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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:MetaVolcanoR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings MetaVolcanoR_1.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/MetaVolcanoR.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* 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 ‘MetaVolcanoR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MetaVolcanoR’ version ‘1.18.0’
* 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 ‘MetaVolcanoR’ 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 whether startup messages can be suppressed ... 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
combining_mv: no visible binding for global variable ‘study’
combining_mv: no visible binding for global variable ‘value’
combining_mv: no visible binding for global variable ‘metap’
combining_mv: no visible binding for global variable ‘idx’
draw_cum_freq: no visible binding for global variable ‘ndatasets’
draw_cum_freq: no visible binding for global variable ‘DEGs’
draw_degbar: no visible binding for global variable ‘dataset’
draw_degbar: no visible binding for global variable ‘Regulation’
draw_forest: no visible binding for global variable ‘group’
plot_mv: no visible binding for global variable ‘metap’
plot_mv: no visible binding for global variable ‘degcomb’
plot_mv: no visible binding for global variable ‘ddeg’
plot_mv: no visible binding for global variable ‘ndeg’
plot_mv: no visible binding for global variable ‘degvcount’
plot_rem: no visible binding for global variable ‘signcon’
plot_rem: no visible binding for global variable ‘randomCi.ub’
plot_rem: no visible binding for global variable ‘randomCi.lb’
plot_rem: no visible binding for global variable ‘randomSummary’
plot_rem: no visible binding for global variable ‘randomP’
plot_rem: no visible binding for global variable ‘signcon2’
plot_rem: no visible binding for global variable ‘Ci.ub’
plot_rem: no visible binding for global variable ‘Ci.lb’
rem_mv: no visible binding for global variable ‘error’
rem_mv: no visible binding for global variable ‘randomCi.ub’
rem_mv: no visible binding for global variable ‘randomCi.lb’
rem_mv: no visible binding for global variable ‘index’
rem_mv: no visible global function definition for ‘head’
votecount_mv: no visible binding for global variable ‘ddeg’
votecount_mv: no visible binding for global variable ‘ndeg’
votecount_mv: no visible binding for global variable ‘idx’
Undefined global functions or variables:
  Ci.lb Ci.ub dataset ddeg degcomb DEGs degvcount error group head idx
  index metap ndatasets ndeg randomCi.lb randomCi.ub randomP
  randomSummary Regulation signcon signcon2 study value
Consider adding
  importFrom("utils", "head")
to your NAMESPACE file.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... 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
combining_mv 4.526  0.471   5.006
* 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 ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘MetaVolcano.Rmd’ using rmarkdown

Quitting from lines  at lines 64-66 [unnamed-chunk-1] (MetaVolcano.Rmd)
Error: processing vignette 'MetaVolcano.Rmd' failed with diagnostics:
there is no package called 'BiocManager'
--- failed re-building ‘MetaVolcano.Rmd’

--- re-building ‘PrepareDatasets.Rmd’ using rmarkdown
[WARNING] This document format requires a nonempty <title> element.
  Please specify either 'title' or 'pagetitle' in the metadata,
  e.g. by using --metadata pagetitle="..." on the command line.
  Falling back to 'PrepareDatasets.knit'
--- finished re-building ‘PrepareDatasets.Rmd’

SUMMARY: processing the following file failed:
  ‘MetaVolcano.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

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

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL MetaVolcanoR
###
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* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘MetaVolcanoR’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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
Warning in fun(libname, pkgname) :
  Package 'MetaVolcanoR' is deprecated and will be removed from
  Bioconductor version 3.20
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'MetaVolcanoR' is deprecated and will be removed from
  Bioconductor version 3.20
** testing if installed package keeps a record of temporary installation path
* DONE (MetaVolcanoR)

R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
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(MetaVolcanoR)
Warning message:
In fun(libname, pkgname) :
  Package 'MetaVolcanoR' is deprecated and will be removed from
  Bioconductor version 3.20
> 
> test_check('MetaVolcanoR')
  index  Symbol   Log2FC_1     CI.L_1     CI.R_1       vi_1   Log2FC_2
1  4795   MXRA5  0.8150851  0.3109324  1.3192377 0.06616251  1.3001104
2  2166  COL6A6 -1.7480348 -2.5780749 -0.9179947 0.17934364 -0.8388366
3  2053   CIDEA         NA         NA         NA         NA         NA
4  7115 SULT1A4  0.9689025  0.5103475  1.4274575 0.05473571  0.7513323
5   130   ACACB -0.8431142 -1.4708480 -0.2153804 0.10257437 -1.1119841
6  6528 SLC27A2 -0.6782948 -0.9931027 -0.3634869 0.02579759 -1.8916655
      CI.L_2     CI.R_2       vi_2   Log2FC_3     CI.L_3     CI.R_3        vi_3
1  0.6603306  1.9398901 0.10654886  1.1895480  0.8401301  1.5389659 0.031781777
2 -1.3578456 -0.3198277 0.07011930 -1.0300519 -1.4730328 -0.5870710 0.051080819
3         NA         NA         NA -1.0111528 -1.3226326 -0.6996729 0.025255027
4  0.4707021  1.0319624 0.02050012         NA         NA         NA          NA
5 -1.7417389 -0.4822293 0.10323592 -0.5305046 -0.6957455 -0.3652637 0.007107599
6 -2.6822584 -1.1010726 0.16270229 -1.2126830 -1.6702908 -0.7550753 0.054509799
    Log2FC_4    CI.L_4     CI.R_4      vi_4   Log2FC_5     CI.L_5     CI.R_5
1  0.2188594 -1.052230  1.4899492 0.4205720  0.8051543  0.1367255  1.4735830
2 -1.3755263 -2.162453 -0.5885999 0.1611967 -0.7213490 -1.5714484  0.1287505
3 -1.7991026 -2.918939 -0.6792665 0.3264351 -0.8738120 -1.6373061 -0.1103179
4         NA        NA         NA        NA         NA         NA         NA
5 -0.7991042 -1.457868 -0.1403403 0.1129659 -0.5155929 -0.8606782 -0.1705076
6 -1.3554403 -2.288444 -0.4224370 0.2265970 -1.4905464 -2.5565023 -0.4245905
        vi_5 signcon ntimes randomSummary randomCi.lb randomCi.ub      randomP
1 0.11630493       5      5     1.0333001   0.7882044   1.2783958 1.420312e-16
2 0.18811668      -5      5    -1.0649749  -1.3396138  -0.7903361 2.956522e-14
3 0.15173972      -3      3    -1.0417876  -1.3210774  -0.7624977 2.653168e-13
4         NA       2      2     0.8106154   0.5712566   1.0499741 3.187477e-11
5 0.03099851      -5      5    -0.5830624  -0.7212245  -0.4449003 1.324963e-16
6 0.29577833      -5      5    -1.2207058  -1.6760435  -0.7653680 1.484852e-07
     het_QE    het_QEp   het_QM      het_QMp error         se rank
1  4.179945 0.38220032 68.27752 1.420312e-16 FALSE 0.12504883    1
2  4.580708 0.33308457 57.76318 2.956522e-14 FALSE 0.14012185    2
3  1.980047 0.37156797 53.44957 2.653168e-13 FALSE 0.14249482    3
4  0.629179 0.42765661 44.05825 3.187477e-11 FALSE 0.12212181    4
5  4.317851 0.36469506 68.41455 1.324963e-16 FALSE 0.07049086    5
6 11.099093 0.02547263 27.60901 1.484852e-07 FALSE 0.23231516    6
[ FAIL 0 | WARN 20 | SKIP 0 | PASS 6 ]

[ FAIL 0 | WARN 20 | SKIP 0 | PASS 6 ]
> 
> proc.time()
   user  system elapsed 
106.527   3.063 109.612