Stefano de Pretis
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 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 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:49 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
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. |
| Package 939/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| INSPEcT 1.25.0 (landing page) Stefano de Pretis
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: INSPEcT |
| Version: 1.25.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:INSPEcT.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings INSPEcT_1.25.0.tar.gz |
| StartedAt: 2022-03-17 19:22:39 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:29:02 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 382.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: INSPEcT.Rcheck |
| Warnings: 0 |
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### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:INSPEcT.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings INSPEcT_1.25.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/INSPEcT.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'INSPEcT' can be installed ... OK
* checking installed package size ... NOTE
installed size is 7.5Mb
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 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
makeSimModel 23.55 0.06 23.61
newINSPEcT 16.76 0.02 16.78
quantifyExpressionsFromTrCounts 16.13 0.00 16.14
processingDelay 12.81 0.00 12.81
compareSteadyNoNascent 7.13 0.05 7.17
makeOscillatorySimModel 6.43 0.16 6.59
* 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
'D:/biocbuild/bbs-3.15-bioc/meat/INSPEcT.Rcheck/00check.log'
for details.
INSPEcT.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL INSPEcT
###
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* installing to library 'D:/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
converting help for package 'INSPEcT'
finding HTML links ... done
AIC-INSPEcT-method html
Extract html
INSPEcT-class html
finding level-2 HTML links ... done
INSPEcT-shinyApps html
INSPEcT html
INSPEcT_diffsteady-class html
INSPEcT_model-class html
INSPEcT_steadyNoNascent-class html
PTratio html
PTreg html
allcounts html
calculateRatePvals html
chisqmodel html
chisqtest html
combine html
compareSteady html
compareSteadyNoNascent html
computeConfidenceIntervals html
convergence html
correlationPlot html
dim-INSPEcT-method html
featureNames-INSPEcT-method html
featureWidths html
geneClass html
inHeatmap html
inspectFromBAM html
inspectFromPCR html
labeledSF html
libsizes html
logLik html
makeModelRates html
makeOscillatorySimModel html
makeSimDataset html
makeSimModel html
mature html
matureVar html
modelRates html
modelRatesNF html
modelSelection html
modelingParams html
nGenes html
nTpts html
newINSPEcT html
plotGene html
plotMA html
plotPMgene html
plotPMtrend html
premature html
prematureVar html
processingDelay html
quantifyExpressionsFromBAMs html
quantifyExpressionsFromBWs html
quantifyExpressionsFromTrAbundance html
quantifyExpressionsFromTrCounts html
ratePvals html
ratesFirstGuess html
ratesFirstGuessVar html
removeModel html
rocCurve html
rocThresholds html
setConfidenceIntervals html
simData3rep_Nascent html
simData3rep_NoNascent html
simData4rep_Nascent html
simData4rep_NoNascent html
split html
tpts html
viewConfidenceIntervals html
viewModelRates html
** 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)
Making 'packages.html' ... done
INSPEcT.Rcheck/INSPEcT-Ex.timings
| name | user | system | elapsed | |
| AIC-INSPEcT-method | 0.20 | 0.03 | 0.24 | |
| Extract | 0.30 | 0.00 | 0.29 | |
| INSPEcT_diffsteady-class | 0 | 0 | 0 | |
| calculateRatePvals | 0.16 | 0.01 | 0.17 | |
| chisqmodel | 0.22 | 0.00 | 0.22 | |
| chisqtest | 0.14 | 0.00 | 0.14 | |
| combine | 0.29 | 0.00 | 0.30 | |
| compareSteady | 0 | 0 | 0 | |
| compareSteadyNoNascent | 7.13 | 0.05 | 7.17 | |
| convergence | 0.22 | 0.00 | 0.22 | |
| geneClass | 0.15 | 0.03 | 0.19 | |
| inHeatmap | 0.19 | 0.00 | 0.18 | |
| inspectFromPCR | 0 | 0 | 0 | |
| labeledSF | 0.11 | 0.03 | 0.14 | |
| logLik | 0.22 | 0.02 | 0.24 | |
| makeModelRates | 0.19 | 0.01 | 0.20 | |
| makeOscillatorySimModel | 6.43 | 0.16 | 6.59 | |
| makeSimDataset | 0 | 0 | 0 | |
| makeSimModel | 23.55 | 0.06 | 23.61 | |
| modelRates | 0 | 0 | 0 | |
| modelRatesNF | 0 | 0 | 0 | |
| modelSelection | 0.16 | 0.00 | 0.16 | |
| modelingParams | 0.14 | 0.02 | 0.16 | |
| nGenes | 0.15 | 0.01 | 0.17 | |
| nTpts | 0.21 | 0.02 | 0.22 | |
| newINSPEcT | 16.76 | 0.02 | 16.78 | |
| plotGene | 0.17 | 0.03 | 0.20 | |
| plotMA | 0.02 | 0.00 | 0.02 | |
| processingDelay | 12.81 | 0.00 | 12.81 | |
| quantifyExpressionsFromBAMs | 0 | 0 | 0 | |
| quantifyExpressionsFromTrCounts | 16.13 | 0.00 | 16.14 | |
| ratePvals | 0.23 | 0.01 | 0.25 | |
| ratesFirstGuess | 0.19 | 0.02 | 0.20 | |
| ratesFirstGuessVar | 0.20 | 0.00 | 0.21 | |
| removeModel | 0.28 | 0.01 | 0.29 | |
| rocCurve | 0 | 0 | 0 | |
| rocThresholds | 0 | 0 | 0 | |
| split | 0.35 | 0.00 | 0.35 | |
| tpts | 0.22 | 0.00 | 0.22 | |
| viewConfidenceIntervals | 0.17 | 0.02 | 0.18 | |
| viewModelRates | 0.19 | 0.02 | 0.20 | |