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 12:01 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
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 60/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
AMARETTO 1.22.0 (landing page) Olivier Gevaert
| 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 AMARETTO package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/AMARETTO.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: AMARETTO |
Version: 1.22.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:AMARETTO.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings AMARETTO_1.22.0.tar.gz |
StartedAt: 2024-11-19 22:45:16 -0500 (Tue, 19 Nov 2024) |
EndedAt: 2024-11-19 22:49:25 -0500 (Tue, 19 Nov 2024) |
EllapsedTime: 249.0 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: AMARETTO.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:AMARETTO.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings AMARETTO_1.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/AMARETTO.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘AMARETTO/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘AMARETTO’ version ‘1.22.0’ * 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 ‘AMARETTO’ can be installed ... OK * checking installed package size ... NOTE installed size is 6.1Mb sub-directories of 1Mb or more: data 1.5Mb extdata 3.8Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License components with restrictions not permitted: Apache License (== 2.0) + file LICENSE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘knitr’ A package should be listed in only one of these fields. 'LinkingTo' field is unused: package has no 'src' directory * 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 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 AMARETTO_HTMLreport: no visible binding for global variable ‘ModuleNr’ AMARETTO_HTMLreport: no visible binding for global variable ‘Weights’ AMARETTO_HTMLreport: no visible binding for global variable ‘RegulatorIDs’ AMARETTO_HTMLreport: no visible binding for global variable ‘TargetIDs’ AMARETTO_HTMLreport: no visible binding for global variable ‘moduleNr’ AMARETTO_HTMLreport: no visible binding for global variable ‘Testset’ AMARETTO_HTMLreport: no visible binding for global variable ‘padj’ AMARETTO_HTMLreport: no visible binding for global variable ‘n_Overlapping’ AMARETTO_HTMLreport: no visible binding for global variable ‘NumberGenes’ AMARETTO_HTMLreport: no visible binding for global variable ‘overlap_perc’ AMARETTO_HTMLreport: no visible binding for global variable ‘Geneset’ AMARETTO_HTMLreport: no visible binding for global variable ‘Description’ AMARETTO_HTMLreport: no visible binding for global variable ‘Geneset_length’ AMARETTO_HTMLreport: no visible binding for global variable ‘Overlapping_genes’ AMARETTO_HTMLreport: no visible binding for global variable ‘p_value’ AMARETTO_HTMLreport: no visible binding for global variable ‘p.value’ AMARETTO_HTMLreport: no visible binding for global variable ‘q.value’ AMARETTO_HTMLreport: no visible binding for global variable ‘Genes’ AMARETTO_HTMLreport: no visible binding for global variable ‘value’ AMARETTO_HTMLreport: no visible binding for global variable ‘Type’ AMARETTO_HTMLreport: no visible binding for global variable ‘Color’ AMARETTO_HTMLreport: no visible binding for global variable ‘Modules’ AMARETTO_HTMLreport: no visible binding for global variable ‘dt_gensesetsall’ GeneSetDescription: no visible binding for global variable ‘MsigdbMapping’ GeneSetDescription : <anonymous>: no visible binding for global variable ‘MsigdbMapping’ GmtFromModules: no visible binding for global variable ‘value’ GmtFromModules: no visible binding for global variable ‘variable’ GmtFromModules: no visible binding for global variable ‘GeneNames’ HyperGTestGeneEnrichment: no visible binding for global variable ‘i’ HyperGTestGeneEnrichment: no visible binding for global variable ‘j’ read_gct: no visible binding for global variable ‘Description’ Undefined global functions or variables: Color Description GeneNames Genes Geneset Geneset_length ModuleNr Modules MsigdbMapping NumberGenes Overlapping_genes RegulatorIDs TargetIDs Testset Type Weights dt_gensesetsall i j moduleNr n_Overlapping overlap_perc p.value p_value padj q.value value variable * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... WARNING Codoc mismatches from Rd file 'get_firehoseData.Rd': get_firehoseData Code: function(TargetDirectory = "./", TCGA_acronym_uppercase = "LUAD", dataType = "stddata", dataFileTag = "mRNAseq_Preprocess.Level_3", FFPE = FALSE, fileType = "tar.gz", gdacURL = "https://gdac.broadinstitute.org/runs/", untarUngzip = TRUE, printDisease_abbr = FALSE) Docs: function(TargetDirectory = "./", TCGA_acronym_uppercase = "LUAD", dataType = "stddata", dataFileTag = "mRNAseq_Preprocess.Level_3", FFPE = FALSE, fileType = "tar.gz", gdacURL = "http://gdac.broadinstitute.org/runs/", untarUngzip = TRUE, printDisease_abbr = FALSE) Mismatches in argument default values: Name: 'gdacURL' Code: "https://gdac.broadinstitute.org/runs/" Docs: "http://gdac.broadinstitute.org/runs/" * 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 ... NOTE Note: found 152 marked UTF-8 strings * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed AMARETTO_Download 6.79 0.737 9.447 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 4 NOTEs See ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/AMARETTO.Rcheck/00check.log’ for details.
AMARETTO.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL AMARETTO ### ############################################################################## ############################################################################## * installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘AMARETTO’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (AMARETTO)
AMARETTO.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 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. > library(testthat) > library(AMARETTO) Loading required package: impute Loading required package: doParallel Loading required package: foreach Loading required package: iterators Loading required package: parallel 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 Loading required package: ComplexHeatmap Loading required package: grid ======================================== ComplexHeatmap version 2.22.0 Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/ Github page: https://github.com/jokergoo/ComplexHeatmap Documentation: http://jokergoo.github.io/ComplexHeatmap-reference If you use it in published research, please cite either one: - Gu, Z. Complex Heatmap Visualization. iMeta 2022. - Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics 2016. The new InteractiveComplexHeatmap package can directly export static complex heatmaps into an interactive Shiny app with zero effort. Have a try! This message can be suppressed by: suppressPackageStartupMessages(library(ComplexHeatmap)) ======================================== > > test_check("AMARETTO") Found 10 CNV driver genes. Found 89 MethylMix driver genes. Found a total of 96 unique drivers with your selected method. Running AMARETTO on 402 genes and 45 samples. Stopping if less then 4.02 genes reassigned. Autoregulation is turned ON. Elapsed time is 1.774000 seconds Average nr of regulators per module: 9.200000 Elapsed time is 0.086000 seconds Nr of reassignments is: 48 Elapsed time is 0.892000 seconds Average nr of regulators per module: 9.100000 Elapsed time is 0.071000 seconds Nr of reassignments is: 9 Elapsed time is 1.604000 seconds Average nr of regulators per module: 9.600000 Elapsed time is 0.088000 seconds Nr of reassignments is: 8 Elapsed time is 0.820000 seconds Average nr of regulators per module: 9.700000 Elapsed time is 0.071000 seconds Nr of reassignments is: 8 Elapsed time is 0.807000 seconds Average nr of regulators per module: 9.300000 Elapsed time is 0.071000 seconds Nr of reassignments is: 4 Elapsed time is 6.285000 seconds [ FAIL 0 | WARN 0 | SKIP 0 | PASS 39 ] > > proc.time() user system elapsed 15.964 0.692 16.652
AMARETTO.Rcheck/AMARETTO-Ex.timings
name | user | system | elapsed | |
AMARETTO_CreateModuleData | 1.022 | 0.055 | 1.308 | |
AMARETTO_CreateRegulatorPrograms | 0.635 | 0.004 | 0.639 | |
AMARETTO_Download | 6.790 | 0.737 | 9.447 | |
AMARETTO_EvaluateTestSet | 0.622 | 0.013 | 0.636 | |
AMARETTO_ExportResults | 0.665 | 0.100 | 0.771 | |
AMARETTO_HTMLreport | 0 | 0 | 0 | |
AMARETTO_Initialize | 0.833 | 0.001 | 0.834 | |
AMARETTO_Preprocess | 0 | 0 | 0 | |
AMARETTO_Run | 0.689 | 0.003 | 0.694 | |
AMARETTO_VisualizeModule | 2.064 | 0.001 | 2.068 | |
plot_run_history | 1.307 | 0.004 | 1.312 | |
read_gct | 0.001 | 0.000 | 0.000 | |