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 11:05:22 -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 TRONCO package: - Please 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 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 2103/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
TRONCO 2.30.0 (landing page) Luca De Sano
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
Package: TRONCO |
Version: 2.30.0 |
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:TRONCO.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings TRONCO_2.30.0.tar.gz |
StartedAt: 2023-04-11 00:41:40 -0400 (Tue, 11 Apr 2023) |
EndedAt: 2023-04-11 00:45:09 -0400 (Tue, 11 Apr 2023) |
EllapsedTime: 208.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: TRONCO.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:TRONCO.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings TRONCO_2.30.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/TRONCO.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 ‘TRONCO/DESCRIPTION’ ... OK * this is package ‘TRONCO’ version ‘2.30.0’ * 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 ‘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 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 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.bootstrap 0.123 0.016 9.228 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘vignette.Rnw’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: OK
TRONCO.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL TRONCO ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-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 4.2.3 (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. > 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 53 (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:01s *** 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 8 edges out of 56 (14%) *** Performing likelihood-fit with regularization: no_reg . *** Evaluating BIC / AIC / LogLik informations. The reconstruction has been successfully completed in 00h:00m:01s *** 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 7 edges out of 51 (14%) *** 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:01s *** 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 53 (9%) *** Performing likelihood-fit with regularization: no_reg . *** Evaluating BIC / AIC / LogLik informations. The reconstruction has been successfully completed in 00h:00m:01s [ FAIL 0 | WARN 14 | SKIP 0 | PASS 225 ] [ FAIL 0 | WARN 14 | SKIP 0 | PASS 225 ] > > proc.time() user system elapsed 34.073 0.964 75.915
TRONCO.Rcheck/TRONCO-Ex.timings
name | user | system | elapsed | |
TCGA.multiple.samples | 0.017 | 0.000 | 0.017 | |
TCGA.remove.multiple.samples | 0.011 | 0.004 | 0.014 | |
TCGA.shorten.barcodes | 0.070 | 0.004 | 0.073 | |
annotate.description | 0.009 | 0.000 | 0.008 | |
annotate.stages | 0.006 | 0.000 | 0.006 | |
as.adj.matrix | 0.004 | 0.005 | 0.010 | |
as.alterations | 0.002 | 0.002 | 0.003 | |
as.bootstrap.scores | 0.182 | 0.001 | 0.181 | |
as.colors | 0.002 | 0.000 | 0.001 | |
as.confidence | 0.003 | 0.008 | 0.010 | |
as.description | 0.002 | 0.000 | 0.001 | |
as.events | 0.002 | 0.000 | 0.001 | |
as.events.in.patterns | 0.000 | 0.003 | 0.003 | |
as.events.in.sample | 0.000 | 0.003 | 0.003 | |
as.gene | 0.003 | 0.001 | 0.003 | |
as.genes | 0.001 | 0.000 | 0.002 | |
as.genes.in.patterns | 0.003 | 0.000 | 0.003 | |
as.genotypes | 0.007 | 0.000 | 0.007 | |
as.hypotheses | 0.003 | 0.000 | 0.003 | |
as.joint.probs | 0.009 | 0.000 | 0.009 | |
as.kfold.eloss | 0.064 | 0.000 | 0.064 | |
as.kfold.posterr | 0.082 | 0.000 | 0.082 | |
as.kfold.prederr | 0.079 | 0.004 | 0.082 | |
as.marginal.probs | 0.000 | 0.003 | 0.004 | |
as.models | 0.009 | 0.007 | 0.017 | |
as.parameters | 0.003 | 0.001 | 0.002 | |
as.pathway | 0.001 | 0.004 | 0.006 | |
as.patterns | 0.001 | 0.000 | 0.002 | |
as.samples | 0.001 | 0.000 | 0.002 | |
as.selective.advantage.relations | 0.081 | 0.004 | 0.085 | |
as.stages | 0.006 | 0.000 | 0.005 | |
as.types | 0.001 | 0.000 | 0.001 | |
as.types.in.patterns | 0.003 | 0.000 | 0.004 | |
change.color | 0.002 | 0.000 | 0.002 | |
consolidate.data | 0.024 | 0.000 | 0.023 | |
delete.event | 0.000 | 0.004 | 0.004 | |
delete.gene | 0.004 | 0.000 | 0.004 | |
delete.hypothesis | 0.021 | 0.003 | 0.025 | |
delete.model | 0.003 | 0.001 | 0.003 | |
delete.pattern | 0.01 | 0.00 | 0.01 | |
delete.samples | 0.002 | 0.000 | 0.003 | |
delete.type | 0.004 | 0.000 | 0.004 | |
duplicates | 0.002 | 0.000 | 0.001 | |
enforce.numeric | 0.002 | 0.000 | 0.002 | |
enforce.string | 0.002 | 0.000 | 0.002 | |
events.selection | 0.003 | 0.000 | 0.003 | |
export.graphml | 0.068 | 0.000 | 0.068 | |
export.mutex | 0.008 | 0.000 | 0.008 | |
has.duplicates | 0.001 | 0.000 | 0.002 | |
has.model | 0.007 | 0.001 | 0.007 | |
has.stages | 0.001 | 0.006 | 0.008 | |
import.GISTIC | 0.006 | 0.001 | 0.006 | |
import.MAF | 0.082 | 0.063 | 0.145 | |
intersect.datasets | 0.002 | 0.001 | 0.001 | |
is.compliant | 0.003 | 0.000 | 0.002 | |
join.events | 0.001 | 0.003 | 0.004 | |
join.types | 0.035 | 0.008 | 0.043 | |
keysToNames | 0.005 | 0.000 | 0.004 | |
nameToKey | 0.003 | 0.000 | 0.002 | |
nevents | 0.001 | 0.000 | 0.001 | |
ngenes | 0.001 | 0.000 | 0.002 | |
nhypotheses | 0.002 | 0.000 | 0.001 | |
npatterns | 0.001 | 0.000 | 0.001 | |
nsamples | 0.002 | 0.000 | 0.001 | |
ntypes | 0.001 | 0.000 | 0.001 | |
oncoprint.cbio | 0.002 | 0.003 | 0.005 | |
order.frequency | 0.003 | 0.004 | 0.007 | |
pheatmap | 0.028 | 0.004 | 0.033 | |
rank.recurrents | 0.003 | 0.000 | 0.004 | |
rename.gene | 0.002 | 0.000 | 0.002 | |
rename.type | 0.002 | 0.000 | 0.002 | |
samples.selection | 0.002 | 0.000 | 0.003 | |
trim | 0.001 | 0.001 | 0.003 | |
tronco.bootstrap | 0.123 | 0.016 | 9.228 | |
tronco.caprese | 0.124 | 0.000 | 0.125 | |
tronco.capri | 1.669 | 0.052 | 1.720 | |
tronco.chowliu | 1.122 | 0.004 | 1.126 | |
tronco.edmonds | 0.994 | 0.004 | 0.997 | |
tronco.gabow | 1.066 | 0.000 | 1.065 | |
tronco.kfold.eloss | 0.063 | 0.020 | 0.082 | |
tronco.kfold.posterr | 0.137 | 0.025 | 2.781 | |
tronco.kfold.prederr | 0.124 | 0.030 | 2.495 | |
tronco.plot | 0.115 | 0.012 | 0.127 | |
tronco.prim | 2.246 | 0.092 | 2.338 | |
view | 0.004 | 0.000 | 0.004 | |
which.samples | 0.002 | 0.000 | 0.002 | |