Greg Gloor
| Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/ALDEx2 |
| git_branch: RELEASE_3_17 |
| git_last_commit: ba32b9a |
| git_last_commit_date: 2023-04-25 10:34:57 -0400 (Tue, 25 Apr 2023) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:35:10 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| 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 50/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ALDEx2 1.32.0 (landing page) Greg Gloor
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the ALDEx2 package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ALDEx2.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: ALDEx2 |
| Version: 1.32.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ALDEx2.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings ALDEx2_1.32.0.tar.gz |
| StartedAt: 2023-10-15 19:08:19 -0400 (Sun, 15 Oct 2023) |
| EndedAt: 2023-10-15 19:12:02 -0400 (Sun, 15 Oct 2023) |
| EllapsedTime: 222.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: ALDEx2.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ALDEx2.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings ALDEx2_1.32.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/ALDEx2.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘ALDEx2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ALDEx2’ version ‘1.32.0’
* 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 ‘ALDEx2’ 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 ... WARNING
checkRd: (5) aldex.clr-class.Rd:17-21: \item in \describe must have non-empty label
checkRd: (5) aldex.clr-class.Rd:22-27: \item in \describe must have non-empty label
checkRd: (5) aldex.clr-class.Rd:28-32: \item in \describe must have non-empty label
checkRd: (5) aldex.clr-class.Rd:33-36: \item in \describe must have non-empty label
checkRd: (5) aldex.clr-class.Rd:37-40: \item in \describe must have non-empty label
checkRd: (5) aldex.clr-class.Rd:41-44: \item in \describe must have non-empty label
checkRd: (5) aldex.clr-class.Rd:45-48: \item in \describe must have non-empty label
checkRd: (5) aldex.clr-class.Rd:49-52: \item in \describe must have non-empty label
checkRd: (5) aldex.clr-class.Rd:53-57: \item in \describe must have non-empty label
checkRd: (5) aldex.clr-class.Rd:58-62: \item in \describe must have non-empty label
* 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
aldex.corr 15.051 0.747 15.799
* 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 ...
‘ALDEx2_vignette.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING
See
‘/home/biocbuild/bbs-3.17-bioc/meat/ALDEx2.Rcheck/00check.log’
for details.
ALDEx2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL ALDEx2 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’ * installing *source* package ‘ALDEx2’ ... ** 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 (ALDEx2)
ALDEx2.Rcheck/tests/testthat.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
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(ALDEx2)
Loading required package: zCompositions
Loading required package: MASS
Loading required package: NADA
Loading required package: survival
Attaching package: 'NADA'
The following object is masked from 'package:stats':
cor
Loading required package: truncnorm
>
> test_check("ALDEx2")
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 22 ]
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 22 ]
>
> proc.time()
user system elapsed
28.812 0.917 29.717
ALDEx2.Rcheck/ALDEx2-Ex.timings
| name | user | system | elapsed | |
| ALDEx2m-package | 0.000 | 0.000 | 0.001 | |
| aldex | 0.278 | 0.012 | 0.291 | |
| aldex.clr-class | 0.021 | 0.000 | 0.021 | |
| aldex.clr.function-methods | 0.016 | 0.004 | 0.020 | |
| aldex.corr | 15.051 | 0.747 | 15.799 | |
| aldex.effect | 0.124 | 0.001 | 0.124 | |
| aldex.glm | 3.133 | 0.000 | 3.133 | |
| aldex.glm.effect | 0.284 | 0.011 | 0.296 | |
| aldex.kw | 1.499 | 0.001 | 1.499 | |
| aldex.plotFeature | 0.059 | 0.003 | 0.063 | |
| aldex.set.mode | 0.019 | 0.000 | 0.019 | |
| aldex.ttest | 0.077 | 0.000 | 0.077 | |
| expectedDistance | 0.393 | 0.009 | 0.401 | |
| getDenom-method | 0.062 | 0.000 | 0.062 | |
| getDirichletInstances-method | 0.017 | 0.003 | 0.021 | |
| getDirichletReplicate-method | 0.021 | 0.000 | 0.021 | |
| getDirichletSample-method | 0.022 | 0.001 | 0.021 | |
| getFeatureNames-method | 0.021 | 0.000 | 0.021 | |
| getFeatures-method | 0.02 | 0.00 | 0.02 | |
| getMonteCarloInstances-method | 0.026 | 0.003 | 0.030 | |
| getMonteCarloReplicate-method | 0.024 | 0.001 | 0.025 | |
| getMonteCarloSample-method | 0.022 | 0.003 | 0.026 | |
| getReads-method | 0.025 | 0.001 | 0.025 | |
| getSampleIDs-method | 0.023 | 0.000 | 0.024 | |
| numConditions-method | 0.024 | 0.000 | 0.024 | |
| numFeatures-method | 0.021 | 0.000 | 0.021 | |
| numMCInstances-method | 0.022 | 0.000 | 0.022 | |
| plot.aldex | 0 | 0 | 0 | |