Keegan Korthauer
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/scDD |
| git_branch: master |
| git_last_commit: e96d5c3 |
| git_last_commit_date: 2021-11-21 00:52:11 -0400 (Sun, 21 Nov 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:37 -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 scDD package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scDD.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 1727/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| scDD 1.19.1 (landing page) Keegan Korthauer
| 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: scDD |
| Version: 1.19.1 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:scDD.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings scDD_1.19.1.tar.gz |
| StartedAt: 2022-03-17 20:12:00 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 20:18:57 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 416.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: scDD.Rcheck |
| Warnings: 0 |
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### Running command:
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### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:scDD.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings scDD_1.19.1.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/scDD.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 'scDD/DESCRIPTION' ... OK
* this is package 'scDD' version '1.19.1'
* 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 'scDD' can be installed ... OK
* checking installed package size ... OK
* 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 ... NOTE
Namespaces in Imports field not imported from:
'grDevices' 'graphics' 'stats'
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
calcMV: no visible global function definition for 'var'
classifyDD: no visible global function definition for 'quantile'
classifyDD: no visible global function definition for 'rt'
classifyDD: no visible global function definition for 'lm'
classifyDD: no visible global function definition for 't.test'
feDP: no visible global function definition for 'runif'
feDP: no visible global function definition for 'lm'
feDP: no visible global function definition for 't.test'
feDP: no visible global function definition for 'fisher.test'
feDP: no visible global function definition for 'p.adjust'
findFC : createFindFC: no visible global function definition for
'quantile'
findFC : createFindFC : f: no visible global function definition for
'runif'
findFC: no visible global function definition for 'par'
findFC: no visible global function definition for 'points'
mclustRestricted: no visible global function definition for 'runif'
permMclustCov: no visible global function definition for 'model.matrix'
permMclustCov: no visible global function definition for 'lm'
permMclustCov : getPerm: no visible global function definition for
'residuals'
permMclustGene: no visible global function definition for
'model.matrix'
permMclustGene: no visible global function definition for 'lm'
permMclustGene: no visible global function definition for 'residuals'
scDD: no visible global function definition for 'p.adjust'
scDD : fishersCombinedPval: no visible global function definition for
'pchisq'
sideHist : ggplotColours: no visible global function definition for
'hcl'
sideHist: no visible global function definition for 'hist'
sideHist: no visible global function definition for 'axis'
sideHist: no visible global function definition for 'rect'
sideHist: no visible global function definition for 'lines'
sideHist: no visible global function definition for 'density'
simuDB: no visible global function definition for 'rnbinom'
simuDE: no visible global function definition for 'rnbinom'
simuDE: no visible global function definition for 'var'
simuDM: no visible global function definition for 'rnbinom'
simuDP: no visible global function definition for 'rbinom'
simuDP: no visible global function definition for 'rnbinom'
simulateSet: no visible global function definition for 'pdf'
simulateSet: no visible global function definition for 'dev.off'
simulateSet: no visible global function definition for 'runif'
singleCellSimu: no visible global function definition for 'var'
singleCellSimu: no visible global function definition for 'lm'
testKS : onegene: no visible global function definition for 'ks.test'
testKS: no visible global function definition for 'p.adjust'
testZeroes : onegene: no visible global function definition for
'binomial'
validation : <anonymous>: no visible global function definition for
'var'
validation: no visible binding for global variable 'var'
validation: no visible global function definition for 'par'
validation: no visible global function definition for 'abline'
validation: no visible global function definition for 'points'
Undefined global functions or variables:
abline axis binomial density dev.off fisher.test hcl hist ks.test
lines lm model.matrix p.adjust par pchisq pdf points quantile rbinom
rect residuals rnbinom rt runif t.test var
Consider adding
importFrom("grDevices", "dev.off", "hcl", "pdf")
importFrom("graphics", "abline", "axis", "hist", "lines", "par",
"points", "rect")
importFrom("stats", "binomial", "density", "fisher.test", "ks.test",
"lm", "model.matrix", "p.adjust", "pchisq", "quantile",
"rbinom", "residuals", "rnbinom", "rt", "runif", "t.test",
"var")
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
scDD 8.03 0.05 70.64
results 7.05 0.14 36.64
simulateSet 2.18 0.02 80.61
testKS 0.93 0.05 18.14
* 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/scDD.Rcheck/00check.log'
for details.
scDD.Rcheck/00install.out
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### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL scDD
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'scDD' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'scDD'
finding HTML links ... done
calcMV html
calcRP html
classifyDD html
feDP html
findFC html
findIndex html
findOutliers html
getPosteriorParams html
jointPosterior html
lu html
luOutlier html
mclustRestricted html
permMclust html
permMclustCov html
permMclustGene html
permZero html
preprocess html
results html
scDD html
scDatEx html
scDatExList html
scDatExSim html
sideHist html
sideViolin html
simuDB html
simuDE html
simuDM html
simuDP html
simulateSet html
singleCellSimu html
testKS html
testZeroes html
validation 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 (scDD)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'trigger' is missing or broken
done
scDD.Rcheck/scDD-Ex.timings
| name | user | system | elapsed | |
| preprocess | 0.89 | 0.05 | 0.94 | |
| results | 7.05 | 0.14 | 36.64 | |
| scDD | 8.03 | 0.05 | 70.64 | |
| scDatEx | 0.03 | 0.00 | 0.03 | |
| scDatExList | 0 | 0 | 0 | |
| scDatExSim | 0 | 0 | 0 | |
| sideViolin | 1.21 | 0.07 | 1.28 | |
| simulateSet | 2.18 | 0.02 | 80.61 | |
| testKS | 0.93 | 0.05 | 18.14 | |