Luca De Sano
| Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024) |
| git_url: https://git.bioconductor.org/packages/TRONCO |
| git_branch: devel |
| git_last_commit: 3152235 |
| git_last_commit_date: 2024-04-30 10:41:10 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-06-11 15:41 -0400 (Tue, 11 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
| 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 2155/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| TRONCO 2.37.0 (landing page) Luca De Sano
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the TRONCO package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TRONCO.git to reflect on this report. See Troubleshooting Build Report for more information. - 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: TRONCO |
| Version: 2.37.0 |
| Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TRONCO.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings TRONCO_2.37.0.tar.gz |
| StartedAt: 2024-06-10 11:41:16 -0400 (Mon, 10 Jun 2024) |
| EndedAt: 2024-06-10 11:51:21 -0400 (Mon, 10 Jun 2024) |
| EllapsedTime: 605.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: TRONCO.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TRONCO.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings TRONCO_2.37.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/TRONCO.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'TRONCO/DESCRIPTION' ... OK
* this is package 'TRONCO' version '2.37.0'
* 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 'TRONCO' 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 code 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 whether startup messages can be suppressed ... 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 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
tronco.kfold.prederr 0.11 0.09 9.39
tronco.kfold.posterr 0.14 0.05 9.28
tronco.bootstrap 0.11 0.04 16.10
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'testthat.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
TRONCO.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL TRONCO ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'TRONCO' ... ** using staged installation ** R ** data ** 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 (TRONCO)
TRONCO.Rcheck/tests/testthat.Rout
R version 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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.
> Sys.setenv("R_TESTS" = "")
>
> library(testthat)
> library(TRONCO)
>
> test_check("TRONCO")
*** Checking input events.
*** Inferring a progression model with the following settings.
Dataset size: n = 40, m = 30.
Algorithm: CAPRESE with shrinkage coefficient: 0.5.
*** Evaluating LogLik informations.
The reconstruction has been successfully completed in 00h:00m:00s
*** Checking input events.
*** Inferring a progression model with the following settings.
Dataset size: n = 40, m = 30.
Algorithm: Edmonds with "no_reg" regularization Random seed: NULL.
Bootstrap iterations (Wilcoxon): 1.
exhaustive bootstrap: TRUE.
p-value: 0.05.
minimum bootstrapped scores: 3.
*** Bootstraping selective advantage scores (prima facie).
....
Evaluating "temporal priority" (Wilcoxon, p-value 0.05)
Evaluating "probability raising" (Wilcoxon, p-value 0.05)
*** Loop detection found loops to break.
Removed 10 edges out of 54 (19%)
*** Performing likelihood-fit with regularization: no_reg and score: pmi .
*** Evaluating BIC / AIC / LogLik informations.
The reconstruction has been successfully completed in 00h:00m:02s
*** Checking input events.
*** Inferring a progression model with the following settings.
Dataset size: n = 40, m = 30.
Algorithm: Gabow with "no_reg" regularization Random seed: NULL.
Bootstrap iterations (Wilcoxon): 1.
exhaustive bootstrap: TRUE.
p-value: 0.05.
minimum bootstrapped scores: 3.
*** Bootstraping selective advantage scores (prima facie).
.......
Evaluating "temporal priority" (Wilcoxon, p-value 0.05)
Evaluating "probability raising" (Wilcoxon, p-value 0.05)
*** Loop detection found loops to break.
Removed 7 edges out of 50 (14%)
*** Performing likelihood-fit with regularization: no_reg .
*** Evaluating BIC / AIC / LogLik informations.
The reconstruction has been successfully completed in 00h:00m:02s
*** Checking input events.
*** Inferring a progression model with the following settings.
Dataset size: n = 40, m = 30.
Algorithm: Chow Liu with "bic, aic" regularization Random seed: NULL.
Bootstrap iterations (Wilcoxon): 1.
exhaustive bootstrap: TRUE.
p-value: 0.05.
minimum bootstrapped scores: 3.
*** Bootstraping selective advantage scores (prima facie).
.......
Evaluating "temporal priority" (Wilcoxon, p-value 0.05)
Evaluating "probability raising" (Wilcoxon, p-value 0.05)
*** Loop detection found loops to break.
Removed 3 edges out of 46 (7%)
*** Performing likelihood-fit with regularization bic .
*** Performing likelihood-fit with regularization aic .
*** Evaluating BIC / AIC / LogLik informations.
The reconstruction has been successfully completed in 00h:00m:02s
*** Checking input events.
*** Inferring a progression model with the following settings.
Dataset size: n = 40, m = 30.
Algorithm: Prim with "no_reg" regularization Random seed: NULL.
Bootstrap iterations (Wilcoxon): 1.
exhaustive bootstrap: TRUE.
p-value: 0.05.
minimum bootstrapped scores: 3.
*** Bootstraping selective advantage scores (prima facie).
....
Evaluating "temporal priority" (Wilcoxon, p-value 0.05)
Evaluating "probability raising" (Wilcoxon, p-value 0.05)
*** Loop detection found loops to break.
Removed 5 edges out of 50 (10%)
*** Performing likelihood-fit with regularization: no_reg .
*** Evaluating BIC / AIC / LogLik informations.
The reconstruction has been successfully completed in 00h:00m:02s
[ FAIL 0 | WARN 23 | SKIP 0 | PASS 225 ]
[ FAIL 0 | WARN 23 | SKIP 0 | PASS 225 ]
>
> proc.time()
user system elapsed
42.53 9.17 211.75
TRONCO.Rcheck/TRONCO-Ex.timings
| name | user | system | elapsed | |
| TCGA.multiple.samples | 0.01 | 0.42 | 0.49 | |
| TCGA.remove.multiple.samples | 0.03 | 0.00 | 0.03 | |
| TCGA.shorten.barcodes | 0.03 | 0.00 | 0.03 | |
| annotate.description | 0.00 | 0.02 | 0.02 | |
| annotate.stages | 0.02 | 0.02 | 0.03 | |
| as.adj.matrix | 0.01 | 0.01 | 0.03 | |
| as.alterations | 0.02 | 0.00 | 0.02 | |
| as.bootstrap.scores | 0.17 | 0.00 | 0.17 | |
| as.colors | 0.00 | 0.02 | 0.01 | |
| as.confidence | 0.03 | 0.00 | 0.03 | |
| as.description | 0.00 | 0.01 | 0.02 | |
| as.events | 0 | 0 | 0 | |
| as.events.in.patterns | 0.02 | 0.00 | 0.02 | |
| as.events.in.sample | 0.01 | 0.00 | 0.01 | |
| as.gene | 0 | 0 | 0 | |
| as.genes | 0.02 | 0.00 | 0.02 | |
| as.genes.in.patterns | 0.01 | 0.00 | 0.01 | |
| as.genotypes | 0.02 | 0.00 | 0.02 | |
| as.hypotheses | 0.00 | 0.02 | 0.01 | |
| as.joint.probs | 0.01 | 0.00 | 0.02 | |
| as.kfold.eloss | 0.07 | 0.00 | 0.06 | |
| as.kfold.posterr | 0.12 | 0.00 | 0.13 | |
| as.kfold.prederr | 0.08 | 0.00 | 0.08 | |
| as.marginal.probs | 0.01 | 0.00 | 0.01 | |
| as.models | 0.02 | 0.03 | 0.05 | |
| as.parameters | 0 | 0 | 0 | |
| as.pathway | 0.00 | 0.00 | 0.01 | |
| as.patterns | 0 | 0 | 0 | |
| as.samples | 0.00 | 0.00 | 0.02 | |
| as.selective.advantage.relations | 0.09 | 0.03 | 0.12 | |
| as.stages | 0.00 | 0.02 | 0.02 | |
| as.types | 0 | 0 | 0 | |
| as.types.in.patterns | 0.02 | 0.00 | 0.02 | |
| change.color | 0.00 | 0.01 | 0.01 | |
| consolidate.data | 0.02 | 0.03 | 0.05 | |
| delete.event | 0 | 0 | 0 | |
| delete.gene | 0.01 | 0.00 | 0.01 | |
| delete.hypothesis | 0.05 | 0.02 | 0.07 | |
| delete.model | 0.00 | 0.01 | 0.01 | |
| delete.pattern | 0.00 | 0.02 | 0.02 | |
| delete.samples | 0 | 0 | 0 | |
| delete.type | 0 | 0 | 0 | |
| duplicates | 0 | 0 | 0 | |
| enforce.numeric | 0.00 | 0.01 | 0.02 | |
| enforce.string | 0 | 0 | 0 | |
| events.selection | 0.01 | 0.00 | 0.01 | |
| export.graphml | 0.13 | 0.00 | 0.13 | |
| export.mutex | 0.00 | 0.02 | 0.01 | |
| has.duplicates | 0 | 0 | 0 | |
| has.model | 0 | 0 | 0 | |
| has.stages | 0.00 | 0.02 | 0.02 | |
| import.GISTIC | 0.00 | 0.01 | 0.01 | |
| import.MAF | 0.08 | 0.02 | 0.10 | |
| intersect.datasets | 0 | 0 | 0 | |
| is.compliant | 0 | 0 | 0 | |
| join.events | 0.01 | 0.00 | 0.01 | |
| join.types | 0.03 | 0.01 | 0.05 | |
| keysToNames | 0.00 | 0.02 | 0.01 | |
| nameToKey | 0.02 | 0.00 | 0.02 | |
| nevents | 0 | 0 | 0 | |
| ngenes | 0 | 0 | 0 | |
| nhypotheses | 0 | 0 | 0 | |
| npatterns | 0 | 0 | 0 | |
| nsamples | 0 | 0 | 0 | |
| ntypes | 0 | 0 | 0 | |
| oncoprint.cbio | 0 | 0 | 0 | |
| order.frequency | 0.03 | 0.00 | 0.03 | |
| pheatmap | 0.02 | 0.00 | 0.02 | |
| rank.recurrents | 0.01 | 0.00 | 0.01 | |
| rename.gene | 0 | 0 | 0 | |
| rename.type | 0.02 | 0.00 | 0.02 | |
| samples.selection | 0 | 0 | 0 | |
| trim | 0.00 | 0.02 | 0.01 | |
| tronco.bootstrap | 0.11 | 0.04 | 16.10 | |
| tronco.caprese | 0.14 | 0.00 | 0.14 | |
| tronco.capri | 1.78 | 0.08 | 1.86 | |
| tronco.chowliu | 1.12 | 0.02 | 1.15 | |
| tronco.edmonds | 1.11 | 0.08 | 1.19 | |
| tronco.gabow | 1.13 | 0.01 | 1.14 | |
| tronco.kfold.eloss | 0.09 | 0.02 | 0.11 | |
| tronco.kfold.posterr | 0.14 | 0.05 | 9.28 | |
| tronco.kfold.prederr | 0.11 | 0.09 | 9.39 | |
| tronco.plot | 0.14 | 0.00 | 0.16 | |
| tronco.prim | 2.49 | 0.44 | 2.97 | |
| view | 0 | 0 | 0 | |
| which.samples | 0.00 | 0.02 | 0.01 | |