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This page was generated on 2024-12-23 11:40 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4372
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 1026/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
INSPEcT 1.37.0  (landing page)
Stefano de Pretis
Snapshot Date: 2024-12-22 13:40 -0500 (Sun, 22 Dec 2024)
git_url: https://git.bioconductor.org/packages/INSPEcT
git_branch: devel
git_last_commit: 7d70bac
git_last_commit_date: 2024-10-29 10:02:14 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'DESeq2' which is only available as a source package that needs compilation
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  NO, package depends on 'DESeq2' which is only available as a source package that needs compilation
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  NO, package depends on 'DESeq2' which is only available as a source package that needs compilation
kunpeng2Linux (openEuler 22.03 LTS-SP1) / 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: 1.37.0
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_1.37.0.tar.gz
StartedAt: 2024-12-22 23:07:50 -0500 (Sun, 22 Dec 2024)
EndedAt: 2024-12-22 23:27:35 -0500 (Sun, 22 Dec 2024)
EllapsedTime: 1185.0 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_1.37.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/INSPEcT.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* 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 ‘1.37.0’
* 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                  72.813  0.248  73.074
modelRates                      36.518  0.010  36.528
quantifyExpressionsFromBAMs     31.414  1.007  32.509
INSPEcT_diffsteady-class        27.726  0.520  28.259
rocCurve                        25.426  0.327  25.754
makeSimModel                    24.372  0.011  24.384
rocThresholds                   24.204  0.173  24.377
plotMA                          23.183  0.003  23.187
compareSteady                   22.491  0.054  22.546
quantifyExpressionsFromTrCounts 16.049  0.402  16.451
newINSPEcT                      14.208  0.002  14.209
processingDelay                 12.990  0.006  12.996
inspectFromPCR                   6.420  0.058   6.478
makeOscillatorySimModel          5.791  0.043   5.835
compareSteadyNoNascent           5.154  0.054   5.209
* 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’ ...
** 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-method0.1820.0110.194
Extract0.3510.0070.358
INSPEcT_diffsteady-class27.726 0.52028.259
calculateRatePvals0.2180.0070.225
chisqmodel0.1820.0030.185
chisqtest0.1770.0060.184
combine0.3400.0040.343
compareSteady22.491 0.05422.546
compareSteadyNoNascent5.1540.0545.209
convergence0.1800.0030.184
geneClass0.2120.0080.220
inHeatmap0.2120.0070.218
inspectFromPCR6.4200.0586.478
labeledSF0.1790.0090.188
logLik0.1800.0050.185
makeModelRates0.2210.0040.225
makeOscillatorySimModel5.7910.0435.835
makeSimDataset72.813 0.24873.074
makeSimModel24.372 0.01124.384
modelRates36.518 0.01036.528
modelRatesNF3.8600.0063.867
modelSelection0.1810.0030.184
modelingParams0.1810.0010.183
nGenes0.1810.0010.182
nTpts0.1790.0020.182
newINSPEcT14.208 0.00214.209
plotGene0.220.000.22
plotMA23.183 0.00323.187
processingDelay12.990 0.00612.996
quantifyExpressionsFromBAMs31.414 1.00732.509
quantifyExpressionsFromTrCounts16.049 0.40216.451
ratePvals0.1840.0020.186
ratesFirstGuess0.1820.0050.187
ratesFirstGuessVar0.1820.0040.185
removeModel0.2740.0020.276
rocCurve25.426 0.32725.754
rocThresholds24.204 0.17324.377
split0.2630.0040.267
tpts0.1790.0020.181
viewConfidenceIntervals0.1790.0050.185
viewModelRates0.1790.0040.182