Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-05-17 11:37:05 -0400 (Fri, 17 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4663 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4398 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4425 |
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 2108/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
TOP 1.5.0 (landing page) Harry Robertson
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | see weekly results here | ||||||||||||
To the developers/maintainers of the TOP package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TOP.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: TOP |
Version: 1.5.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:TOP.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings TOP_1.5.0.tar.gz |
StartedAt: 2024-05-16 03:17:36 -0400 (Thu, 16 May 2024) |
EndedAt: 2024-05-16 03:22:01 -0400 (Thu, 16 May 2024) |
EllapsedTime: 265.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: TOP.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:TOP.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings TOP_1.5.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/TOP.Rcheck’ * using R version 4.4.0 RC (2024-04-16 r86468) * using platform: x86_64-pc-linux-gnu * 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 ‘TOP/DESCRIPTION’ ... OK * this is package ‘TOP’ version ‘1.5.0’ * package encoding: UTF-8 * 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 ‘TOP’ 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 loading without being on the library search path ... 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 Surv_TOP_CI: no visible binding for global variable ‘offset’ TOP_coefPlot: no visible binding for global variable ‘lambda.min’ TOP_coefPlot: no visible binding for global variable ‘Features’ TOP_lambdaPlot: no visible binding for global variable ‘variable’ TOP_lambdaPlot: no visible binding for global variable ‘value’ TOP_lambdaPlot: no visible binding for global variable ‘Feature’ TOP_model: no visible binding for global variable ‘value’ TOP_model: no visible binding for global variable ‘SampleGroup’ TOP_model: no visible binding for global variable ‘n’ TOP_model: no visible binding for global variable ‘freq’ TOP_model: no visible binding for global variable ‘sd’ TOP_survival: no visible binding for global variable ‘coef’ TOP_survival: no visible binding for global variable ‘value’ TOP_survival: no visible binding for global variable ‘freq’ TOP_survival: no visible binding for global variable ‘sd’ TOP_survival: no visible binding for global variable ‘.’ TOP_survival: no visible binding for global variable ‘SampleGroup’ TOP_survival: no visible binding for global variable ‘n’ TOP_survivalPrediction: no visible binding for global variable ‘offset’ coefNetworkPlot: no visible binding for global variable ‘Features’ coefNetworkPlot: no visible binding for global variable ‘lambda.min’ coefNetworkPlot: no visible binding for global variable ‘score’ colCoxTests_combine: no visible binding for global variable ‘coef’ extractAUC: no visible binding for global variable ‘variable’ extractAUC: no visible binding for global variable ‘value’ simplenetworkPlot: no visible binding for global variable ‘Features’ simplenetworkPlot: no visible binding for global variable ‘lambda.min’ simplenetworkPlot: no visible binding for global variable ‘coef_abs’ simplenetworkPlot: no visible binding for global variable ‘from’ simplenetworkPlot: no visible binding for global variable ‘to’ simplenetworkPlot: no visible binding for global variable ‘name’ Undefined global functions or variables: . Feature Features SampleGroup coef coef_abs freq from lambda.min n name offset score sd to value variable Consider adding importFrom("stats", "coef", "offset", "sd") to your NAMESPACE file. * 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 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.20-bioc/meat/TOP.Rcheck/00check.log’ for details.
TOP.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL TOP ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘TOP’ ... ** 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 (TOP)
TOP.Rcheck/TOP-Ex.timings
name | user | system | elapsed | |
ROC_Plot | 1.282 | 0.164 | 1.446 | |
Surv_Frank_CI | 0.919 | 0.056 | 0.976 | |
TOP_coefPlot | 0.396 | 0.024 | 0.420 | |
TOP_lambdaPlot | 0.641 | 0.056 | 0.698 | |
TOP_model | 0.13 | 0.00 | 0.13 | |
TOP_survival | 0.947 | 0.024 | 0.971 | |
TOP_survivalPrediction | 0.921 | 0.008 | 0.929 | |
coefNetworkPlot | 0.663 | 0.004 | 0.667 | |
filterFeatures | 0.043 | 0.000 | 0.044 | |
logit-expit | 0.028 | 0.004 | 0.033 | |
pairwise_col_diff | 0.001 | 0.000 | 0.001 | |
performance_TOP | 0.192 | 0.004 | 0.196 | |
predict_TOP | 0.150 | 0.008 | 0.158 | |
simplenetworkPlot | 0.433 | 0.016 | 0.449 | |