Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2024-04-17 11:36:02 -0400 (Wed, 17 Apr 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4676 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4437 |
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 |
Package 1003/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
IFAA 1.4.0 (landing page) Zhigang Li
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
To the developers/maintainers of the IFAA package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/IFAA.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: IFAA |
Version: 1.4.0 |
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:IFAA.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings IFAA_1.4.0.tar.gz |
StartedAt: 2024-04-15 23:54:48 -0400 (Mon, 15 Apr 2024) |
EndedAt: 2024-04-16 00:06:08 -0400 (Tue, 16 Apr 2024) |
EllapsedTime: 679.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: IFAA.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:IFAA.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings IFAA_1.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/IFAA.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘IFAA/DESCRIPTION’ ... OK * this is package ‘IFAA’ version ‘1.4.0’ * 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 ‘IFAA’ 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed IFAA 23.633 0.969 109.733 MZILN 1.534 0.149 22.736 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘IFAA.Rmd’ using ‘UTF-8’... OK OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: OK
IFAA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL IFAA ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’ * installing *source* package ‘IFAA’ ... ** using staged installation ** R ** 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 (IFAA)
IFAA.Rcheck/tests/runTests.Rout
R version 4.3.3 (2024-02-29) -- "Angel Food Cake" Copyright (C) 2024 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. > BiocGenerics:::testPackage("IFAA") Data dimensions (after removing missing data if any): 40 samples 20 taxa/OTU/ASV 2 testCov variables in the analysis These are the testCov variables: x1, x2 1 ctrlCov variables in the analysis These are the ctrlCov variables: x3 1 binary covariates in the analysis These are the binary covariates: x2 25 percent of microbiome sequencing reads are zero Start Phase 1 analysis 2 parallel jobs are registered for the analysis. 33 percent of phase 1 analysis has been done and it took 0.28 minutes 2 parallel jobs are registered for the analysis. 100 percent of phase 1 analysis has been done and it took 0.52 minutes Start Phase 2 parameter estimation 2 parallel jobs are registered for analyzing reference taxa in Phase 2 50 percent of Phase 2 is done and it took 0.2 minutes 2 parallel jobs are registered for analyzing reference taxa in Phase 2 Entire Phase 2 parameter estimation done and took 0.389 minutes. The entire analysis took 0.91 minutes Data dimensions (after removing missing data if any): 40 samples 20 taxa/OTU/ASV 3 testCov variables in the analysis These are the testCov variables: x1, x2, x3 0 ctrlCov variables in the analysis 1 binary covariates in the analysis These are the binary covariates: x2 25 percent of microbiome sequencing reads are zero 2 parallel jobs are registered for analyzing reference taxa in Phase 2 Estimation done for the 1th denominator taxon: rawCount10 and it took 0.19 minutes The entire analysis took 0.19 minutes Data dimensions (after removing missing data if any): 5 samples 20 taxa/OTU/ASV 2 testCov variables in the analysis These are the testCov variables: x1, x2 4 ctrlCov variables in the analysis These are the ctrlCov variables: x3, x4, x5, x6 1 binary covariates in the analysis These are the binary covariates: x2 0 percent of microbiome sequencing reads are zero Start Phase 1 analysis 2 parallel jobs are registered for the analysis. 33 percent of phase 1 analysis has been done and it took 0.24 minutes 2 parallel jobs are registered for the analysis. 67 percent of phase 1 analysis has been done and it took 0.47 minutes 2 parallel jobs are registered for the analysis. 100 percent of phase 1 analysis has been done and it took 0.71 minutes Start Phase 2 parameter estimation 2 parallel jobs are registered for analyzing reference taxa in Phase 2 50 percent of Phase 2 is done and it took 0.559 minutes 2 parallel jobs are registered for analyzing reference taxa in Phase 2 Entire Phase 2 parameter estimation done and took 1.046 minutes. The entire analysis took 1.75 minutes RUNIT TEST PROTOCOL -- Tue Apr 16 00:02:50 2024 *********************************************** Number of test functions: 3 Number of errors: 0 Number of failures: 0 1 Test Suite : IFAA RUnit Tests - 3 test functions, 0 errors, 0 failures Number of test functions: 3 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 35.267 2.945 180.637
IFAA.Rcheck/IFAA-Ex.timings
name | user | system | elapsed | |
IFAA | 23.633 | 0.969 | 109.733 | |
MZILN | 1.534 | 0.149 | 22.736 | |