Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2024-04-17 11:36:03 -0400 (Wed, 17 Apr 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4676 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4437 |
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 1066/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
iterativeBMAsurv 1.60.0 (landing page) Ka Yee Yeung
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
To the developers/maintainers of the iterativeBMAsurv package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/iterativeBMAsurv.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: iterativeBMAsurv |
Version: 1.60.0 |
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:iterativeBMAsurv.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings iterativeBMAsurv_1.60.0.tar.gz |
StartedAt: 2024-04-16 00:11:44 -0400 (Tue, 16 Apr 2024) |
EndedAt: 2024-04-16 00:13:16 -0400 (Tue, 16 Apr 2024) |
EllapsedTime: 92.0 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: iterativeBMAsurv.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:iterativeBMAsurv.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings iterativeBMAsurv_1.60.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/iterativeBMAsurv.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘iterativeBMAsurv/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘iterativeBMAsurv’ version ‘1.60.0’ * 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 ‘iterativeBMAsurv’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘survival’ A package should be listed in only one of these fields. * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R 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 ... NOTE Packages in Depends field not imported from: ‘BMA’ ‘leaps’ ‘splines’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE iterateBMAsurv.train: no visible global function definition for ‘bic.surv’ iterateBMAsurv.train.wrapper: no visible global function definition for ‘bic.surv’ Undefined global functions or variables: bic.surv * checking Rd files ... WARNING checkRd: (-1) crossVal.Rd:74: Escaped LaTeX specials: \_ \_ \_ \_ checkRd: (5) iterateBMAsurv.train.Rd:67-98: \item in \value must have non-empty label prepare_Rd: predictBicSurv.Rd:46: Dropping empty section \note prepare_Rd: predictiveAssessCategory.Rd:52: Dropping empty section \note prepare_Rd: printTopGenes.Rd:49: Dropping empty section \note checkRd: (-1) printTopGenes.Rd:22: Escaped LaTeX specials: \_ \_ prepare_Rd: singleGeneCoxph.Rd:54: Dropping empty section \note checkRd: (-1) singleGeneCoxph.Rd:32: Escaped LaTeX specials: \_ prepare_Rd: testCens.Rd:13-14: Dropping empty section \details prepare_Rd: testSurv.Rd:13-14: Dropping empty section \details prepare_Rd: trainCens.Rd:13-14: Dropping empty section \details prepare_Rd: trainSurv.Rd:13-14: Dropping empty section \details * 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 imageplot.iterate.bma.surv 9.105 0 9.105 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘iterativeBMAsurv.Rnw’... OK OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 3 NOTEs See ‘/home/biocbuild/bbs-3.18-bioc/meat/iterativeBMAsurv.Rcheck/00check.log’ for details.
iterativeBMAsurv.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL iterativeBMAsurv ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’ * installing *source* package ‘iterativeBMAsurv’ ... ** using staged installation ** R ** data ** 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 (iterativeBMAsurv)
iterativeBMAsurv.Rcheck/iterativeBMAsurv-Ex.timings
name | user | system | elapsed | |
crossVal | 1.183 | 0.008 | 1.191 | |
imageplot.iterate.bma.surv | 9.105 | 0.000 | 9.105 | |
iterateBMAsurv.train | 4.689 | 0.004 | 4.693 | |
iterateBMAsurv.train.predict.assess | 0.485 | 0.000 | 0.485 | |
iterateBMAsurv.train.wrapper | 4.294 | 0.000 | 4.294 | |
iterativeBMAsurv-package | 1.639 | 0.012 | 1.651 | |
predictBicSurv | 4.402 | 0.012 | 4.414 | |
predictiveAssessCategory | 4.696 | 0.032 | 4.729 | |
printTopGenes | 0.290 | 0.128 | 0.418 | |
singleGeneCoxph | 0.238 | 0.012 | 0.250 | |