Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-02-08 01:15:02 -0000 (Wed, 08 Feb 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
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To the developers/maintainers of the EnMCB package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/EnMCB.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 599/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
EnMCB 1.11.1 (landing page) Xin Yu
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
Package: EnMCB |
Version: 1.11.1 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:EnMCB.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings EnMCB_1.11.1.tar.gz |
StartedAt: 2023-02-07 00:47:36 -0000 (Tue, 07 Feb 2023) |
EndedAt: 2023-02-07 00:54:19 -0000 (Tue, 07 Feb 2023) |
EllapsedTime: 402.9 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: EnMCB.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:EnMCB.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings EnMCB_1.11.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/EnMCB.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘EnMCB/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘EnMCB’ version ‘1.11.1’ * 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 ‘EnMCB’ 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’ ... OK * checking examples ... ERROR Running examples in ‘EnMCB-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: ensemble_prediction > ### Title: fitting function using stacking ensemble model for Methylation > ### Correlation Block > ### Aliases: ensemble_prediction > > ### ** Examples > > library(survival) > #import datasets > data(demo_survival_data) > datamatrix<-create_demo() > data(demo_MCBinformation) > #select MCB with at least 3 CpGs. > demo_MCBinformation<-demo_MCBinformation[demo_MCBinformation[,"CpGs_num"]>2,] > trainingset<-colnames(datamatrix) %in% sample(colnames(datamatrix),0.6*length(colnames(datamatrix))) > testingset<-!trainingset > #select one MCB > select_single_one=1 > em<-ensemble_model(t(demo_MCBinformation[select_single_one,]), + training_set=datamatrix[,trainingset], + Surv_training=demo_survival_data[trainingset]) Killed * 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.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: ... --- re-building ‘vignette.Rmd’ using rmarkdown Killed * checking PDF version of manual ... OK * DONE Status: 2 ERRORs See ‘/home/biocbuild/bbs-3.17-bioc/meat/EnMCB.Rcheck/00check.log’ for details.
EnMCB.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL EnMCB ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘EnMCB’ ... ** 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 (EnMCB)
EnMCB.Rcheck/tests/testthat.Rout
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-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. > library(testthat) > library(EnMCB) > > test_check("EnMCB") Start calculating the correlation, this may take a while... (or you can try to use IdentifyMCB_parallel function instead) | | | 0% | |################## | 25% | |################################### | 50% | |#################################################### | 75% | |######################################################################| 100% Now gathering the results, please wait ... Statistics ( 4 MCBs in total): chr2 : total MCBs: 1 Mean Length: 167 (Range: 167 167 ) chr6 : total MCBs: 1 Mean Length: 129 (Range: 129 129 ) chr8 : total MCBs: 2 Mean Length: 303.5 (Range: 181 426 ) [ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ] > > proc.time() user system elapsed 26.234 1.414 33.550
EnMCB.Rcheck/EnMCB-Ex.timings
name | user | system | elapsed | |
CompareMCB | 0.031 | 0.000 | 0.031 | |
DiffMCB | 0.259 | 0.000 | 0.259 | |
IdentifyMCB | 22.566 | 0.452 | 23.057 | |
IdentifyMCB_parallel | 10.716 | 0.136 | 10.940 | |
create_demo | 1.053 | 0.012 | 1.066 | |
draw_survival_curve | 3.608 | 0.033 | 3.727 | |
ensemble_model | 13.046 | 0.247 | 13.551 | |