Luca De Sano
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/TRONCO |
| git_branch: master |
| git_last_commit: 6080e92 |
| git_last_commit_date: 2021-10-26 12:18:20 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:55 -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 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? 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 2015/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| TRONCO 2.27.0 (landing page) Luca De Sano
| 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: TRONCO |
| Version: 2.27.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TRONCO.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings TRONCO_2.27.0.tar.gz |
| StartedAt: 2022-03-17 20:32:43 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 20:36:07 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 204.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: TRONCO.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TRONCO.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings TRONCO_2.27.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/TRONCO.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 'TRONCO/DESCRIPTION' ... OK
* this is package 'TRONCO' version '2.27.0'
* 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 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 data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... NOTE
Files named as vignettes but with no recognized vignette engine:
'vignettes/1_introduction.Rmd'
'vignettes/2_loading_data.Rmd'
'vignettes/3_data_visualization.Rmd'
'vignettes/4_data_manipulation.Rmd'
'vignettes/5_model_inference.Rmd'
'vignettes/6_post_reconstruction.Rmd'
'vignettes/7_import_export.Rmd'
(Is a VignetteBuilder field missing?)
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
tronco.kfold.posterr 0.16 0.05 5.04
tronco.bootstrap 0.12 0.00 12.24
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
'D:/biocbuild/bbs-3.15-bioc/meat/TRONCO.Rcheck/00check.log'
for details.
TRONCO.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL TRONCO
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-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
converting help for package 'TRONCO'
finding HTML links ... done
AND html
OR html
TCGA.map.clinical.data html
TCGA.multiple.samples html
TCGA.remove.multiple.samples html
TCGA.shorten.barcodes html
XOR html
aCML html
annotate.description html
annotate.stages html
as.adj.matrix html
as.alterations html
as.bootstrap.scores html
as.colors html
as.conditional.probs html
as.confidence html
as.description html
as.events html
as.events.in.patterns html
as.events.in.sample html
as.gene html
as.genes html
as.genes.in.patterns html
as.genotypes html
as.hypotheses html
as.joint.probs html
as.kfold.eloss html
as.kfold.posterr html
as.kfold.prederr html
as.marginal.probs html
as.models html
as.parameters html
as.pathway html
as.patterns html
as.samples html
as.selective.advantage.relations html
as.stages html
as.types html
as.types.in.patterns html
cbio.query html
change.color html
consolidate.data html
crc_gistic html
crc_maf html
crc_plain html
delete.event html
delete.gene html
delete.hypothesis html
delete.model html
delete.pattern html
delete.samples html
delete.type html
duplicates html
ebind html
enforce.numeric html
enforce.string html
events.selection html
export.graphml html
export.mutex html
export.nbs.input html
extract.MAF.HuGO.Entrez.map html
genes.table.report html
has.duplicates html
has.model html
has.stages html
hypothesis.add html
hypothesis.add.group html
hypothesis.add.homologous html
import.GISTIC html
import.MAF html
import.genotypes html
import.model html
import.mutex.groups html
intersect.datasets html
is.compliant html
join.events html
join.types html
keysToNames html
maf html
muts html
nameToKey html
nevents html
ngenes html
nhypotheses html
npatterns html
nsamples html
ntypes html
oncoprint html
oncoprint.cbio html
order.frequency html
pathway.visualization html
pheatmap html
rank.recurrents html
rename.gene html
rename.type html
samples.selection html
sbind html
ssplit html
stage html
test_dataset html
test_dataset_no_hypos html
test_model html
test_model_kfold html
trim html
tronco.bootstrap html
tronco.caprese html
tronco.capri html
tronco.chowliu html
tronco.edmonds html
tronco.gabow html
tronco.kfold.eloss html
tronco.kfold.posterr html
tronco.kfold.prederr html
tronco.pattern.plot html
tronco.plot html
tronco.prim html
view html
which.samples 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 (TRONCO)
Making 'packages.html' ... done
TRONCO.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.
> 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 6 edges out of 56 (11%)
*** 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 9 edges out of 58 (16%)
*** 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 7 edges out of 48 (15%)
*** 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 8 edges out of 50 (16%)
*** 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 28 | SKIP 0 | PASS 225 ]
[ FAIL 0 | WARN 28 | SKIP 0 | PASS 225 ]
>
> proc.time()
user system elapsed
39.54 0.95 90.95
TRONCO.Rcheck/TRONCO-Ex.timings
| name | user | system | elapsed | |
| TCGA.multiple.samples | 0.03 | 0.00 | 0.03 | |
| TCGA.remove.multiple.samples | 0.00 | 0.02 | 0.02 | |
| TCGA.shorten.barcodes | 0.00 | 0.01 | 0.01 | |
| annotate.description | 0.01 | 0.00 | 0.02 | |
| annotate.stages | 0.02 | 0.00 | 0.02 | |
| as.adj.matrix | 0.00 | 0.02 | 0.01 | |
| as.alterations | 0 | 0 | 0 | |
| as.bootstrap.scores | 0.02 | 0.03 | 0.05 | |
| as.colors | 0 | 0 | 0 | |
| as.confidence | 0.03 | 0.00 | 0.03 | |
| as.description | 0 | 0 | 0 | |
| as.events | 0.01 | 0.00 | 0.01 | |
| as.events.in.patterns | 0 | 0 | 0 | |
| as.events.in.sample | 0.02 | 0.00 | 0.02 | |
| as.gene | 0 | 0 | 0 | |
| as.genes | 0.00 | 0.01 | 0.02 | |
| as.genes.in.patterns | 0 | 0 | 0 | |
| as.genotypes | 0.01 | 0.00 | 0.01 | |
| as.hypotheses | 0 | 0 | 0 | |
| as.joint.probs | 0.02 | 0.00 | 0.01 | |
| as.kfold.eloss | 0.06 | 0.01 | 0.08 | |
| as.kfold.posterr | 0.10 | 0.02 | 0.11 | |
| as.kfold.prederr | 0.07 | 0.00 | 0.07 | |
| as.marginal.probs | 0.00 | 0.01 | 0.02 | |
| as.models | 0.02 | 0.02 | 0.03 | |
| as.parameters | 0 | 0 | 0 | |
| as.pathway | 0 | 0 | 0 | |
| as.patterns | 0.00 | 0.01 | 0.02 | |
| as.samples | 0 | 0 | 0 | |
| as.selective.advantage.relations | 0.05 | 0.00 | 0.04 | |
| as.stages | 0.00 | 0.02 | 0.02 | |
| as.types | 0 | 0 | 0 | |
| as.types.in.patterns | 0.01 | 0.00 | 0.01 | |
| change.color | 0 | 0 | 0 | |
| consolidate.data | 0.02 | 0.00 | 0.02 | |
| delete.event | 0.00 | 0.01 | 0.02 | |
| delete.gene | 0.01 | 0.00 | 0.01 | |
| delete.hypothesis | 0.00 | 0.04 | 0.03 | |
| delete.model | 0 | 0 | 0 | |
| delete.pattern | 0.02 | 0.00 | 0.02 | |
| delete.samples | 0 | 0 | 0 | |
| delete.type | 0.01 | 0.00 | 0.01 | |
| duplicates | 0 | 0 | 0 | |
| enforce.numeric | 0 | 0 | 0 | |
| enforce.string | 0.02 | 0.00 | 0.02 | |
| events.selection | 0 | 0 | 0 | |
| export.graphml | 0.06 | 0.00 | 0.06 | |
| export.mutex | 0.02 | 0.00 | 0.02 | |
| has.duplicates | 0 | 0 | 0 | |
| has.model | 0 | 0 | 0 | |
| has.stages | 0.00 | 0.01 | 0.01 | |
| import.GISTIC | 0 | 0 | 0 | |
| import.MAF | 0.10 | 0.00 | 0.09 | |
| intersect.datasets | 0 | 0 | 0 | |
| is.compliant | 0 | 0 | 0 | |
| join.events | 0.00 | 0.02 | 0.02 | |
| join.types | 0.04 | 0.00 | 0.05 | |
| keysToNames | 0.02 | 0.00 | 0.01 | |
| nameToKey | 0 | 0 | 0 | |
| nevents | 0.02 | 0.00 | 0.02 | |
| ngenes | 0 | 0 | 0 | |
| nhypotheses | 0 | 0 | 0 | |
| npatterns | 0.00 | 0.01 | 0.01 | |
| nsamples | 0 | 0 | 0 | |
| ntypes | 0 | 0 | 0 | |
| oncoprint.cbio | 0 | 0 | 0 | |
| order.frequency | 0.00 | 0.02 | 0.02 | |
| pheatmap | 0.03 | 0.00 | 0.03 | |
| rank.recurrents | 0 | 0 | 0 | |
| rename.gene | 0 | 0 | 0 | |
| rename.type | 0 | 0 | 0 | |
| samples.selection | 0 | 0 | 0 | |
| trim | 0 | 0 | 0 | |
| tronco.bootstrap | 0.12 | 0.00 | 12.24 | |
| tronco.caprese | 0.14 | 0.00 | 0.39 | |
| tronco.capri | 2.14 | 0.19 | 2.81 | |
| tronco.chowliu | 1.11 | 0.05 | 1.16 | |
| tronco.edmonds | 0.86 | 0.00 | 0.86 | |
| tronco.gabow | 0.80 | 0.00 | 0.79 | |
| tronco.kfold.eloss | 0.09 | 0.01 | 0.11 | |
| tronco.kfold.posterr | 0.16 | 0.05 | 5.04 | |
| tronco.kfold.prederr | 0.16 | 0.03 | 3.84 | |
| tronco.plot | 0.12 | 0.00 | 0.12 | |
| tronco.prim | 1.56 | 0.10 | 1.66 | |
| view | 0 | 0 | 0 | |
| which.samples | 0 | 0 | 0 | |