Dipen P. Sangurdekar
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/Rnits |
| git_branch: master |
| git_last_commit: f913d43 |
| git_last_commit_date: 2021-10-26 12:15:38 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:10:33 -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 Rnits package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rnits.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 1647/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Rnits 1.29.0 (landing page) Dipen P. Sangurdekar
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: Rnits |
| Version: 1.29.0 |
| Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Rnits.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings Rnits_1.29.0.tar.gz |
| StartedAt: 2022-03-18 02:43:11 -0400 (Fri, 18 Mar 2022) |
| EndedAt: 2022-03-18 02:44:33 -0400 (Fri, 18 Mar 2022) |
| EllapsedTime: 82.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: Rnits.Rcheck |
| Warnings: 1 |
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### Running command:
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### F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Rnits.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings Rnits_1.29.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/Rnits.Rcheck'
* using R Under development (unstable) (2022-02-17 r81757 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'Rnits/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Rnits' version '1.29.0'
* 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 'Rnits' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
build.Rnits: no visible global function definition for 'median'
build.Rnits: no visible global function definition for 'sd'
finds0: no visible global function definition for 'rnorm'
finds0: no visible global function definition for 'quantile'
finds0: no visible global function definition for 'mad'
finds0 : <anonymous>: no visible global function definition for 'sd'
modelfit: no visible global function definition for 'hat'
ranknormalization: no visible binding for global variable 'median'
ranknormalization: no visible global function definition for
'smooth.spline'
ranknormalization: no visible global function definition for 'predict'
ranknormalization: no visible global function definition for 'par'
solvemat: no visible global function definition for 'hat'
tsFit: no visible global function definition for 'txtProgressBar'
tsFit: no visible global function definition for 'setTxtProgressBar'
calculateGCV,Rnits: no visible global function definition for 'glm'
calculateGCV,Rnits: no visible binding for global variable 'gaussian'
fit,Rnits: no visible global function definition for 'kmeans'
fit,Rnits : <anonymous>: no visible global function definition for
'p.adjust'
fit,Rnits: no visible global function definition for 'par'
fit,Rnits: no visible global function definition for 'hist'
getCID,Rnits: no visible global function definition for 'setNames'
getPval,Rnits: no visible global function definition for 'setNames'
getStat,Rnits: no visible global function definition for 'setNames'
plotResults,Rnits: no visible global function definition for 'aes'
plotResults,Rnits: no visible binding for global variable 'Time'
plotResults,Rnits: no visible binding for global variable 'value'
plotResults,Rnits: no visible global function definition for
'geom_point'
plotResults,Rnits: no visible binding for global variable 'Sample'
plotResults,Rnits: no visible global function definition for
'geom_smooth'
plotResults,Rnits: no visible global function definition for 'ylab'
plotResults,Rnits: no visible global function definition for 'theme_bw'
plotResults,Rnits: no visible global function definition for 'theme'
plotResults,Rnits: no visible global function definition for
'scale_color_brewer'
plotResults,Rnits: no visible global function definition for
'facet_wrap'
plotResults,Rnits: no visible global function definition for 'dev.off'
summary,Rnits: no visible global function definition for 'hist'
timeAlign,Rnits: no visible global function definition for 'quantile'
timeAlign,Rnits: no visible global function definition for 'mvfft'
timeAlign,Rnits: no visible global function definition for 'abline'
Undefined global functions or variables:
Sample Time abline aes dev.off facet_wrap gaussian geom_point
geom_smooth glm hat hist kmeans mad median mvfft p.adjust par predict
quantile rnorm scale_color_brewer sd setNames setTxtProgressBar
smooth.spline theme theme_bw txtProgressBar value ylab
Consider adding
importFrom("grDevices", "dev.off")
importFrom("graphics", "abline", "hist", "par")
importFrom("stats", "gaussian", "glm", "hat", "kmeans", "mad",
"median", "mvfft", "p.adjust", "predict", "quantile",
"rnorm", "sd", "setNames", "smooth.spline")
importFrom("utils", "setTxtProgressBar", "txtProgressBar")
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 ... WARNING
Documented arguments not in \usage in documentation object 'plotResults':
'...'
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 LazyData ... 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
calculateGCV-methods 6.11 0.19 6.3
* 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: 1 WARNING, 1 NOTE
See
'F:/biocbuild/bbs-3.15-bioc/meat/Rnits.Rcheck/00check.log'
for details.
Rnits.Rcheck/00install.out
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### Running command:
###
### F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL Rnits
###
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* installing to library 'F:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'Rnits' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'Rnits'
finding HTML links ... done
Rnits-class html
build.Rnits html
finding level-2 HTML links ... done
calculateGCV-methods html
extract-methods html
fit-methods html
getCID-methods html
getFitModel-methods html
getLR-methods html
getNormTwoChannel-methods html
getPval-methods html
getStat-methods html
plotResults-methods html
rnits html
summarizeProbes-methods html
summary-methods html
timeAlign-methods html
topData-methods html
yeastchemostat 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 (Rnits)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'geneRxCluster' is missing or broken
done
Rnits.Rcheck/Rnits-Ex.timings
| name | user | system | elapsed | |
| build.Rnits | 0.42 | 0.01 | 0.43 | |
| calculateGCV-methods | 6.11 | 0.19 | 6.30 | |
| fit-methods | 0.35 | 0.03 | 0.38 | |
| getCID-methods | 0.37 | 0.05 | 0.42 | |
| getFitModel-methods | 0.27 | 0.03 | 0.31 | |
| getLR-methods | 0.20 | 0.06 | 0.28 | |
| getPval-methods | 0.30 | 0.02 | 0.31 | |
| getStat-methods | 0.28 | 0.03 | 0.32 | |
| plotResults-methods | 0.32 | 0.01 | 0.32 | |
| summarizeProbes-methods | 0.45 | 0.05 | 0.50 | |
| summary-methods | 0.19 | 0.06 | 0.25 | |
| timeAlign-methods | 1.09 | 0.25 | 1.35 | |
| topData-methods | 0.3 | 0.0 | 0.3 | |