Hamed Haselimashhadi
| Snapshot Date: 2024-05-18 09:00:01 -0400 (Sat, 18 May 2024) |
| git_url: https://git.bioconductor.org/packages/PhenStat |
| git_branch: devel |
| git_last_commit: 0171dda |
| git_last_commit_date: 2024-04-30 10:34:35 -0400 (Tue, 30 Apr 2024) |
| Back to Mac ARM64 build report for BioC 3.20 |
|
This page was generated on 2024-05-20 11:32:17 -0400 (Mon, 20 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4381 |
| 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 1506/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| PhenStat 2.41.0 (landing page) Hamed Haselimashhadi
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the PhenStat package: - 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: 2.41.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PhenStat.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PhenStat_2.41.0.tar.gz |
| StartedAt: 2024-05-19 22:15:54 -0400 (Sun, 19 May 2024) |
| EndedAt: 2024-05-19 22:18:19 -0400 (Sun, 19 May 2024) |
| EllapsedTime: 144.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: PhenStat.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PhenStat.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PhenStat_2.41.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/PhenStat.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PhenStat/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PhenStat’ version ‘2.41.0’
* 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 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
qqplotRotatedResiduals 5.567 0.046 5.636
* 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
‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/PhenStat.Rcheck/00check.log’
for details.
PhenStat.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL PhenStat ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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 -- Sun May 19 22:18:07 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
3.508 0.238 3.727
PhenStat.Rcheck/PhenStat-Ex.timings
| name | user | system | elapsed | |
| FisherExactTest | 0.155 | 0.016 | 0.172 | |
| JSONOutput | 1.090 | 0.033 | 1.124 | |
| LRDataset | 0.063 | 0.005 | 0.068 | |
| PhenList-class | 0.179 | 0.013 | 0.193 | |
| PhenList | 0.176 | 0.008 | 0.192 | |
| PhenStatReport | 0.036 | 0.002 | 0.038 | |
| PhenTestResult-class | 0.961 | 0.016 | 0.976 | |
| PhenTestResult | 0.812 | 0.010 | 0.820 | |
| RRTest | 0.093 | 0.005 | 0.097 | |
| TFDataset | 0.208 | 0.017 | 0.223 | |
| analysedDataset | 0.897 | 0.019 | 0.916 | |
| analysisResults | 0.894 | 0.012 | 0.908 | |
| boxplotResidualBatch | 0.934 | 0.022 | 0.961 | |
| boxplotSexGenotype | 0.077 | 0.008 | 0.084 | |
| boxplotSexGenotypeBatch | 0.121 | 0.006 | 0.127 | |
| boxplotSexGenotypeBatchAdjusted | 0.065 | 0.003 | 0.068 | |
| boxplotSexGenotypeResult | 1.411 | 0.027 | 1.438 | |
| boxplotSexGenotypeWeightBatchAdjusted | 0.059 | 0.004 | 0.062 | |
| categoricalBarplot | 0.129 | 0.019 | 0.148 | |
| checkDataset | 0.033 | 0.001 | 0.034 | |
| classificationTag | 0.872 | 0.015 | 0.887 | |
| determiningLambda | 1.116 | 0.236 | 1.353 | |
| dim | 0.033 | 0.001 | 0.034 | |
| finalLRModel | 0.497 | 0.015 | 0.511 | |
| finalModel | 0.802 | 0.012 | 0.814 | |
| finalTFModel | 0.419 | 0.020 | 0.440 | |
| htestPhenStat-class | 0.130 | 0.012 | 0.141 | |
| modelFormula | 0 | 0 | 0 | |
| modelFormulaLR | 0 | 0 | 0 | |
| parserOutputSummary | 0.874 | 0.016 | 0.889 | |
| parserOutputSummaryLR | 0.446 | 0.013 | 0.459 | |
| parserOutputTFSummary | 0.088 | 0.001 | 0.090 | |
| performReverseTransformation | 0.001 | 0.000 | 0.000 | |
| performTransformation | 0 | 0 | 0 | |
| plot.PhenList | 2.899 | 0.089 | 2.995 | |
| plot.PhenTestResult | 2.844 | 0.062 | 2.907 | |
| plotResidualPredicted | 0.931 | 0.033 | 0.966 | |
| printLROutput | 0.427 | 0.013 | 0.440 | |
| printTabStyle | 0.000 | 0.001 | 0.001 | |
| qqplotGenotype | 0.915 | 0.017 | 0.933 | |
| qqplotRandomEffects | 0.907 | 0.013 | 0.920 | |
| qqplotRotatedResiduals | 5.567 | 0.046 | 5.636 | |
| recommendMethod | 0.494 | 0.007 | 0.501 | |
| scatterplotGenotypeWeight | 0.174 | 0.006 | 0.180 | |
| scatterplotGenotypeWeightResult | 1.114 | 0.024 | 1.140 | |
| scatterplotSexGenotypeBatch | 0.087 | 0.005 | 0.091 | |
| scatterplotSexGenotypeBatchResult | 1.085 | 0.012 | 1.098 | |
| startLRModel | 0.408 | 0.003 | 0.412 | |
| startModel | 0.730 | 0.006 | 0.736 | |
| startTFModel | 0.374 | 0.014 | 0.391 | |
| summaryOutput | 0.991 | 0.028 | 1.019 | |
| summaryPhenListResult | 1.026 | 0.028 | 1.053 | |
| testDataset | 2.828 | 0.075 | 2.925 | |
| testFinalLRModel | 0.431 | 0.015 | 0.448 | |
| testFinalModel | 1.105 | 0.019 | 1.125 | |
| vectorOutput | 0.986 | 0.013 | 1.000 | |
| vectorOutputMatrices | 0.134 | 0.004 | 0.139 | |