Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-06-11 15:41 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
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 2116/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TOP 1.5.0  (landing page)
Harry Robertson
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/TOP
git_branch: devel
git_last_commit: 3d414c4
git_last_commit_date: 2024-04-30 11:49:24 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  NO, package depends on 'ClassifyR' which is only available as a source package that needs compilation
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for TOP on palomino4

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: 1.5.0
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TOP.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings TOP_1.5.0.tar.gz
StartedAt: 2024-06-10 11:20:22 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 11:30:59 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 636.7 seconds
RetCode: 0
Status:   OK  
CheckDir: TOP.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TOP.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings TOP_1.5.0.tar.gz
###
##############################################################################
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* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/TOP.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* 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 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
  'F:/biocbuild/bbs-3.20-bioc/meat/TOP.Rcheck/00check.log'
for details.


Installation output

TOP.Rcheck/00install.out

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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL TOP
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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)

Tests output


Example timings

TOP.Rcheck/TOP-Ex.timings

nameusersystemelapsed
ROC_Plot1.250.041.31
Surv_Frank_CI1.060.071.14
TOP_coefPlot0.570.020.61
TOP_lambdaPlot0.610.030.64
TOP_model0.210.000.20
TOP_survival0.950.000.95
TOP_survivalPrediction0.980.021.00
coefNetworkPlot0.740.321.08
filterFeatures0.030.080.12
logit-expit0.030.000.03
pairwise_col_diff000
performance_TOP0.230.080.33
predict_TOP0.190.000.19
simplenetworkPlot0.490.060.54