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This page was generated on 2023-11-02 11:40:49 -0400 (Thu, 02 Nov 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4729
palomino4Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4463
lconwaymacOS 12.6.5 Montereyx86_644.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" 4478
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.1 (2023-06-16) -- "Beagle Scouts" 4464
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 1003/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IFAA 1.4.0  (landing page)
Zhigang Li
Snapshot Date: 2023-11-01 14:05:06 -0400 (Wed, 01 Nov 2023)
git_url: https://git.bioconductor.org/packages/IFAA
git_branch: RELEASE_3_18
git_last_commit: ca5c2f7
git_last_commit_date: 2023-10-24 11:45:38 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.6.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for IFAA on kunpeng2


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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: IFAA
Version: 1.4.0
Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:IFAA.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings IFAA_1.4.0.tar.gz
StartedAt: 2023-11-02 11:24:25 -0000 (Thu, 02 Nov 2023)
EndedAt: 2023-11-02 11:34:26 -0000 (Thu, 02 Nov 2023)
EllapsedTime: 601.1 seconds
RetCode: 0
Status:   OK  
CheckDir: IFAA.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:IFAA.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings IFAA_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/IFAA.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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  27.640  1.611 137.538
MZILN  1.999  0.239  32.284
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

IFAA.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL IFAA
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.1/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)

Tests output

IFAA.Rcheck/tests/runTests.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
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.

> 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 0.4 minutes
2 parallel jobs are registered for the analysis.
100 percent of phase 1 analysis has been done and it took 0.73 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 0.238 minutes
2 parallel jobs are registered for analyzing reference taxa in Phase 2
Entire Phase 2 parameter estimation done and took 0.477 minutes.
The entire analysis took 1.21 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 0.26 minutes
The entire analysis took 0.26 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 0.29 minutes
2 parallel jobs are registered for the analysis.
67 percent of phase 1 analysis has been done and it took 0.57 minutes
2 parallel jobs are registered for the analysis.
100 percent of phase 1 analysis has been done and it took 0.85 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 0.496 minutes
2 parallel jobs are registered for analyzing reference taxa in Phase 2
Entire Phase 2 parameter estimation done and took 0.973 minutes.
The entire analysis took 1.83 minutes


RUNIT TEST PROTOCOL -- Thu Nov  2 11:34:22 2023 
*********************************************** 
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 
 44.548   3.669 209.022 

Example timings

IFAA.Rcheck/IFAA-Ex.timings

nameusersystemelapsed
IFAA 27.640 1.611137.538
MZILN 1.999 0.23932.284