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This page was generated on 2024-06-18 17:59 -0400 (Tue, 18 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4758
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4492
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4464
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 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 2245/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
VAExprs 1.10.0  (landing page)
Dongmin Jung
Snapshot Date: 2024-06-16 14:00 -0400 (Sun, 16 Jun 2024)
git_url: https://git.bioconductor.org/packages/VAExprs
git_branch: RELEASE_3_19
git_last_commit: e637622
git_last_commit_date: 2024-04-30 11:36:10 -0400 (Tue, 30 Apr 2024)
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
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    NA  


CHECK results for VAExprs on palomino3

To the developers/maintainers of the VAExprs package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/VAExprs.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: VAExprs
Version: 1.10.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:VAExprs.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings VAExprs_1.10.0.tar.gz
StartedAt: 2024-06-17 14:14:28 -0400 (Mon, 17 Jun 2024)
EndedAt: 2024-06-17 14:26:08 -0400 (Mon, 17 Jun 2024)
EllapsedTime: 699.7 seconds
RetCode: 0
Status:   OK  
CheckDir: VAExprs.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:VAExprs.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings VAExprs_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/VAExprs.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'VAExprs/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'VAExprs' version '1.10.0'
* 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 whether package 'VAExprs' 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 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 ... NOTE
fit_vae: no visible binding for global variable 'z_mean'
fit_vae: no visible binding for global variable 'z_log_stddev'
fit_vae : vae_loss: no visible binding for global variable
  'original_dim'
fit_vae : vae_loss: no visible binding for global variable
  'z_log_stddev'
fit_vae : vae_loss: no visible binding for global variable 'z_mean'
Undefined global functions or variables:
  original_dim z_log_stddev z_mean
* 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
fit_vae   9.98   3.19   13.36
plot_aug  7.19   0.51    6.56
gen_exprs 5.88   0.42    5.12
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  'F:/biocbuild/bbs-3.19-bioc/meat/VAExprs.Rcheck/00check.log'
for details.


Installation output

VAExprs.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL VAExprs
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'VAExprs' ...
** using staged installation
** R
** 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 (VAExprs)

Tests output

VAExprs.Rcheck/tests/testthat.Rout


R version 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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(VAExprs)
Loading required package: keras
Loading required package: mclust
Package 'mclust' version 6.1.1
Type 'citation("mclust")' for citing this R package in publications.
> 
> test_check("VAExprs")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
  19.43   19.70   41.95 

Example timings

VAExprs.Rcheck/VAExprs-Ex.timings

nameusersystemelapsed
fit_vae 9.98 3.1913.36
gen_exprs5.880.425.12
plot_aug7.190.516.56
plot_vae3.990.754.11