Back to Multiple platform build/check report for BioC 3.17 |
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This page was generated on 2023-04-12 10:55:28 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
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 PathoStat package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PathoStat.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
Package 1463/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
PathoStat 1.25.0 (landing page) Solaiappan Manimaran
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ||||||||||
Package: PathoStat |
Version: 1.25.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:PathoStat.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings PathoStat_1.25.0.tar.gz |
StartedAt: 2023-04-11 22:17:33 -0400 (Tue, 11 Apr 2023) |
EndedAt: 2023-04-11 22:28:14 -0400 (Tue, 11 Apr 2023) |
EllapsedTime: 641.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: PathoStat.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:PathoStat.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings PathoStat_1.25.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/PathoStat.Rcheck’ * using R version 4.3.0 alpha (2023-04-03 r84154) * using platform: x86_64-pc-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 22.04.2 LTS * using session charset: UTF-8 * checking for file ‘PathoStat/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘PathoStat’ version ‘1.25.0’ * 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 ‘PathoStat’ 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 ... NOTE Namespaces in Imports field not imported from: ‘ComplexHeatmap’ ‘RColorBrewer’ All declared Imports should be used. * 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 Bootstrap_LOOCV_LR_AUC 12.684 0.696 13.477 getSignatureFromMultipleGlmnet 10.099 0.263 11.360 LOOAUC_simple_multiple_one_df 3.873 0.151 9.269 LOOAUC_simple_multiple_noplot_one_df 3.698 0.191 5.763 * 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 ... ‘PathoStat-vignette.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.17-bioc/meat/PathoStat.Rcheck/00check.log’ for details.
PathoStat.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL PathoStat ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’ * installing *source* package ‘PathoStat’ ... ** 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 (PathoStat)
PathoStat.Rcheck/tests/testthat.Rout
R version 4.3.0 alpha (2023-04-03 r84154) 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. > library(testthat) > library(PathoStat) > > test_check("PathoStat") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ] > > proc.time() user system elapsed 17.475 0.774 25.622
PathoStat.Rcheck/PathoStat-Ex.timings
name | user | system | elapsed | |
Bootstrap_LOOCV_LR_AUC | 12.684 | 0.696 | 13.477 | |
Chisq_Test_Pam | 0.008 | 0.000 | 0.007 | |
Fisher_Test_Pam | 0.005 | 0.004 | 0.009 | |
GET_PAM | 0.005 | 0.000 | 0.005 | |
LOOAUC_simple_multiple_noplot_one_df | 3.698 | 0.191 | 5.763 | |
LOOAUC_simple_multiple_one_df | 3.873 | 0.151 | 9.269 | |
PathoStat-class | 0.124 | 0.012 | 0.288 | |
TranslateIdToTaxLevel | 0.002 | 0.003 | 0.005 | |
Wilcox_Test_df | 0.021 | 0.004 | 0.057 | |
findRAfromCount | 0.430 | 0.000 | 0.881 | |
findTaxonMat | 0.159 | 0.017 | 0.370 | |
findTaxonomy | 0.148 | 0.008 | 0.328 | |
findTaxonomy300 | 0.162 | 0.000 | 0.334 | |
getShinyInput | 0.001 | 0.000 | 0.001 | |
getShinyInputCombat | 0 | 0 | 0 | |
getShinyInputOrig | 0 | 0 | 0 | |
getSignatureFromMultipleGlmnet | 10.099 | 0.263 | 11.360 | |
grepTid | 0 | 0 | 0 | |
loadPathoscopeReports | 0.002 | 0.000 | 0.002 | |
loadPstat | 0.003 | 0.000 | 0.002 | |
log2CPM | 0.002 | 0.000 | 0.002 | |
percent | 0.001 | 0.000 | 0.001 | |
phyloseq_to_edgeR | 0.060 | 0.008 | 0.068 | |
plotPCAPlotly | 0.227 | 0.040 | 0.267 | |
plotPCoAPlotly | 0.143 | 0.011 | 0.154 | |
readPathoscopeData | 0.039 | 0.004 | 0.043 | |
runPathoStat | 0.089 | 0.004 | 0.093 | |
savePstat | 0.007 | 0.000 | 0.007 | |
setShinyInput | 0 | 0 | 0 | |
setShinyInputCombat | 0 | 0 | 0 | |
setShinyInputOrig | 0 | 0 | 0 | |
summarizeTable | 0.004 | 0.000 | 0.004 | |