Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:06 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 1559/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
PIUMA 1.2.0 (landing page) Mattia Chiesa
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the PIUMA package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PIUMA.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: PIUMA |
Version: 1.2.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PIUMA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PIUMA_1.2.0.tar.gz |
StartedAt: 2024-11-20 01:12:34 -0500 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 01:19:00 -0500 (Wed, 20 Nov 2024) |
EllapsedTime: 386.0 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: PIUMA.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PIUMA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PIUMA_1.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/PIUMA.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-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 Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘PIUMA/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘PIUMA’ version ‘1.2.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 ‘PIUMA’ 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE makeTDAobjFromSE: no visible global function definition for ‘colData’ makeTDAobjFromSE: no visible global function definition for ‘assay’ plot_ScaleFreeLaw: no visible binding for global variable ‘k’ plot_ScaleFreeLaw: no visible binding for global variable ‘pk’ plot_ScaleFreeLaw: no visible global function definition for ‘stat_smooth’ plot_ScaleFreeLaw: no visible global function definition for ‘scale_x_continuous’ plot_ScaleFreeLaw: no visible binding for global variable ‘.x’ plot_projection_plot: no visible binding for global variable ‘comp1’ plot_projection_plot: no visible binding for global variable ‘comp2’ Undefined global functions or variables: .x assay colData comp1 comp2 k pk scale_x_continuous stat_smooth * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented code objects: ‘jaccard’ ‘plot_ScaleFreeLaw’ ‘plot_projection_plot’ ‘scaleData_01’ All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 files in ‘vignettes’ ... OK * checking examples ... OK * 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 WARNING, 1 NOTE See ‘/Users/biocbuild/bbs-3.20-bioc/meat/PIUMA.Rcheck/00check.log’ for details.
PIUMA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL PIUMA ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘PIUMA’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading in method for ‘getOrigData’ with signature ‘x="TDAobj"’: no definition for class “TDAobj” in method for ‘setOrigData’ with signature ‘x="TDAobj"’: no definition for class “TDAobj” in method for ‘getScaledData’ with signature ‘x="TDAobj"’: no definition for class “TDAobj” in method for ‘setScaledData’ with signature ‘x="TDAobj"’: no definition for class “TDAobj” in method for ‘getOutcomeFact’ with signature ‘x="TDAobj"’: no definition for class “TDAobj” in method for ‘setOutcomeFact’ with signature ‘x="TDAobj"’: no definition for class “TDAobj” in method for ‘getOutcome’ with signature ‘x="TDAobj"’: no definition for class “TDAobj” in method for ‘setOutcome’ with signature ‘x="TDAobj"’: no definition for class “TDAobj” in method for ‘getComp’ with signature ‘x="TDAobj"’: no definition for class “TDAobj” in method for ‘setComp’ with signature ‘x="TDAobj"’: no definition for class “TDAobj” in method for ‘getDistMat’ with signature ‘x="TDAobj"’: no definition for class “TDAobj” in method for ‘setDistMat’ with signature ‘x="TDAobj"’: no definition for class “TDAobj” in method for ‘getDfMapper’ with signature ‘x="TDAobj"’: no definition for class “TDAobj” in method for ‘setDfMapper’ with signature ‘x="TDAobj"’: no definition for class “TDAobj” in method for ‘getJacc’ with signature ‘x="TDAobj"’: no definition for class “TDAobj” in method for ‘setJacc’ with signature ‘x="TDAobj"’: no definition for class “TDAobj” in method for ‘getNodeDataMat’ with signature ‘x="TDAobj"’: no definition for class “TDAobj” in method for ‘setNodeDataMat’ with signature ‘x="TDAobj"’: no definition for class “TDAobj” ** help *** installing help indices *** copying figures ** 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 (PIUMA)
PIUMA.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-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. > library(testthat) > library(PIUMA) Loading required package: ggplot2 > > test_check("PIUMA") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 78 ] > > proc.time() user system elapsed 8.964 0.530 9.532
PIUMA.Rcheck/PIUMA-Ex.timings
name | user | system | elapsed | |
checkNetEntropy | 0.001 | 0.000 | 0.001 | |
checkScaleFreeModel | 0.002 | 0.001 | 0.003 | |
dfToDistance | 0.003 | 0.001 | 0.004 | |
dfToProjection | 0.003 | 0.001 | 0.005 | |
getComp | 0.001 | 0.000 | 0.002 | |
getDfMapper | 0.001 | 0.001 | 0.002 | |
getDistMat | 0.002 | 0.001 | 0.002 | |
getJacc | 0.002 | 0.001 | 0.003 | |
getNodeDataMat | 0.001 | 0.001 | 0.002 | |
getOrigData | 0.001 | 0.001 | 0.002 | |
getOutcome | 0.002 | 0.001 | 0.002 | |
getOutcomeFact | 0.001 | 0.001 | 0.002 | |
getScaledData | 0.001 | 0.001 | 0.002 | |
jaccardMatrix | 0.064 | 0.008 | 0.072 | |
makeTDAobj | 1.635 | 0.056 | 1.694 | |
makeTDAobjFromSE | 1.324 | 0.086 | 1.411 | |
mapperCore | 0.019 | 0.001 | 0.020 | |
setComp | 0.002 | 0.001 | 0.002 | |
setDfMapper | 0.001 | 0.001 | 0.002 | |
setDistMat | 0.001 | 0.001 | 0.002 | |
setJacc | 0.002 | 0.000 | 0.003 | |
setNodeDataMat | 0.001 | 0.000 | 0.002 | |
setOrigData | 0.001 | 0.000 | 0.002 | |
setOutcome | 0.002 | 0.000 | 0.002 | |
setOutcomeFact | 0.001 | 0.001 | 0.002 | |
setScaledData | 0.001 | 0.001 | 0.002 | |
tdaDfEnrichment | 0.006 | 0.001 | 0.007 | |