Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-26 13:07:28 -0500 (Wed, 26 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
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 tokay2


To the developers/maintainers of the TBSignatureProfiler package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TBSignatureProfiler.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1935/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TBSignatureProfiler 1.6.0  (landing page)
Aubrey Odom
Snapshot Date: 2022-01-25 01:55:07 -0500 (Tue, 25 Jan 2022)
git_url: https://git.bioconductor.org/packages/TBSignatureProfiler
git_branch: RELEASE_3_14
git_last_commit: fe6bf5e
git_last_commit_date: 2021-10-26 12:59:18 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: TBSignatureProfiler
Version: 1.6.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TBSignatureProfiler.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings TBSignatureProfiler_1.6.0.tar.gz
StartedAt: 2022-01-26 03:49:46 -0500 (Wed, 26 Jan 2022)
EndedAt: 2022-01-26 03:55:46 -0500 (Wed, 26 Jan 2022)
EllapsedTime: 360.3 seconds
RetCode: 0
Status:   OK  
CheckDir: TBSignatureProfiler.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TBSignatureProfiler.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings TBSignatureProfiler_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/TBSignatureProfiler.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'TBSignatureProfiler/DESCRIPTION' ... OK
* this is package 'TBSignatureProfiler' version '1.6.0'
* 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 ... NOTE
  installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
evaluateOriginalModel 10.82   0.70   11.51
bootstrapAUC           8.06   0.80    8.89
compareAlgs            8.13   0.70    8.83
signatureROCplot_CI    5.58   0.27    5.84
SignatureQuantitative  4.84   0.19    5.03
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
bootstrapAUC          9.96   0.33   10.29
evaluateOriginalModel 7.76   0.59    8.36
compareAlgs           5.61   0.34    5.96
SignatureQuantitative 4.81   0.23    5.05
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'packagecoverage.R'
  Running 'spelling.R'
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/TBSignatureProfiler.Rcheck/00check.log'
for details.



Installation output

TBSignatureProfiler.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/TBSignatureProfiler_1.6.0.tar.gz && rm -rf TBSignatureProfiler.buildbin-libdir && mkdir TBSignatureProfiler.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TBSignatureProfiler.buildbin-libdir TBSignatureProfiler_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL TBSignatureProfiler_1.6.0.zip && rm TBSignatureProfiler_1.6.0.tar.gz TBSignatureProfiler_1.6.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 2823k  100 2823k    0     0  5431k      0 --:--:-- --:--:-- --:--:-- 5440k

install for i386

* 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
  converting help for package 'TBSignatureProfiler'
    finding HTML links ... done
    Bootstrap_LOOCV_LR_AUC                  html  
    COVIDsignatures                         html  
    LOOAUC_simple_multiple_noplot_one_df    html  
    ObtainSampleScore_OriginalModel         html  
    OriginalTrainingData                    html  
    SignatureQuantitative                   html  
    SulimanOriginalModel                    html  
    TBSPapp                                 html  
    TB_hiv                                  html  
    TB_indian                               html  
    TBcommon                                html  
    TBsignatures                            html  
    TBsignaturesSplit                       html  
    addTBsignature                          html  
    bootstrapAUC                            html  
    common_sigAnnotData                     html  
    compareAlgs                             html  
    compareBoxplots                         html  
    cv_glmnet_OriginalModel                 html  
    deseq2_norm_rle                         html  
    distinctColors                          html  
    dot-OriginalModel_NoRetraining          html  
    dot-OriginalModel_Retraining            html  
    evaluateOriginalModel                   html  
    knn_OriginalModel                       html  
    lda_OriginalModel                       html  
    mkAssay                                 html  
    plotQuantitative                        html  
    randomForest_OriginalModel              html  
    ref_combat_impute                       html  
    runTBsigProfiler                        html  
    sigAnnotData                            html  
    signatureBoxplot                        html  
    signatureGeneHeatmap                    html  
    signatureHeatmap                        html  
    signatureROCplot                        html  
    signatureROCplot_CI                     html  
    subsetGeneSet                           html  
    svm_OriginalModel                       html  
    tableAUC                                html  
** 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

install for x64

* installing *source* package 'TBSignatureProfiler' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TBSignatureProfiler' as TBSignatureProfiler_1.6.0.zip
* DONE (TBSignatureProfiler)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'TBSignatureProfiler' successfully unpacked and MD5 sums checked

Tests output

TBSignatureProfiler.Rcheck/tests_i386/packagecoverage.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 
   0.29    0.06    0.32 

TBSignatureProfiler.Rcheck/tests_x64/packagecoverage.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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 
   0.26    0.01    0.26 

TBSignatureProfiler.Rcheck/tests_i386/spelling.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 
   0.25    0.12    0.34 

TBSignatureProfiler.Rcheck/tests_x64/spelling.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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 
   0.23    0.06    0.28 

TBSignatureProfiler.Rcheck/tests_i386/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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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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.

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Estimating GSVA scores for 1 gene sets.
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Estimating ssGSEA scores for 1 gene sets.

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Estimating GSVA scores for 1 gene sets.
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[ FAIL 0 | WARN 0 | SKIP 1 | PASS 153 ]

== Skipped tests ===============================================================
* On CRAN (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 153 ]
> 
> proc.time()
   user  system elapsed 
  67.51    3.12   72.79 

TBSignatureProfiler.Rcheck/tests_x64/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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 GSVA scores for 1 gene sets.
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[ FAIL 0 | WARN 0 | SKIP 1 | PASS 153 ]

== Skipped tests ===============================================================
* On CRAN (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 153 ]
> 
> proc.time()
   user  system elapsed 
  89.57    1.67   91.34 

Example timings

TBSignatureProfiler.Rcheck/examples_i386/TBSignatureProfiler-Ex.timings

nameusersystemelapsed
COVIDsignatures0.010.020.03
OriginalTrainingData000
SignatureQuantitative4.840.195.03
TBSPapp000
TB_hiv000
TB_indian000
TBcommon000
TBsignatures0.000.010.01
TBsignaturesSplit000
addTBsignature0.020.000.02
bootstrapAUC8.060.808.89
common_sigAnnotData000
compareAlgs8.130.708.83
compareBoxplots0.710.240.95
deseq2_norm_rle0.330.000.33
distinctColors000
evaluateOriginalModel10.82 0.7011.51
mkAssay1.790.141.94
plotQuantitative1.970.001.97
runTBsigProfiler0.190.000.18
sigAnnotData000
signatureBoxplot0.590.000.60
signatureGeneHeatmap3.660.003.65
signatureHeatmap0.800.020.82
signatureROCplot0.440.000.44
signatureROCplot_CI5.580.275.84
tableAUC0.560.040.61

TBSignatureProfiler.Rcheck/examples_x64/TBSignatureProfiler-Ex.timings

nameusersystemelapsed
COVIDsignatures0.000.010.02
OriginalTrainingData0.000.020.01
SignatureQuantitative4.810.235.05
TBSPapp000
TB_hiv000
TB_indian000
TBcommon0.000.020.01
TBsignatures000
TBsignaturesSplit000
addTBsignature0.010.000.02
bootstrapAUC 9.96 0.3310.29
common_sigAnnotData000
compareAlgs5.610.345.96
compareBoxplots0.590.000.59
deseq2_norm_rle0.270.020.28
distinctColors000
evaluateOriginalModel7.760.598.36
mkAssay1.440.031.47
plotQuantitative1.910.122.03
runTBsigProfiler0.20.00.2
sigAnnotData000
signatureBoxplot0.610.030.64
signatureGeneHeatmap3.740.023.75
signatureHeatmap0.620.010.64
signatureROCplot0.470.000.47
signatureROCplot_CI4.880.024.89
tableAUC0.620.050.67