Back to Multiple platform build/check report for BioC 3.16:   simplified   long
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This page was generated on 2023-04-12 11:05:21 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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 nebbiolo2


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? 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 2025/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TBSignatureProfiler 1.10.0  (landing page)
Aubrey R. Odom-Mabey
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/TBSignatureProfiler
git_branch: RELEASE_3_16
git_last_commit: d5d3e43
git_last_commit_date: 2022-11-01 11:21:57 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    ERROR  
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: TBSignatureProfiler
Version: 1.10.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:TBSignatureProfiler.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings TBSignatureProfiler_1.10.0.tar.gz
StartedAt: 2023-04-11 00:29:53 -0400 (Tue, 11 Apr 2023)
EndedAt: 2023-04-11 00:33:06 -0400 (Tue, 11 Apr 2023)
EllapsedTime: 193.7 seconds
RetCode: 1
Status:   ERROR  
CheckDir: TBSignatureProfiler.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:TBSignatureProfiler.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings TBSignatureProfiler_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/TBSignatureProfiler.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘TBSignatureProfiler/DESCRIPTION’ ... OK
* this is package ‘TBSignatureProfiler’ version ‘1.10.0’
* 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 ‘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 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 ... 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 9.574  0.496  10.075
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘packagecoverage.R’
  Running ‘spelling.R’
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    1. ├─testthat::expect_is(...) at test-evaluate.R:30:2
    2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. └─TBSignatureProfiler:::Bootstrap_LOOCV_LR_AUC(...)
    5.   ├─base::suppressWarnings(...)
    6.   │ └─base::withCallingHandlers(...)
    7.   └─TBSignatureProfiler:::LOOAUC_simple_multiple_noplot_one_df(...)
    8.     ├─base::suppressWarnings(glmnet::glmnet(train, targetVec[-j], family = "binomial"))
    9.     │ └─base::withCallingHandlers(...)
   10.     └─glmnet::glmnet(train, targetVec[-j], family = "binomial")
   11.       └─glmnet:::lognet(...)
  
  [ FAIL 1 | WARN 3 | SKIP 0 | PASS 143 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘tbspVignette.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/TBSignatureProfiler.Rcheck/00check.log’
for details.


Installation output

TBSignatureProfiler.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL TBSignatureProfiler
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-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 version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 
  0.161   0.024   0.167 

TBSignatureProfiler.Rcheck/tests/spelling.Rout


R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 
  0.151   0.039   0.174 

TBSignatureProfiler.Rcheck/tests/testthat.Rout.fail


R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 absolute values from ranks..."

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

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

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[ FAIL 1 | WARN 3 | SKIP 0 | PASS 143 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-evaluate.R:30:3'): LOOAUC works ────────────────────────────────
Error in `lognet(xd, is.sparse, ix, jx, y, weights, offset, alpha, nobs, 
    nvars, jd, vp, cl, ne, nx, nlam, flmin, ulam, thresh, isd, 
    intr, vnames, maxit, kopt, family, pb)`: one multinomial or binomial class has 1 or 0 observations; not allowed
Backtrace:
     ▆
  1. ├─testthat::expect_is(...) at test-evaluate.R:30:2
  2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
  3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
  4. └─TBSignatureProfiler:::Bootstrap_LOOCV_LR_AUC(...)
  5.   ├─base::suppressWarnings(...)
  6.   │ └─base::withCallingHandlers(...)
  7.   └─TBSignatureProfiler:::LOOAUC_simple_multiple_noplot_one_df(...)
  8.     ├─base::suppressWarnings(glmnet::glmnet(train, targetVec[-j], family = "binomial"))
  9.     │ └─base::withCallingHandlers(...)
 10.     └─glmnet::glmnet(train, targetVec[-j], family = "binomial")
 11.       └─glmnet:::lognet(...)

[ FAIL 1 | WARN 3 | SKIP 0 | PASS 143 ]
Error: Test failures
Execution halted

Example timings

TBSignatureProfiler.Rcheck/TBSignatureProfiler-Ex.timings

nameusersystemelapsed
COVIDsignatures0.0230.0000.023
OriginalTrainingData0.0010.0000.000
SignatureQuantitative3.4190.1633.592
TBSPapp000
TB_hiv0.0010.0000.001
TB_indian0.0010.0000.000
TBcommon0.0010.0000.000
TBsignatures0.0010.0000.000
TBsignaturesSplit0.0010.0000.000
addTBsignature0.0050.0040.010
bootstrapAUC 9.574 0.49610.075
common_sigAnnotData0.0010.0000.000
compareAlgs2.2520.1442.396
compareBoxplots0.8360.0200.855
deseq2_norm_rle0.310.000.31
distinctColors0.0010.0000.001
evaluateOriginalModel0.1760.0040.180
mkAssay2.670.102.77
plotQuantitative2.5150.0522.567
runTBsigProfiler0.2500.0080.258
sigAnnotData0.0010.0000.001
signatureBoxplot0.7190.0120.731
signatureGeneHeatmap3.2320.0483.280
signatureHeatmap0.6540.0000.654
signatureROCplot0.6320.0040.636
signatureROCplot_CI4.5610.0364.597
tableAUC0.5710.0200.592