Back to Mac ARM64 build report for BioC 3.20 |
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This page was generated on 2024-05-13 11:32:15 -0400 (Mon, 13 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" | 4378 |
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 2114/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
TPP2D 1.21.0 (landing page) Nils Kurzawa
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | NA | ||||||||
To the developers/maintainers of the TPP2D 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: TPP2D |
Version: 1.21.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TPP2D.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TPP2D_1.21.0.tar.gz |
StartedAt: 2024-05-13 05:39:39 -0400 (Mon, 13 May 2024) |
EndedAt: 2024-05-13 05:41:36 -0400 (Mon, 13 May 2024) |
EllapsedTime: 117.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: TPP2D.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TPP2D.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TPP2D_1.21.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/TPP2D.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 ‘TPP2D/DESCRIPTION’ ... OK * this is package ‘TPP2D’ version ‘1.21.0’ * package encoding: UTF-8 * 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 ‘TPP2D’ 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 dependencies in R code ... NOTE There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘.min_RSS_h0’ ‘.min_RSS_h1_slope_pEC50’ * 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 ... 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 R/sysdata.rda ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed computeFStatFromParams 5.541 0.097 5.68 getModelParamsDf 5.486 0.095 5.60 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.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: 1 NOTE See ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/TPP2D.Rcheck/00check.log’ for details.
TPP2D.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL TPP2D ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘TPP2D’ ... ** using staged installation ** R ** data ** 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 (TPP2D)
TPP2D.Rcheck/tests/testthat.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. > Sys.setenv("R_TESTS" = "") > library(testthat) > library(TPP2D) Loading required package: dplyr Attaching package: 'dplyr' The following object is masked from 'package:testthat': matches The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union > > test_check("TPP2D") [1] "Warning: You have specificed B < 20, it is recommended to use at least B = 20 in order to obtain reliable results." | | | 0% | |======================================================================| 100% [ FAIL 0 | WARN 2 | SKIP 0 | PASS 18 ] [ FAIL 0 | WARN 2 | SKIP 0 | PASS 18 ] > > proc.time() user system elapsed 6.087 0.267 6.419
TPP2D.Rcheck/TPP2D-Ex.timings
name | user | system | elapsed | |
TPP_importCheckConfigTable | 0.025 | 0.004 | 0.030 | |
annotateDataList | 0.715 | 0.023 | 0.743 | |
bootstrapNull | 0.072 | 0.011 | 2.023 | |
bootstrapNullAlternativeModel | 1.767 | 0.028 | 1.800 | |
bootstrapNullAlternativeModelFast | 1.781 | 0.018 | 1.803 | |
competeModels | 2.517 | 0.059 | 2.583 | |
computeFStatFromParams | 5.541 | 0.097 | 5.680 | |
computeFstat | 4.053 | 0.079 | 4.144 | |
configWide2Long | 0.007 | 0.002 | 0.009 | |
filterOutContaminants | 0.037 | 0.002 | 0.040 | |
findHits | 1.005 | 0.022 | 4.455 | |
fitAndEvalDataset | 4.706 | 0.102 | 4.837 | |
fitH0Model | 0.113 | 0.002 | 0.116 | |
fitH1Model | 0.765 | 0.016 | 0.784 | |
getFDR | 1.032 | 0.023 | 4.328 | |
getModelParamsDf | 5.486 | 0.095 | 5.600 | |
getPEC504Temperature | 0.356 | 0.006 | 0.363 | |
getPvalues | 0.614 | 0.023 | 3.678 | |
gg_qq | 0.057 | 0.002 | 0.059 | |
import2dDataset | 0.446 | 0.007 | 0.454 | |
import2dMain | 0.176 | 0.004 | 0.182 | |
plot2dTppFcHeatmap | 0.256 | 0.007 | 0.265 | |
plot2dTppFit | 0.291 | 0.004 | 0.298 | |
plot2dTppProfile | 0.277 | 0.004 | 0.282 | |
plot2dTppRelProfile | 0.268 | 0.004 | 0.273 | |
plot2dTppVolcano | 4.055 | 0.054 | 4.149 | |
recomputeSignalFromRatios | 0.058 | 0.001 | 0.060 | |
renameColumns | 0.423 | 0.006 | 0.431 | |
resolveAmbiguousProteinNames | 0.03 | 0.00 | 0.03 | |
runTPP2D | 1.539 | 0.019 | 1.561 | |
tpp2dExperiment-class | 0 | 0 | 0 | |