Hamed Haselimashhadi
| Snapshot Date: 2025-01-10 13:40 -0500 (Fri, 10 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/PhenStat |
| git_branch: devel |
| git_last_commit: 59cb12c |
| git_last_commit_date: 2024-10-29 09:49:35 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-01-11 11:42 -0500 (Sat, 11 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4760 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4479 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4443 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4398 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4391 |
| 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 1536/2277 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| PhenStat 2.43.0 (landing page) Hamed Haselimashhadi
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the PhenStat package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PhenStat.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. |
| Package: PhenStat |
| Version: 2.43.0 |
| Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:PhenStat.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings PhenStat_2.43.0.tar.gz |
| StartedAt: 2025-01-11 04:06:04 -0500 (Sat, 11 Jan 2025) |
| EndedAt: 2025-01-11 04:08:51 -0500 (Sat, 11 Jan 2025) |
| EllapsedTime: 167.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: PhenStat.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:PhenStat.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings PhenStat_2.43.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/PhenStat.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'PhenStat/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PhenStat' version '2.43.0'
* 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 'PhenStat' 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 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: 'SmoothWin'
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 ... OK
* checking Rd files ... NOTE
checkRd: (-1) plot.PhenList.Rd:49-53: Lost braces
49 | \item boxplotSexGenotype. See documentations for {
| ^
checkRd: (-1) plot.PhenList.Rd:54-58: Lost braces
54 | \item boxplotSexGenotypeBatchAdjusted. See documentations for {
| ^
checkRd: (-1) plot.PhenList.Rd:59-63: Lost braces
59 | \item boxplotSexGenotypeWeightBatchAdjusted. See documentations for {
| ^
checkRd: (-1) plot.PhenList.Rd:64-68: Lost braces
64 | \item scatterplotSexGenotypeBatch. See documentations for {
| ^
checkRd: (-1) plot.PhenList.Rd:69-73: Lost braces
69 | \item scatterplotGenotypeWeight. See documentations for {
| ^
checkRd: (-1) plot.PhenList.Rd:74-78: Lost braces
74 | \item boxplotSexGenotypeBatch. See documentations for {
| ^
checkRd: (-1) plot.PhenTestResult.Rd:41-45: Lost braces
41 | \item boxplotSexGenotypeResult. See documentations for {
| ^
checkRd: (-1) plot.PhenTestResult.Rd:46-50: Lost braces
46 | \item scatterplotSexGenotypeBatchResult. See documentations for {
| ^
checkRd: (-1) plot.PhenTestResult.Rd:51-55: Lost braces
51 | \item scatterplotGenotypeWeightResult. See documentations for {
| ^
checkRd: (-1) plot.PhenTestResult.Rd:56-60: Lost braces
56 | \item plotResidualPredicted. See documentations for {
| ^
checkRd: (-1) plot.PhenTestResult.Rd:61-65: Lost braces
61 | \item qqplotRandomEffects. See documentations for {
| ^
checkRd: (-1) plot.PhenTestResult.Rd:66-70: Lost braces
66 | \item boxplotResidualBatch. See documentations for {
| ^
checkRd: (-1) plot.PhenTestResult.Rd:71-75: Lost braces
71 | \item qqplotRotatedResiduals. See documentations for {
| ^
checkRd: (-1) plot.PhenTestResult.Rd:76-80: Lost braces
76 | \item qqplotGenotype. See documentations for {
| ^
checkRd: (-1) plot.PhenTestResult.Rd:81-85: Lost braces
81 | \item categoricalBarplot. See documentations for {
| ^
checkRd: (-1) qqplotRotatedResiduals.Rd:18: Lost braces
18 | Houseman, E. A., Ryan, L. M., Coull, B. A. (2004): Cholesky residuals for assessing normal errors in a linear model with correlated outcomes. \emph{Journal of the American Statistical Association} \bold{99}{466}: pg 383-394. Doi 10.1198
| ^
* 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 ... NOTE
Documented arguments not in \usage in Rd file 'printLROutput.Rd':
'effectValues'
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 ... NOTE
Argument items with no description in Rd file 'plot.PhenList.Rd':
'\dots'
Argument items with no description in Rd file 'plot.PhenTestResult.Rd':
'\dots'
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'runTests.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 4 NOTEs
See
'E:/biocbuild/bbs-3.21-bioc/meat/PhenStat.Rcheck/00check.log'
for details.
PhenStat.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL PhenStat ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library' * installing *source* package 'PhenStat' ... ** using staged installation ** R ** 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 (PhenStat)
PhenStat.Rcheck/tests/runTests.Rout
R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> BiocGenerics:::testPackage("PhenStat")
>=========================================================================<
This version of PhenStat includes *FEWER* functions than the previous ones
You *still* can use the previous functions by using `:::`. For example :
PhenStat:::boxplotSexGenotype or PhenStat:::FisherExactTest
*** Want to know what is new in this version? run PhenStat:::WhatIsNew()
>=========================================================================<
RUNIT TEST PROTOCOL -- Sat Jan 11 04:08:34 2025
***********************************************
Number of test functions: 0
Number of errors: 0
Number of failures: 0
1 Test Suite :
PhenStat RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
3.10 0.45 3.50
PhenStat.Rcheck/PhenStat-Ex.timings
| name | user | system | elapsed | |
| FisherExactTest | 0.40 | 0.03 | 0.45 | |
| JSONOutput | 1.30 | 0.03 | 1.33 | |
| LRDataset | 0.08 | 0.00 | 0.08 | |
| PhenList-class | 0.20 | 0.00 | 0.22 | |
| PhenList | 0.28 | 0.00 | 0.28 | |
| PhenStatReport | 0.05 | 0.00 | 0.04 | |
| PhenTestResult-class | 1.34 | 0.03 | 1.38 | |
| PhenTestResult | 0.94 | 0.02 | 0.96 | |
| RRTest | 0.09 | 0.00 | 0.09 | |
| TFDataset | 0.20 | 0.04 | 0.25 | |
| analysedDataset | 1.1 | 0.0 | 1.1 | |
| analysisResults | 1.22 | 0.02 | 1.23 | |
| boxplotResidualBatch | 0.98 | 0.03 | 1.02 | |
| boxplotSexGenotype | 0.13 | 0.00 | 0.12 | |
| boxplotSexGenotypeBatch | 0.2 | 0.0 | 0.2 | |
| boxplotSexGenotypeBatchAdjusted | 0.09 | 0.01 | 0.11 | |
| boxplotSexGenotypeResult | 1.49 | 0.05 | 1.53 | |
| boxplotSexGenotypeWeightBatchAdjusted | 0.31 | 0.00 | 0.32 | |
| categoricalBarplot | 0.13 | 0.00 | 0.12 | |
| checkDataset | 0.03 | 0.00 | 0.03 | |
| classificationTag | 0.89 | 0.03 | 0.92 | |
| determiningLambda | 1.14 | 0.28 | 1.42 | |
| dim | 0.04 | 0.02 | 0.06 | |
| finalLRModel | 0.88 | 0.02 | 0.91 | |
| finalModel | 1.06 | 0.03 | 1.09 | |
| finalTFModel | 0.53 | 0.06 | 0.60 | |
| htestPhenStat-class | 0.19 | 0.00 | 0.19 | |
| modelFormula | 0 | 0 | 0 | |
| modelFormulaLR | 0 | 0 | 0 | |
| parserOutputSummary | 1.28 | 0.03 | 1.31 | |
| parserOutputSummaryLR | 0.69 | 0.00 | 0.69 | |
| parserOutputTFSummary | 0.09 | 0.00 | 0.09 | |
| performReverseTransformation | 0 | 0 | 0 | |
| performTransformation | 0 | 0 | 0 | |
| plot.PhenList | 2.93 | 0.03 | 2.95 | |
| plot.PhenTestResult | 2.92 | 0.13 | 3.05 | |
| plotResidualPredicted | 1.20 | 0.07 | 1.28 | |
| printLROutput | 0.72 | 0.00 | 0.72 | |
| printTabStyle | 0 | 0 | 0 | |
| qqplotGenotype | 1 | 0 | 1 | |
| qqplotRandomEffects | 0.97 | 0.02 | 0.98 | |
| qqplotRotatedResiduals | 4.67 | 0.03 | 4.71 | |
| recommendMethod | 0.18 | 0.00 | 0.19 | |
| scatterplotGenotypeWeight | 0.17 | 0.00 | 0.17 | |
| scatterplotGenotypeWeightResult | 1.22 | 0.03 | 1.25 | |
| scatterplotSexGenotypeBatch | 0.1 | 0.0 | 0.1 | |
| scatterplotSexGenotypeBatchResult | 1.28 | 0.05 | 1.32 | |
| startLRModel | 0.51 | 0.02 | 0.54 | |
| startModel | 0.74 | 0.01 | 0.75 | |
| startTFModel | 0.42 | 0.00 | 0.42 | |
| summaryOutput | 1.58 | 0.09 | 1.67 | |
| summaryPhenListResult | 1.26 | 0.08 | 1.34 | |
| testDataset | 2.93 | 0.10 | 3.02 | |
| testFinalLRModel | 0.76 | 0.03 | 0.80 | |
| testFinalModel | 1.35 | 0.04 | 1.39 | |
| vectorOutput | 1.23 | 0.04 | 1.26 | |
| vectorOutputMatrices | 0.11 | 0.01 | 0.13 | |