Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2025-03-17 11:39 -0400 (Mon, 17 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" 4545
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4576
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4528
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4459
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 2184/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TOP 1.7.0  (landing page)
Harry Robertson
Snapshot Date: 2025-03-16 13:40 -0400 (Sun, 16 Mar 2025)
git_url: https://git.bioconductor.org/packages/TOP
git_branch: devel
git_last_commit: ade71fe
git_last_commit_date: 2024-10-29 11:20:53 -0400 (Tue, 29 Oct 2024)
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for TOP on lconway

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.

raw results


Summary

Package: TOP
Version: 1.7.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TOP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TOP_1.7.0.tar.gz
StartedAt: 2025-03-17 00:20:15 -0400 (Mon, 17 Mar 2025)
EndedAt: 2025-03-17 00:24:14 -0400 (Mon, 17 Mar 2025)
EllapsedTime: 239.6 seconds
RetCode: 0
Status:   OK  
CheckDir: TOP.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TOP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TOP_1.7.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/TOP.Rcheck’
* using R Under development (unstable) (2025-03-02 r87868)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TOP/DESCRIPTION’ ... OK
* this is package ‘TOP’ version ‘1.7.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 27 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/TOP.Rcheck/00check.log’
for details.


Installation output

TOP.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL TOP
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘TOP’ ...
** this is package ‘TOP’ version ‘1.7.0’
** 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)

Tests output


Example timings

TOP.Rcheck/TOP-Ex.timings

nameusersystemelapsed
ROC_Plot1.3930.0251.424
Surv_Frank_CI1.1630.0511.222
TOP_coefPlot0.4900.0110.503
TOP_lambdaPlot0.7470.0330.787
TOP_model0.1540.0060.161
TOP_survival1.1210.0121.140
TOP_survivalPrediction1.2180.0201.248
coefNetworkPlot0.7500.0380.794
filterFeatures0.0480.0030.052
logit-expit0.0380.0020.039
pairwise_col_diff0.0010.0000.001
performance_TOP0.2330.0150.249
predict_TOP0.1580.0050.163
simplenetworkPlot0.5210.0150.545