| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:06:29 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (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 | ||||
|
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. |
| Package 2025/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| TBSignatureProfiler 1.10.0 (landing page) Aubrey R. Odom-Mabey
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK |  | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: TBSignatureProfiler |
| Version: 1.10.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TBSignatureProfiler.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TBSignatureProfiler_1.10.0.tar.gz |
| StartedAt: 2023-04-10 23:03:10 -0400 (Mon, 10 Apr 2023) |
| EndedAt: 2023-04-10 23:05:46 -0400 (Mon, 10 Apr 2023) |
| EllapsedTime: 155.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: TBSignatureProfiler.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TBSignatureProfiler.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TBSignatureProfiler_1.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/TBSignatureProfiler.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 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 8.472 0.416 8.902
signatureROCplot_CI 5.132 0.635 5.787
* 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: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL TBSignatureProfiler ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/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)
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-apple-darwin17.0 (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
0.175 0.062 0.233
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-apple-darwin17.0 (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
0.178 0.059 0.226
TBSignatureProfiler.Rcheck/tests/testthat.Rout
R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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")
|
| | 0%
|
|======================================================================| 100%
|
| | 0%
|
|======================================================================| 100%
|
| | 0%
|
|======================================================================| 100%
|
| | 0%
|
|======================================================================| 100%
|
| | 0%
|
|======================================================================| 100%
|
| | 0%
|
|======================================================================| 100%
|
| | 0%
|
|======================================================================| 100%
Estimating ssGSEA scores for 1 gene sets.
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
|
| | 0%
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%
|
|=============================================================== | 90%
|
|======================================================================| 100%
[1] "Normalizing..."
Estimating ssGSEA scores for 1 gene sets.
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
|
| | 0%
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%
|
|=============================================================== | 90%
|
|======================================================================| 100%
[1] "Normalizing..."
|
| | 0%
|
|======================================================================| 100%
|
| | 0%
|
|======================================================================| 100%
|
| | 0%
|
|======================================================================| 100%
|
| | 0%
|
|======================================================================| 100%
|
| | 0%
|
|======================================================================| 100%
|
| | 0%
|
|======================================================================| 100%
|
| | 0%
|
|======================================================================| 100%
|
| | 0%
|
|======================================================================| 100%
Estimating ssGSEA scores for 1 gene sets.
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
|
| | 0%
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%
|
|=============================================================== | 90%
|
|======================================================================| 100%
[1] "Normalizing..."
Estimating ssGSEA scores for 1 gene sets.
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
|
| | 0%
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%
|
|=============================================================== | 90%
|
|======================================================================| 100%
[1] "Normalizing..."
Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels
|
| | 0%
|
|======================================================================| 100%
Estimating ssGSEA scores for 1 gene sets.
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
|
| | 0%
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%
|
|=============================================================== | 90%
|
|======================================================================| 100%
[1] "Normalizing..."
================================================================================
Estimating PLAGE scores for 1 gene sets.
|
| | 0%
|
|======================================================================| 100%
Estimating combined z-scores for 1 gene sets.
|
| | 0%
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%
|
|=============================================================== | 90%
|
|======================================================================| 100%
Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels
|
| | 0%
|
|======================================================================| 100%
Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels
|
| | 0%
|
|======================================================================| 100%
Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels
|
| | 0%
|
|======================================================================| 100%
Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels
|
| | 0%
|
|======================================================================| 100%
Estimating ssGSEA scores for 1 gene sets.
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
|
| | 0%
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%
|
|=============================================================== | 90%
|
|======================================================================| 100%
[1] "Normalizing..."
Estimating combined z-scores for 1 gene sets.
|
| | 0%
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%
|
|=============================================================== | 90%
|
|======================================================================| 100%
Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels
|
| | 0%
|
|======================================================================| 100%
Estimating ssGSEA scores for 1 gene sets.
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
|
| | 0%
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%
|
|=============================================================== | 90%
|
|======================================================================| 100%
[1] "Normalizing..."
Estimating combined z-scores for 1 gene sets.
|
| | 0%
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%
|
|=============================================================== | 90%
|
|======================================================================| 100%
Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels
|
| | 0%
|
|======================================================================| 100%
Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels
|
| | 0%
|
|======================================================================| 100%
Estimating ssGSEA scores for 1 gene sets.
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
|
| | 0%
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%
|
|=============================================================== | 90%
|
|======================================================================| 100%
[1] "Normalizing..."
================================================================================
Estimating PLAGE scores for 1 gene sets.
|
| | 0%
|
|======================================================================| 100%
Estimating combined z-scores for 1 gene sets.
|
| | 0%
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%
|
|=============================================================== | 90%
|
|======================================================================| 100%
Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels
|
| | 0%
|
|======================================================================| 100%
Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels
|
| | 0%
|
|======================================================================| 100%
Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels
|
| | 0%
|
|======================================================================| 100%
Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels
|
| | 0%
|
|======================================================================| 100%
Estimating ssGSEA scores for 1 gene sets.
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
|
| | 0%
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%
|
|=============================================================== | 90%
|
|======================================================================| 100%
[1] "Normalizing..."
Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels
|
| | 0%
|
|======================================================================| 100%
Estimating ssGSEA scores for 1 gene sets.
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
|
| | 0%
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%
|
|=============================================================== | 90%
|
|======================================================================| 100%
[1] "Normalizing..."
================================================================================
Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels
|
| | 0%
|
|======================================================================| 100%
Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels
|
| | 0%
|
|======================================================================| 100%
Estimating ssGSEA scores for 1 gene sets.
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
|
| | 0%
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%
|
|=============================================================== | 90%
|
|======================================================================| 100%
[1] "Normalizing..."
Estimating ssGSEA scores for 1 gene sets.
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
|
| | 0%
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%
|
|=============================================================== | 90%
|
|======================================================================| 100%
[1] "Normalizing..."
================================================================================
================================================================================
Estimating PLAGE scores for 1 gene sets.
|
| | 0%
|
|======================================================================| 100%
Estimating PLAGE scores for 1 gene sets.
|
| | 0%
|
|======================================================================| 100%
Estimating combined z-scores for 1 gene sets.
|
| | 0%
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%
|
|=============================================================== | 90%
|
|======================================================================| 100%
Estimating combined z-scores for 1 gene sets.
|
| | 0%
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%
|
|=============================================================== | 90%
|
|======================================================================| 100%
Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels
|
| | 0%
|
|======================================================================| 100%
Estimating combined z-scores for 1 gene sets.
|
| | 0%
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%
|
|=============================================================== | 90%
|
|======================================================================| 100%
Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels
|
| | 0%
|
|======================================================================| 100%
Estimating combined z-scores for 1 gene sets.
|
| | 0%
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%
|
|=============================================================== | 90%
|
|======================================================================| 100%
Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels
|
| | 0%
|
|======================================================================| 100%
Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels
|
| | 0%
|
|======================================================================| 100%
Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels
|
| | 0%
|
|======================================================================| 100%
Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels
|
| | 0%
|
|======================================================================| 100%
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 144 ]
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 144 ]
>
> proc.time()
user system elapsed
59.498 3.326 62.965
TBSignatureProfiler.Rcheck/TBSignatureProfiler-Ex.timings
| name | user | system | elapsed | |
| COVIDsignatures | 0.018 | 0.004 | 0.022 | |
| OriginalTrainingData | 0.001 | 0.001 | 0.001 | |
| SignatureQuantitative | 3.120 | 0.177 | 3.314 | |
| TBSPapp | 0 | 0 | 0 | |
| TB_hiv | 0.000 | 0.001 | 0.001 | |
| TB_indian | 0.000 | 0.001 | 0.001 | |
| TBcommon | 0.000 | 0.001 | 0.001 | |
| TBsignatures | 0.000 | 0.001 | 0.002 | |
| TBsignaturesSplit | 0.000 | 0.001 | 0.001 | |
| addTBsignature | 0.005 | 0.002 | 0.007 | |
| bootstrapAUC | 8.472 | 0.416 | 8.902 | |
| common_sigAnnotData | 0.001 | 0.001 | 0.002 | |
| compareAlgs | 2.224 | 0.131 | 2.361 | |
| compareBoxplots | 0.845 | 0.025 | 0.872 | |
| deseq2_norm_rle | 0.258 | 0.017 | 0.277 | |
| distinctColors | 0.000 | 0.000 | 0.001 | |
| evaluateOriginalModel | 0.222 | 0.010 | 0.232 | |
| mkAssay | 3.343 | 0.181 | 3.529 | |
| plotQuantitative | 1.586 | 0.020 | 1.610 | |
| runTBsigProfiler | 0.248 | 0.007 | 0.255 | |
| sigAnnotData | 0.001 | 0.002 | 0.002 | |
| signatureBoxplot | 0.715 | 0.022 | 0.738 | |
| signatureGeneHeatmap | 2.929 | 0.031 | 2.962 | |
| signatureHeatmap | 0.703 | 0.018 | 0.723 | |
| signatureROCplot | 0.624 | 0.010 | 0.635 | |
| signatureROCplot_CI | 5.132 | 0.635 | 5.787 | |
| tableAUC | 0.609 | 0.040 | 0.652 | |