Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-10-16 12:32:15 -0400 (Wed, 16 Oct 2019).
Package 1682/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
TRONCO 2.16.2 Luca De Sano
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: TRONCO |
Version: 2.16.2 |
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TRONCO.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings TRONCO_2.16.2.tar.gz |
StartedAt: 2019-10-16 07:43:02 -0400 (Wed, 16 Oct 2019) |
EndedAt: 2019-10-16 07:52:24 -0400 (Wed, 16 Oct 2019) |
EllapsedTime: 561.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: TRONCO.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TRONCO.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings TRONCO_2.16.2.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/TRONCO.Rcheck' * using R version 3.6.1 (2019-07-05) * 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 '2.16.2' * 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 * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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' ... OK * checking examples ... ** running examples for arch 'i386' ... OK Examples with CPU or elapsed time > 5s user system elapsed tronco.kfold.posterr 0.28 0.19 15.56 tronco.bootstrap 0.19 0.16 23.39 tronco.kfold.prederr 0.20 0.13 14.55 ** running examples for arch 'x64' ... OK Examples with CPU or elapsed time > 5s user system elapsed tronco.kfold.posterr 0.41 0.15 15.95 tronco.bootstrap 0.30 0.11 24.81 tronco.kfold.prederr 0.31 0.06 16.19 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'testthat.R' OK ** running tests for arch 'x64' ... 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
TRONCO.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/TRONCO_2.16.2.tar.gz && rm -rf TRONCO.buildbin-libdir && mkdir TRONCO.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TRONCO.buildbin-libdir TRONCO_2.16.2.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL TRONCO_2.16.2.zip && rm TRONCO_2.16.2.tar.gz TRONCO_2.16.2.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 254k 100 254k 0 0 3706k 0 --:--:-- --:--:-- --:--:-- 4169k install for i386 * installing *source* package 'TRONCO' ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 install for x64 * installing *source* package 'TRONCO' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'TRONCO' as TRONCO_2.16.2.zip * DONE (TRONCO) * installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library' package 'TRONCO' successfully unpacked and MD5 sums checked
TRONCO.Rcheck/tests_i386/testthat.Rout R version 3.6.1 (2019-07-05) -- "Action of the Toes" Copyright (C) 2019 The R Foundation for Statistical Computing Platform: i386-w64-mingw32/i386 (32-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 9 edges out of 51 (18%) *** 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 8 edges out of 54 (15%) *** 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 6 edges out of 50 (12%) *** 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 7 edges out of 51 (14%) *** Performing likelihood-fit with regularization: no_reg . *** Evaluating BIC / AIC / LogLik informations. The reconstruction has been successfully completed in 00h:00m:01s == testthat results =========================================================== [ OK: 225 | SKIPPED: 0 | WARNINGS: 31 | FAILED: 0 ] > > proc.time() user system elapsed 44.78 0.87 148.06 |
TRONCO.Rcheck/tests_x64/testthat.Rout R version 3.6.1 (2019-07-05) -- "Action of the Toes" Copyright (C) 2019 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 11 edges out of 58 (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 6 edges out of 51 (12%) *** 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 52 (13%) *** 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 6 edges out of 48 (12%) *** Performing likelihood-fit with regularization: no_reg . *** Evaluating BIC / AIC / LogLik informations. The reconstruction has been successfully completed in 00h:00m:02s == testthat results =========================================================== [ OK: 225 | SKIPPED: 0 | WARNINGS: 28 | FAILED: 0 ] > > proc.time() user system elapsed 53.00 0.71 153.57 |
TRONCO.Rcheck/examples_i386/TRONCO-Ex.timings
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TRONCO.Rcheck/examples_x64/TRONCO-Ex.timings
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