Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 106/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ASSET 2.24.0 (landing page) Samsiddhi Bhattacharjee
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the ASSET package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ASSET.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: ASSET |
Version: 2.24.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ASSET.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ASSET_2.24.0.tar.gz |
StartedAt: 2024-12-20 11:28:28 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 11:30:30 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 121.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ASSET.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ASSET.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ASSET_2.24.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ASSET.Rcheck’ * using R version 4.4.2 (2024-10-31) * 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 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ASSET/DESCRIPTION’ ... OK * this is package ‘ASSET’ version ‘2.24.0’ * 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 ‘ASSET’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License components with restrictions not permitted: GPL-2 + file LICENSE * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... NOTE Problems with news in ‘NEWS’: Cannot process chunk/lines: The stochastic p-value calculation with p-value screening appears to be unacceptably slow in many cases. Cannot process chunk/lines: Reverting to older deterministic p-value calculation used till ASSET 1.8.0. P-value screening option Cannot process chunk/lines: is not supported for now but may be included in future releases. Cannot process chunk/lines: A new p-value screening option p.bound introduced and stochastic p-value calculation incorporated to allow Cannot process chunk/lines: p-value screening. * 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 ... OK * checking Rd files ... NOTE checkRd: (-1) fast_asset.Rd:29: Lost braces; missing escapes or markup? 29 | \item{cor}{A matrix of dimension k by k storing the correlation of z-statistics under the null hypothesis. It can be estimated using LD score regression (https://github.com/bulik/ldsc). For example, element \code{(j,k)} is the LD score regression intercept between traits \code{j} and {k}. Diagonal elements are equal to 1. Set to identity matrix if different studies do not have overlapping samples.} | ^ * 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed fast_asset 41.886 1.831 43.764 h.types 7.359 0.346 7.733 * 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: 3 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/ASSET.Rcheck/00check.log’ for details.
ASSET.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ASSET ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘ASSET’ ... ** 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 (ASSET)
ASSET.Rcheck/tests/runTests.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 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("ASSET") RUNIT TEST PROTOCOL -- Fri Dec 20 11:30:20 2024 *********************************************** Number of test functions: 4 Number of errors: 0 Number of failures: 0 1 Test Suite : ASSET RUnit Tests - 4 test functions, 0 errors, 0 failures Number of test functions: 4 Number of errors: 0 Number of failures: 0 Warning messages: 1: In formula.character(object, env = baseenv()) : Using formula(x) is deprecated when x is a character vector of length > 1. Consider formula(paste(x, collapse = " ")) instead. 2: In formula.character(object, env = baseenv()) : Using formula(x) is deprecated when x is a character vector of length > 1. Consider formula(paste(x, collapse = " ")) instead. 3: In formula.character(object, env = baseenv()) : Using formula(x) is deprecated when x is a character vector of length > 1. Consider formula(paste(x, collapse = " ")) instead. 4: In formula.character(object, env = baseenv()) : Using formula(x) is deprecated when x is a character vector of length > 1. Consider formula(paste(x, collapse = " ")) instead. > > proc.time() user system elapsed 8.936 0.444 9.391
ASSET.Rcheck/ASSET-Ex.timings
name | user | system | elapsed | |
create_blocks | 0.021 | 0.004 | 0.026 | |
ex_fast_asset | 0.004 | 0.002 | 0.006 | |
ex_trait | 0.007 | 0.002 | 0.008 | |
ex_types | 0.022 | 0.001 | 0.024 | |
fast_asset | 41.886 | 1.831 | 43.764 | |
h.forestPlot | 0.413 | 0.008 | 0.433 | |
h.summary | 0.273 | 0.003 | 0.283 | |
h.traits | 0.288 | 0.005 | 0.314 | |
h.types | 7.359 | 0.346 | 7.733 | |
p.dlm | 0.021 | 0.000 | 0.021 | |
z.max | 0.015 | 0.000 | 0.016 | |