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 12:08 -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 2119/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
TargetScore 1.44.0 (landing page) Yue Li
| 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 TargetScore package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TargetScore.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: TargetScore |
Version: 1.44.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TargetScore.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TargetScore_1.44.0.tar.gz |
StartedAt: 2024-12-21 11:38:45 -0500 (Sat, 21 Dec 2024) |
EndedAt: 2024-12-21 11:39:34 -0500 (Sat, 21 Dec 2024) |
EllapsedTime: 49.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: TargetScore.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TargetScore.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TargetScore_1.44.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/TargetScore.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 ‘TargetScore/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘TargetScore’ version ‘1.44.0’ * 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 ‘TargetScore’ 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 dot.ext: no visible global function definition for ‘size’ getTargetScores: no visible global function definition for ‘get_TargetScanHuman_contextScore’ getTargetScores: no visible global function definition for ‘get_TargetScanHuman_PCT’ getTargetScores: no visible global function definition for ‘get_validated_targets’ getTargetScores: no visible global function definition for ‘get_miRNA_family_info’ getTargetScores: no visible binding for global variable ‘logFC.imputed’ getTargetScores : <anonymous>: no visible global function definition for ‘cor’ getTargetScores: no visible global function definition for ‘aggregate’ logmvgamma: no visible global function definition for ‘size’ targetScore: no visible global function definition for ‘as.roman’ targetScore : <anonymous>: no visible global function definition for ‘as.roman’ targetScore: no visible global function definition for ‘sigmoid’ Undefined global functions or variables: aggregate as.roman cor get_TargetScanHuman_PCT get_TargetScanHuman_contextScore get_miRNA_family_info get_validated_targets logFC.imputed sigmoid size Consider adding importFrom("stats", "aggregate", "cor") importFrom("utils", "as.roman") to your NAMESPACE file. * checking Rd files ... NOTE checkRd: (-1) targetScore.Rd:28: Lost braces 28 | sigmoid(-log{FC}) (1/K+1) sum_{x in \{x_f, x_1, ..., x_L\} p(t | x)), | ^ checkRd: (-1) targetScore.Rd:28-31: Lost braces 28 | sigmoid(-log{FC}) (1/K+1) sum_{x in \{x_f, x_1, ..., x_L\} p(t | x)), | ^ checkRd: (-1) targetScore.Rd:30: Lost braces 30 | where sigmoid(-log{FC}) = 1/(1 + exp(log{FC})) and p(t | x) is the posterior of the first component computed by \code{\link{vbgmm}}. | ^ checkRd: (-1) targetScore.Rd:30: Lost braces 30 | where sigmoid(-log{FC}) = 1/(1 + exp(log{FC})) and p(t | x) is the posterior of the first component computed by \code{\link{vbgmm}}. | ^ * 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... 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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/TargetScore.Rcheck/00check.log’ for details.
TargetScore.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL TargetScore ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘TargetScore’ ... ** using staged installation ** R ** 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 (TargetScore)
TargetScore.Rcheck/TargetScore-Ex.timings
name | user | system | elapsed | |
TargetScore-package | 0 | 0 | 0 | |
bsxfun.se | 0.001 | 0.000 | 0.001 | |
dot.ext | 0.001 | 0.000 | 0.001 | |
getTargetScores | 0.002 | 0.000 | 0.002 | |
initialization | 0.011 | 0.001 | 0.012 | |
logmvgamma | 0.002 | 0.000 | 0.001 | |
logsumexp | 0.001 | 0.000 | 0.001 | |
sort_components | 0.079 | 0.010 | 0.090 | |
targetScore | 0.425 | 0.014 | 0.459 | |
vbgmm | 0.066 | 0.000 | 0.067 | |
vbound | 0.073 | 0.001 | 0.074 | |
vexp | 0.066 | 0.001 | 0.066 | |
vmax | 0.069 | 0.000 | 0.069 | |