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This page was generated on 2024-03-28 11:36:10 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4708
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4446
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4471
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4426
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 52/2270HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ALDEx2 1.35.0  (landing page)
Greg Gloor
Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/ALDEx2
git_branch: devel
git_last_commit: 9e689b5
git_last_commit_date: 2023-10-24 10:38:50 -0400 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for ALDEx2 on nebbiolo1


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.

raw results


Summary

Package: ALDEx2
Version: 1.35.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ALDEx2.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ALDEx2_1.35.0.tar.gz
StartedAt: 2024-03-27 20:10:23 -0400 (Wed, 27 Mar 2024)
EndedAt: 2024-03-27 20:15:37 -0400 (Wed, 27 Mar 2024)
EllapsedTime: 314.0 seconds
RetCode: 0
Status:   OK  
CheckDir: ALDEx2.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ALDEx2.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ALDEx2_1.35.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/ALDEx2.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-pc-linux-gnu
* 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 ‘ALDEx2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ALDEx2’ version ‘1.35.0’
* 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 code 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 ... NOTE
Invalid package aliases in Rd file 'ALDEx2m-package.Rd':
  ‘ALDEx2m-package’
* 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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/ALDEx2.Rcheck/00check.log’
for details.


Installation output

ALDEx2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL ALDEx2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-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)

Tests output

ALDEx2.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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
Loading required package: lattice
Loading required package: latticeExtra
> 
> test_check("ALDEx2")
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 34 ]

[ FAIL 0 | WARN 5 | SKIP 0 | PASS 34 ]
> 
> proc.time()
   user  system elapsed 
 63.056   1.641  64.689 

Example timings

ALDEx2.Rcheck/ALDEx2-Ex.timings

nameusersystemelapsed
ALDEx2m-package000
aldex0.3170.0310.349
aldex.clr-class0.0260.0000.026
aldex.corr0.9650.0911.057
aldex.effect0.1210.0000.122
aldex.expectedDistance0.8200.0120.832
aldex.glm3.2030.0243.227
aldex.glm.effect0.2510.0070.259
aldex.glm.plot0.0010.0010.000
aldex.kw1.4250.0231.449
aldex.makeScaleMatrix0.0120.0000.012
aldex.plot000
aldex.plotFeature0.0620.0010.062
aldex.set.mode0.0210.0000.021
aldex.ttest0.0840.0000.083
getConditions-method0.0200.0000.021
getDenom-method0.0430.0030.048
getDirichletInstances-method0.020.000.02
getDirichletReplicate-method0.0200.0000.019
getDirichletSample-method0.0160.0040.020
getFeatureNames-method0.0170.0030.020
getFeatures-method0.0190.0000.020
getMonteCarloInstances-method0.020.000.02
getMonteCarloReplicate-method0.0210.0000.020
getMonteCarloSample-method0.0330.0040.038
getReads-method0.0420.0040.045
getSampleIDs-method0.0360.0000.036
getScaleSamples-method0.0340.0000.035
numConditions-method0.0210.0000.021
numFeatures-method0.020.000.02
numMCInstances-method0.0200.0000.021