| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:13 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 | ||||
| Package 2074/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| TBSignatureProfiler 1.12.0 (landing page) Aubrey R. Odom-Mabey
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK |  | |||||||
|
To the developers/maintainers of the TBSignatureProfiler package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: TBSignatureProfiler |
| Version: 1.12.0 |
| 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_1.12.0.tar.gz |
| StartedAt: 2023-10-19 06:09:13 -0400 (Thu, 19 Oct 2023) |
| EndedAt: 2023-10-19 06:14:39 -0400 (Thu, 19 Oct 2023) |
| EllapsedTime: 326.8 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_1.12.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/TBSignatureProfiler.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TBSignatureProfiler/DESCRIPTION’ ... OK
* this is package ‘TBSignatureProfiler’ version ‘1.12.0’
* 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 11.486 0.586 21.644
signatureROCplot_CI 7.138 0.117 12.090
signatureGeneHeatmap 4.551 0.097 8.274
SignatureQuantitative 4.072 0.210 7.712
mkAssay 2.820 0.094 5.172
* 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/4.3-arm64/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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
0.207 0.064 0.444
TBSignatureProfiler.Rcheck/tests/spelling.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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
0.209 0.069 0.450
TBSignatureProfiler.Rcheck/tests/testthat.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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 141 ]
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 141 ]
>
> proc.time()
user system elapsed
70.344 1.867 128.487
TBSignatureProfiler.Rcheck/TBSignatureProfiler-Ex.timings
| name | user | system | elapsed | |
| COVIDsignatures | 0.022 | 0.004 | 0.051 | |
| OriginalTrainingData | 0.001 | 0.001 | 0.004 | |
| SignatureQuantitative | 4.072 | 0.210 | 7.712 | |
| TBSPapp | 0.000 | 0.000 | 0.004 | |
| TB_hiv | 0.001 | 0.001 | 0.002 | |
| TB_indian | 0.001 | 0.001 | 0.002 | |
| TBcommon | 0.001 | 0.001 | 0.006 | |
| TBsignatures | 0.001 | 0.001 | 0.001 | |
| TBsignaturesSplit | 0.001 | 0.001 | 0.002 | |
| addTBsignature | 0.008 | 0.002 | 0.019 | |
| bootstrapAUC | 11.486 | 0.586 | 21.644 | |
| common_sigAnnotData | 0.001 | 0.001 | 0.001 | |
| compareAlgs | 1.864 | 0.177 | 3.930 | |
| compareBoxplots | 1.100 | 0.033 | 2.030 | |
| deseq2_norm_rle | 0.268 | 0.019 | 0.514 | |
| distinctColors | 0.001 | 0.000 | 0.001 | |
| evaluateOriginalModel | 1.113 | 0.016 | 1.942 | |
| mkAssay | 2.820 | 0.094 | 5.172 | |
| plotQuantitative | 2.232 | 0.101 | 3.948 | |
| runTBsigProfiler | 0.349 | 0.011 | 0.572 | |
| sigAnnotData | 0.001 | 0.001 | 0.002 | |
| signatureBoxplot | 0.982 | 0.035 | 1.658 | |
| signatureGeneHeatmap | 4.551 | 0.097 | 8.274 | |
| signatureHeatmap | 0.904 | 0.027 | 1.689 | |
| signatureROCplot | 0.868 | 0.019 | 1.523 | |
| signatureROCplot_CI | 7.138 | 0.117 | 12.090 | |
| tableAUC | 0.807 | 0.058 | 1.341 | |