0030.189
removeModel0.2700.0120.282
rocCurve24.450 0.35224.803
rocThresholds23.905 0.14024.045
split0.2640.0160.280
tpts0.1860.0040.189
viewConfidenceIntervals0.2620.0000.262
viewModelRates0.1810.0080.190