Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-24 11:42 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 106/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ASSET 2.25.0 (landing page) Samsiddhi Bhattacharjee
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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: 2.25.0 |
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_2.25.0.tar.gz |
StartedAt: 2024-12-23 18:55:06 -0500 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 18:57:15 -0500 (Mon, 23 Dec 2024) |
EllapsedTime: 128.8 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_2.25.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/ASSET.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * 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 ‘ASSET/DESCRIPTION’ ... OK * this is package ‘ASSET’ version ‘2.25.0’ * 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 48.285 0.626 49.191 h.types 6.031 0.321 6.385 * 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-3.21-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/4.5-x86_64/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 Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 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. > BiocGenerics:::testPackage("ASSET") RUNIT TEST PROTOCOL -- Mon Dec 23 18:57:06 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 7.915 0.509 8.464
ASSET.Rcheck/ASSET-Ex.timings
name | user | system | elapsed | |
create_blocks | 0.018 | 0.006 | 0.025 | |
ex_fast_asset | 0.003 | 0.003 | 0.006 | |
ex_trait | 0.005 | 0.002 | 0.007 | |
ex_types | 0.009 | 0.001 | 0.011 | |
fast_asset | 48.285 | 0.626 | 49.191 | |
h.forestPlot | 0.460 | 0.006 | 0.467 | |
h.summary | 0.311 | 0.004 | 0.318 | |
h.traits | 0.335 | 0.005 | 0.342 | |
h.types | 6.031 | 0.321 | 6.385 | |
p.dlm | 0.023 | 0.001 | 0.024 | |
z.max | 0.015 | 0.001 | 0.016 | |