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This page was generated on 2022-01-28 11:06:17 -0500 (Fri, 28 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4167
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4062
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4004
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4121
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

CHECK results for INSPEcT on nebbiolo1


To the developers/maintainers of the INSPEcT package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 935/2077HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
INSPEcT 1.25.0  (landing page)
Stefano de Pretis
Snapshot Date: 2022-01-27 13:55:17 -0500 (Thu, 27 Jan 2022)
git_url: https://git.bioconductor.org/packages/INSPEcT
git_branch: master
git_last_commit: e99d196
git_last_commit_date: 2021-10-26 12:21:19 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'Biobase' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: INSPEcT
Version: 1.25.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:INSPEcT.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings INSPEcT_1.25.0.tar.gz
StartedAt: 2022-01-27 19:39:48 -0500 (Thu, 27 Jan 2022)
EndedAt: 2022-01-27 19:51:03 -0500 (Thu, 27 Jan 2022)
EllapsedTime: 675.1 seconds
RetCode: 0
Status:   OK  
CheckDir: INSPEcT.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:INSPEcT.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings INSPEcT_1.25.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/INSPEcT.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘INSPEcT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘INSPEcT’ version ‘1.25.0’
* 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 R 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 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                  73.064  0.440  73.504
modelRates                      35.840  0.120  35.960
quantifyExpressionsFromBAMs     30.045  3.229  33.378
INSPEcT_diffsteady-class        25.836  0.615  26.464
rocCurve                        23.906  0.092  23.998
rocThresholds                   23.897  0.036  23.933
makeSimModel                    23.619  0.064  23.683
compareSteady                   22.997  0.220  23.218
plotMA                          22.318  0.056  22.374
quantifyExpressionsFromTrCounts 15.023  0.096  15.119
newINSPEcT                      14.480  0.128  14.607
processingDelay                 12.385  0.067  12.452
inspectFromPCR                   6.930  0.112   7.043
makeOscillatorySimModel          5.738  0.013   5.754
compareSteadyNoNascent           5.150  0.056   5.206
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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-3.15-bioc/meat/INSPEcT.Rcheck/00check.log’
for details.



Installation output

INSPEcT.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL INSPEcT
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/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-method0.1730.0080.182
Extract0.3100.0120.322
INSPEcT_diffsteady-class25.836 0.61526.464
calculateRatePvals0.2200.0040.224
chisqmodel0.1730.0040.177
chisqtest0.1750.0040.178
combine0.3440.0040.348
compareSteady22.997 0.22023.218
compareSteadyNoNascent5.1500.0565.206
convergence0.1830.0020.184
geneClass0.2130.0020.216
inHeatmap0.2100.0000.211
inspectFromPCR6.9300.1127.043
labeledSF0.1740.0030.177
logLik0.1760.0040.180
makeModelRates0.2080.0060.214
makeOscillatorySimModel5.7380.0135.754
makeSimDataset73.064 0.44073.504
makeSimModel23.619 0.06423.683
modelRates35.84 0.1235.96
modelRatesNF4.1060.0244.131
modelSelection0.1780.0040.181
modelingParams0.1760.0040.181
nGenes0.180.000.18
nTpts0.1870.0080.194
newINSPEcT14.480 0.12814.607
plotGene0.2190.0040.222
plotMA22.318 0.05622.374
processingDelay12.385 0.06712.452
quantifyExpressionsFromBAMs30.045 3.22933.378
quantifyExpressionsFromTrCounts15.023 0.09615.119
ratePvals0.1770.0000.176
ratesFirstGuess0.1760.0010.177
ratesFirstGuessVar0.1730.0070.180
removeModel0.2600.0020.261
rocCurve23.906 0.09223.998
rocThresholds23.897 0.03623.933
split0.2680.0040.271
tpts0.1720.0000.173
viewConfidenceIntervals0.1650.0120.177
viewModelRates0.1710.0040.174