Back to Build/check report for BioC 3.17
ABCDEFGHIJKLMNOPQRS[T]UVWXYZ

This page was generated on 2023-01-02 09:00:53 -0500 (Mon, 02 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
palomino5Windows Server 2022 Datacenterx64R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" 4165
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

CHECK results for TBSignatureProfiler on palomino5


To the developers/maintainers of the TBSignatureProfiler package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 2006/2158HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TBSignatureProfiler 1.11.0  (landing page)
Aubrey R. Odom-Mabey
Snapshot Date: 2022-12-28 11:00:06 -0500 (Wed, 28 Dec 2022)
git_url: https://git.bioconductor.org/packages/TBSignatureProfiler
git_branch: master
git_last_commit: 282d5a1
git_last_commit_date: 2022-11-01 11:21:57 -0500 (Tue, 01 Nov 2022)
palomino5Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  

Summary

Package: TBSignatureProfiler
Version: 1.11.0
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TBSignatureProfiler.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings TBSignatureProfiler_1.11.0.tar.gz
StartedAt: 2022-12-29 04:07:37 -0500 (Thu, 29 Dec 2022)
EndedAt: 2022-12-29 04:10:09 -0500 (Thu, 29 Dec 2022)
EllapsedTime: 151.4 seconds
RetCode: 0
Status:   OK  
CheckDir: TBSignatureProfiler.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TBSignatureProfiler.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings TBSignatureProfiler_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/TBSignatureProfiler.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'TBSignatureProfiler/DESCRIPTION' ... OK
* this is package 'TBSignatureProfiler' version '1.11.0'
* 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 'TBSignatureProfiler' 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 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 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 ... OK
* 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 LazyData ... 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
bootstrapAUC 7.14   0.33    7.53
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'packagecoverage.R'
  Running 'spelling.R'
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

TBSignatureProfiler.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL TBSignatureProfiler
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'TBSignatureProfiler' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (TBSignatureProfiler)

Tests output

TBSignatureProfiler.Rcheck/tests/packagecoverage.Rout


R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # Coverage Script
> # Run tests and generate Code Coverage Report
> 
> # Look at a specific script ---------------------------------------------------
> #test_for_me <- function(codefile, testfile) {
> #  test_file(testfile)
> #  res <- covr::file_coverage(codefile, testfile)
> #  print(res)
> #  covr::report(res)
> #}
> 
> #test_for_me("R/evaluate.R", "tests/testthat/test-evaluate.R")
> # Look at whole package -------------------------------------------------------
> # Gets percent coverage for entire package, by script
> #covr::package_coverage()
> #
> # Report with gui (probably the best here)
> #covr::report()
> 
> proc.time()
   user  system elapsed 
   0.07    0.12    0.17 

TBSignatureProfiler.Rcheck/tests/spelling.Rout


R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> if (requireNamespace("spelling", quietly = TRUE))
+   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+                              skip_on_cran = TRUE)
NULL
> 
> proc.time()
   user  system elapsed 
   0.20    0.04    0.23 

TBSignatureProfiler.Rcheck/tests/testthat.Rout


R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(TBSignatureProfiler)
> 
> test_check("TBSignatureProfiler")

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Estimating ssGSEA scores for 1 gene sets.
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[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."

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[1] "Normalizing..."
Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels

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  |======================================================================| 100%

Estimating ssGSEA scores for 1 gene sets.
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."

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[1] "Normalizing..."
================================================================================
Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels

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Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels

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Estimating ssGSEA scores for 1 gene sets.
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."

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[1] "Normalizing..."
Estimating ssGSEA scores for 1 gene sets.
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."

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[1] "Normalizing..."
================================================================================
================================================================================
Estimating PLAGE scores for 1 gene sets.

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Estimating PLAGE scores for 1 gene sets.

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Estimating combined z-scores for 1 gene sets.

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  |======================================================================| 100%

Estimating combined z-scores for 1 gene sets.

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Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels

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  |======================================================================| 100%

Estimating combined z-scores for 1 gene sets.

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Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels

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  |======================================================================| 100%

Estimating combined z-scores for 1 gene sets.

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Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels

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  |======================================================================| 100%

Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels

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  |======================================================================| 100%

Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels

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  |======================================================================| 100%

Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels

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  |======================================================================| 100%

[ FAIL 0 | WARN 3 | SKIP 0 | PASS 144 ]

[ FAIL 0 | WARN 3 | SKIP 0 | PASS 144 ]
> 
> proc.time()
   user  system elapsed 
  61.98    1.82   63.98 

Example timings

TBSignatureProfiler.Rcheck/TBSignatureProfiler-Ex.timings

nameusersystemelapsed
COVIDsignatures0.000.010.02
OriginalTrainingData0.020.000.01
SignatureQuantitative2.910.153.05
TBSPapp000
TB_hiv000
TB_indian000
TBcommon000
TBsignatures000
TBsignaturesSplit000
addTBsignature000
bootstrapAUC7.140.337.53
common_sigAnnotData000
compareAlgs1.950.232.18
compareBoxplots0.830.030.86
deseq2_norm_rle0.170.040.21
distinctColors000
evaluateOriginalModel0.120.010.14
mkAssay2.310.022.33
plotQuantitative1.360.011.38
runTBsigProfiler0.250.000.25
sigAnnotData0.020.000.01
signatureBoxplot0.690.030.72
signatureGeneHeatmap3.390.103.49
signatureHeatmap0.540.010.56
signatureROCplot0.560.020.58
signatureROCplot_CI3.770.093.86
tableAUC0.550.080.70