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This page was generated on 2024-11-20 12:02 -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 1033/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
INSPEcT 1.36.0  (landing page)
Stefano de Pretis
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/INSPEcT
git_branch: RELEASE_3_20
git_last_commit: ce54116
git_last_commit_date: 2024-10-29 10:02:14 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
palomino8Windows 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 INSPEcT on teran2

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: 1.36.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:INSPEcT.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings INSPEcT_1.36.0.tar.gz
StartedAt: 2024-11-20 04:40:07 -0500 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 04:54:15 -0500 (Wed, 20 Nov 2024)
EllapsedTime: 848.0 seconds
RetCode: 0
Status:   OK  
CheckDir: INSPEcT.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:INSPEcT.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings INSPEcT_1.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/INSPEcT.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘INSPEcT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘INSPEcT’ version ‘1.36.0’
* 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                  55.899  0.054  55.991
modelRates                      26.128  0.015  26.156
quantifyExpressionsFromBAMs     24.750  0.217  26.314
rocCurve                        21.020  0.062  21.081
INSPEcT_diffsteady-class        20.879  0.131  21.011
rocThresholds                   18.585  0.232  18.819
makeSimModel                    18.075  0.000  18.089
plotMA                          16.676  0.014  16.699
compareSteady                   16.427  0.018  16.452
quantifyExpressionsFromTrCounts 14.411  0.121  14.533
newINSPEcT                       9.816  0.007   9.834
processingDelay                  9.238  0.003   9.246
makeOscillatorySimModel          5.246  0.064   5.315
* 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
  ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/INSPEcT.Rcheck/00check.log’
for details.


Installation output

INSPEcT.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL INSPEcT
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-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-method0.1520.0090.162
Extract0.2550.0070.262
INSPEcT_diffsteady-class20.879 0.13121.011
calculateRatePvals0.1650.0090.174
chisqmodel0.1310.0020.133
chisqtest0.1270.0050.132
combine0.2450.0050.250
compareSteady16.427 0.01816.452
compareSteadyNoNascent3.6920.0023.695
convergence0.1290.0070.136
geneClass0.1710.0050.176
inHeatmap0.1490.0020.151
inspectFromPCR4.5090.0114.525
labeledSF0.1270.0100.136
logLik0.1250.0080.132
makeModelRates0.1550.0050.159
makeOscillatorySimModel5.2460.0645.315
makeSimDataset55.899 0.05455.991
makeSimModel18.075 0.00018.089
modelRates26.128 0.01526.156
modelRatesNF2.7850.0172.802
modelSelection0.1280.0090.137
modelingParams0.1270.0040.131
nGenes0.1270.0030.131
nTpts0.1440.0060.150
newINSPEcT9.8160.0079.834
plotGene0.1530.0070.161
plotMA16.676 0.01416.699
processingDelay9.2380.0039.246
quantifyExpressionsFromBAMs24.750 0.21726.314
quantifyExpressionsFromTrCounts14.411 0.12114.533
ratePvals0.1280.0010.130
ratesFirstGuess0.4230.0160.438
ratesFirstGuessVar0.1260.0010.128
removeModel0.1950.0010.196
rocCurve21.020 0.06221.081
rocThresholds18.585 0.23218.819
split0.5740.0010.575
tpts0.1260.0000.126
viewConfidenceIntervals0.1270.0000.128
viewModelRates0.1260.0010.127