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 12:07 -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 2013/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SparseSignatures 2.16.0 (landing page) Luca De Sano
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the SparseSignatures package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SparseSignatures.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: SparseSignatures |
Version: 2.16.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SparseSignatures.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SparseSignatures_2.16.0.tar.gz |
StartedAt: 2024-11-20 02:54:32 -0500 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 03:08:44 -0500 (Wed, 20 Nov 2024) |
EllapsedTime: 852.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: SparseSignatures.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SparseSignatures.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SparseSignatures_2.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/SparseSignatures.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 ‘SparseSignatures/DESCRIPTION’ ... OK * this is package ‘SparseSignatures’ version ‘2.16.0’ * 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 ‘SparseSignatures’ 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 import.trinucleotides.counts: no visible global function definition for ‘.’ patients.plot: no visible binding for global variable ‘Context’ patients.plot: no visible binding for global variable ‘alt’ patients.plot: no visible binding for global variable ‘patient’ patients.plot: no visible binding for global variable ‘value’ signatures.plot: no visible binding for global variable ‘Context’ signatures.plot: no visible binding for global variable ‘alt’ signatures.plot: no visible binding for global variable ‘value’ Undefined global functions or variables: . Context alt patient value * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed nmfLassoCV 119.694 15.260 136.480 lambdaRangeBetaEvaluation 79.419 7.129 86.964 nmfLassoBootstrap 73.523 10.497 84.763 lambdaRangeAlphaEvaluation 73.180 7.286 80.898 * 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/meat/SparseSignatures.Rcheck/00check.log’ for details.
SparseSignatures.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SparseSignatures ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘SparseSignatures’ ... ** 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 (SparseSignatures)
SparseSignatures.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. > Sys.setenv("R_TESTS" = "") > > library("testthat") > library("SparseSignatures") Loading required package: NMF Loading required package: registry Loading required package: rngtools Loading required package: cluster NMF - BioConductor layer [OK] | Shared memory capabilities [NO: synchronicity] | Cores 2/2 To enable shared memory capabilities, try: install.extras(' NMF ') Attaching package: 'NMF' The following object is masked from 'package:testthat': compare > > test_check("SparseSignatures") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ] > > proc.time() user system elapsed 9.514 0.527 10.121
SparseSignatures.Rcheck/SparseSignatures-Ex.timings
name | user | system | elapsed | |
import.trinucleotides.counts | 2.058 | 0.835 | 4.842 | |
lambdaRangeAlphaEvaluation | 73.180 | 7.286 | 80.898 | |
lambdaRangeBetaEvaluation | 79.419 | 7.129 | 86.964 | |
nmfLasso | 4.342 | 0.322 | 4.682 | |
nmfLassoBootstrap | 73.523 | 10.497 | 84.763 | |
nmfLassoCV | 119.694 | 15.260 | 136.480 | |
patients.plot | 1.004 | 0.013 | 1.022 | |
sigAssignmentCV | 0.661 | 0.090 | 0.768 | |
sigAssignmentEvaluation | 1.780 | 0.159 | 1.949 | |
sigAssignmentLasso | 0.536 | 0.040 | 0.579 | |
signatures.plot | 1.819 | 0.030 | 1.857 | |
startingBetaEstimation | 3.300 | 0.091 | 3.402 | |