Aubrey Odom
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/TBSignatureProfiler |
| git_branch: master |
| git_last_commit: 9ce9d17 |
| git_last_commit_date: 2021-11-21 00:59:28 -0400 (Sun, 21 Nov 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:50 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
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. |
| Package 1940/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| TBSignatureProfiler 1.7.1 (landing page) Aubrey Odom
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: TBSignatureProfiler |
| Version: 1.7.1 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TBSignatureProfiler.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings TBSignatureProfiler_1.7.1.tar.gz |
| StartedAt: 2022-03-17 20:27:16 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 20:30:28 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 191.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: TBSignatureProfiler.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TBSignatureProfiler.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings TBSignatureProfiler_1.7.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/TBSignatureProfiler.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* 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 '1.7.1'
* 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
evaluateOriginalModel 6.85 1.48 8.33
bootstrapAUC 7.46 0.69 8.16
compareAlgs 4.55 0.50 5.05
* 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
TBSignatureProfiler.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL TBSignatureProfiler
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-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
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
* DONE (TBSignatureProfiler)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'supersigs' is missing or broken
done
TBSignatureProfiler.Rcheck/tests/packagecoverage.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
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
0.12 0.06 0.14
TBSignatureProfiler.Rcheck/tests/spelling.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
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
0.12 0.04 0.15
TBSignatureProfiler.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
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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[1] "Normalizing..."
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Estimating GSVA scores for 1 gene sets.
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Estimating GSVA scores for 1 gene sets.
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Estimating GSVA scores for 1 gene sets.
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Estimating GSVA 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
86.37 2.53 89.03
TBSignatureProfiler.Rcheck/TBSignatureProfiler-Ex.timings
| name | user | system | elapsed | |
| COVIDsignatures | 0 | 0 | 0 | |
| OriginalTrainingData | 0 | 0 | 0 | |
| SignatureQuantitative | 3.87 | 0.17 | 4.05 | |
| TBSPapp | 0 | 0 | 0 | |
| TB_hiv | 0 | 0 | 0 | |
| TB_indian | 0.02 | 0.00 | 0.01 | |
| TBcommon | 0 | 0 | 0 | |
| TBsignatures | 0 | 0 | 0 | |
| TBsignaturesSplit | 0 | 0 | 0 | |
| addTBsignature | 0.02 | 0.00 | 0.02 | |
| bootstrapAUC | 7.46 | 0.69 | 8.16 | |
| common_sigAnnotData | 0 | 0 | 0 | |
| compareAlgs | 4.55 | 0.50 | 5.05 | |
| compareBoxplots | 0.84 | 0.09 | 0.94 | |
| deseq2_norm_rle | 0.25 | 0.02 | 0.26 | |
| distinctColors | 0 | 0 | 0 | |
| evaluateOriginalModel | 6.85 | 1.48 | 8.33 | |
| mkAssay | 2.58 | 0.36 | 2.94 | |
| plotQuantitative | 2.43 | 0.16 | 2.59 | |
| runTBsigProfiler | 0.33 | 0.03 | 0.36 | |
| sigAnnotData | 0 | 0 | 0 | |
| signatureBoxplot | 0.85 | 0.03 | 0.87 | |
| signatureGeneHeatmap | 3.82 | 0.10 | 3.92 | |
| signatureHeatmap | 0.64 | 0.00 | 0.64 | |
| signatureROCplot | 0.49 | 0.01 | 0.50 | |
| signatureROCplot_CI | 3.55 | 0.47 | 4.02 | |
| tableAUC | 0.79 | 0.05 | 0.84 | |