| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-31 17:03:08 -0400 (Fri, 31 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4753 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4464 |
| 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 1557/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| PhenStat 2.40.0 (landing page) Hamed Haselimashhadi
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | 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: 2.40.0 |
| Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:PhenStat.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings PhenStat_2.40.0.tar.gz |
| StartedAt: 2024-05-31 06:47:08 -0400 (Fri, 31 May 2024) |
| EndedAt: 2024-05-31 06:49:17 -0400 (Fri, 31 May 2024) |
| EllapsedTime: 129.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: PhenStat.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:PhenStat.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings PhenStat_2.40.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/PhenStat.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘PhenStat/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PhenStat’ version ‘2.40.0’
* 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 ‘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 loading without being on the library search path ... 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 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 4 NOTEs
See
‘/home/biocbuild/bbs-3.19-bioc/meat/PhenStat.Rcheck/00check.log’
for details.
PhenStat.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL PhenStat ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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 version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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 -- Fri May 31 06:49:01 2024
***********************************************
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
2.884 0.222 3.095
PhenStat.Rcheck/PhenStat-Ex.timings
| name | user | system | elapsed | |
| FisherExactTest | 0.129 | 0.024 | 0.154 | |
| JSONOutput | 0.774 | 0.012 | 0.787 | |
| LRDataset | 0.040 | 0.003 | 0.044 | |
| PhenList-class | 0.181 | 0.000 | 0.182 | |
| PhenList | 0.169 | 0.000 | 0.169 | |
| PhenStatReport | 0.045 | 0.000 | 0.045 | |
| PhenTestResult-class | 0.680 | 0.000 | 0.681 | |
| PhenTestResult | 0.539 | 0.000 | 0.539 | |
| RRTest | 0.086 | 0.008 | 0.094 | |
| TFDataset | 0.219 | 0.020 | 0.239 | |
| analysedDataset | 0.635 | 0.040 | 0.675 | |
| analysisResults | 0.648 | 0.004 | 0.652 | |
| boxplotResidualBatch | 0.675 | 0.000 | 0.675 | |
| boxplotSexGenotype | 0.061 | 0.004 | 0.065 | |
| boxplotSexGenotypeBatch | 0.124 | 0.000 | 0.124 | |
| boxplotSexGenotypeBatchAdjusted | 0.061 | 0.004 | 0.065 | |
| boxplotSexGenotypeResult | 1.089 | 0.008 | 1.097 | |
| boxplotSexGenotypeWeightBatchAdjusted | 0.050 | 0.008 | 0.058 | |
| categoricalBarplot | 0.108 | 0.012 | 0.120 | |
| checkDataset | 0.045 | 0.000 | 0.045 | |
| classificationTag | 0.606 | 0.001 | 0.607 | |
| determiningLambda | 0.626 | 0.075 | 0.701 | |
| dim | 0.037 | 0.001 | 0.038 | |
| finalLRModel | 0.480 | 0.010 | 0.492 | |
| finalModel | 0.531 | 0.004 | 0.536 | |
| finalTFModel | 0.370 | 0.004 | 0.374 | |
| htestPhenStat-class | 0.109 | 0.003 | 0.113 | |
| modelFormula | 0.000 | 0.000 | 0.001 | |
| modelFormulaLR | 0 | 0 | 0 | |
| parserOutputSummary | 0.578 | 0.024 | 0.602 | |
| parserOutputSummaryLR | 0.414 | 0.016 | 0.430 | |
| parserOutputTFSummary | 0.079 | 0.000 | 0.079 | |
| performReverseTransformation | 0 | 0 | 0 | |
| performTransformation | 0 | 0 | 0 | |
| plot.PhenList | 2.110 | 0.036 | 2.146 | |
| plot.PhenTestResult | 2.121 | 0.048 | 2.170 | |
| plotResidualPredicted | 0.637 | 0.008 | 0.646 | |
| printLROutput | 0.418 | 0.000 | 0.418 | |
| printTabStyle | 0.001 | 0.000 | 0.001 | |
| qqplotGenotype | 0.641 | 0.000 | 0.641 | |
| qqplotRandomEffects | 0.621 | 0.008 | 0.629 | |
| qqplotRotatedResiduals | 3.945 | 0.084 | 4.029 | |
| recommendMethod | 0.447 | 0.012 | 0.460 | |
| scatterplotGenotypeWeight | 0.143 | 0.000 | 0.142 | |
| scatterplotGenotypeWeightResult | 0.820 | 0.024 | 0.843 | |
| scatterplotSexGenotypeBatch | 0.077 | 0.004 | 0.081 | |
| scatterplotSexGenotypeBatchResult | 0.790 | 0.000 | 0.789 | |
| startLRModel | 0.390 | 0.000 | 0.389 | |
| startModel | 0.446 | 0.000 | 0.446 | |
| startTFModel | 0.322 | 0.008 | 0.330 | |
| summaryOutput | 0.709 | 0.000 | 0.709 | |
| summaryPhenListResult | 0.701 | 0.016 | 0.717 | |
| testDataset | 2.012 | 0.056 | 2.068 | |
| testFinalLRModel | 0.404 | 0.004 | 0.409 | |
| testFinalModel | 0.767 | 0.008 | 0.776 | |
| vectorOutput | 0.716 | 0.008 | 0.724 | |
| vectorOutputMatrices | 0.125 | 0.000 | 0.124 | |