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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:magpie.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings magpie_0.99.8.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/magpie.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘magpie/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘magpie’ version ‘0.99.8’
* 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 ‘magpie’ 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 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 ‘runTest.R’
 ERROR
Running the tests in ‘tests/runTest.R’ failed.
Last 13 lines of output:
  
   
  1 Test Suite : 
  magpie RUnit Tests - 2 test functions, 1 error, 0 failures
  ERROR in test_PowerEval: Error in seq.default(1, ncol(Counts), 2) : 'to' must be of length 1
  
  Test files with failing tests
  
     test_magpie.R 
       test_PowerEval 
  
  
  Error in BiocGenerics:::testPackage("magpie") : 
    unit tests failed for package magpie
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘magpie.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/magpie.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL magpie
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library’
* installing *source* package ‘magpie’ ...
** 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 (magpie)

R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences"
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("magpie")
Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Error in x$.self$finalize() : attempt to apply non-function
Merge bumps from different replicates...
Estimating parameters...
Parameters estimation has finished...
KL divergence calculation has finished...
Parameters simulation has finished for sequencing depth--1x, 2 Controls, 2 Cases.
converting counts to integer mode
using pre-existing size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
converting counts to integer mode
using pre-existing size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
Timing stopped at: 42.18 4.224 37.71
Error in seq.default(1, ncol(Counts), 2) : 'to' must be of length 1
In addition: Warning messages:
1: call dbDisconnect() when finished working with a connection 
2: In aod::betabin(cbind(y, n - y) ~ Pred, ~1, data = dat, link = "logit") :
  
Possible convergence problem. Optimization process code: 10 (see ?optim).

3: In aod::betabin(cbind(y, n - y) ~ Pred, ~1, data = dat, link = "logit") :
  
Possible convergence problem. Optimization process code: 10 (see ?optim).

4: In aod::betabin(cbind(y, n - y) ~ Pred, ~1, data = dat, link = "logit") :
  
Possible convergence problem. Optimization process code: 10 (see ?optim).

5: In aod::betabin(cbind(y, n - y) ~ Pred, ~1, data = dat, link = "logit") :
  
Possible convergence problem. Optimization process code: 10 (see ?optim).

6: In aod::betabin(cbind(y, n - y) ~ Pred, ~1, data = dat, link = "logit") :
  
Possible convergence problem. Optimization process code: 10 (see ?optim).

7: In aod::betabin(cbind(y, n - y) ~ Pred, ~1, data = dat, link = "logit") :
  
Possible convergence problem. Optimization process code: 10 (see ?optim).

8: In aod::betabin(cbind(y, n - y) ~ Pred, ~1, data = dat, link = "logit") :
  
Possible convergence problem. Optimization process code: 10 (see ?optim).

9: In aod::betabin(cbind(y, n - y) ~ Pred, ~1, data = dat, link = "logit") :
  
Possible convergence problem. Optimization process code: 10 (see ?optim).



RUNIT TEST PROTOCOL -- Sat Mar 25 05:48:53 2023 
*********************************************** 
Number of test functions: 2 
Number of errors: 1 
Number of failures: 0 

 
1 Test Suite : 
magpie RUnit Tests - 2 test functions, 1 error, 0 failures
ERROR in test_PowerEval: Error in seq.default(1, ncol(Counts), 2) : 'to' must be of length 1

Test files with failing tests

   test_magpie.R 
     test_PowerEval 


Error in BiocGenerics:::testPackage("magpie") : 
  unit tests failed for package magpie
Execution halted