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This page was generated on 2025-08-04 11:40 -0400 (Mon, 04 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4823
palomino7Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4565
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4603
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4544
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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 1052/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
INSPEcT 1.38.0  (landing page)
Stefano de Pretis
Snapshot Date: 2025-07-31 13:40 -0400 (Thu, 31 Jul 2025)
git_url: https://git.bioconductor.org/packages/INSPEcT
git_branch: RELEASE_3_21
git_last_commit: 7870789
git_last_commit_date: 2025-04-15 10:51:53 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


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: 1.38.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:INSPEcT.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings INSPEcT_1.38.0.tar.gz
StartedAt: 2025-08-03 23:28:15 -0400 (Sun, 03 Aug 2025)
EndedAt: 2025-08-03 23:46:49 -0400 (Sun, 03 Aug 2025)
EllapsedTime: 1114.5 seconds
RetCode: 0
Status:   OK  
CheckDir: INSPEcT.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:INSPEcT.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings INSPEcT_1.38.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/INSPEcT.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘INSPEcT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘INSPEcT’ version ‘1.38.0’
* 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 ... INFO
  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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  INSPEcT-class.Rd: featureNames
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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                  73.459  0.516  73.980
modelRates                      37.974  0.194  38.168
quantifyExpressionsFromBAMs     30.183  0.135  30.425
INSPEcT_diffsteady-class        27.618  0.390  28.010
rocThresholds                   24.925  0.074  24.999
rocCurve                        24.700  0.104  24.803
makeSimModel                    23.990  0.113  24.102
plotMA                          23.705  0.229  23.941
compareSteady                   22.461  0.092  22.556
quantifyExpressionsFromTrCounts 15.858  0.125  15.982
newINSPEcT                      13.566  0.041  13.608
processingDelay                 12.949  0.051  12.999
inspectFromPCR                   6.509  0.006   6.517
makeOscillatorySimModel          5.761  0.035   5.800
compareSteadyNoNascent           5.212  0.091   5.303
* 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-3.21-bioc/meat/INSPEcT.Rcheck/00check.log’
for details.


Installation output

INSPEcT.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL INSPEcT
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘INSPEcT’ ...
** this is package ‘INSPEcT’ version ‘1.38.0’
** 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-method0.1860.0110.198
Extract0.3600.0060.366
INSPEcT_diffsteady-class27.618 0.39028.010
calculateRatePvals0.2220.0110.233
chisqmodel0.1870.0050.191
chisqtest0.1880.0030.190
combine0.3510.0030.354
compareSteady22.461 0.09222.556
compareSteadyNoNascent5.2120.0915.303
convergence0.1940.0050.198
geneClass0.2240.0060.231
inHeatmap0.2180.0040.224
inspectFromPCR6.5090.0066.517
labeledSF0.1850.0050.190
logLik0.1870.0040.191
makeModelRates0.2220.0050.228
makeOscillatorySimModel5.7610.0355.800
makeSimDataset73.459 0.51673.980
makeSimModel23.990 0.11324.102
modelRates37.974 0.19438.168
modelRatesNF4.0450.0284.075
modelSelection0.1850.0030.188
modelingParams0.1850.0030.188
nGenes0.1870.0020.188
nTpts0.2030.0030.206
newINSPEcT13.566 0.04113.608
plotGene0.2230.0030.225
plotMA23.705 0.22923.941
processingDelay12.949 0.05112.999
quantifyExpressionsFromBAMs30.183 0.13530.425
quantifyExpressionsFromTrCounts15.858 0.12515.982
ratePvals0.1880.0000.187
ratesFirstGuess0.1880.0010.189
ratesFirstGuessVar0.1870.0030.189
removeModel0.2850.0010.286
rocCurve24.700 0.10424.803
rocThresholds24.925 0.07424.999
split0.2790.0090.289
tpts0.1880.0000.189
viewConfidenceIntervals0.1860.0050.192
viewModelRates0.1870.0030.190