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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:pairedGSEA.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings pairedGSEA_1.1.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/pairedGSEA.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘pairedGSEA/DESCRIPTION’ ... OK
* this is package ‘pairedGSEA’ version ‘1.1.0’
* 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 ‘pairedGSEA’ 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 ... WARNING
Codoc mismatches from documentation object 'plot_ora':
plot_ora
  Code: function(ora, pattern = NULL, paired = FALSE, plotly = FALSE,
                 cutoff = 0.05, lines = TRUE, colors = c("darkgray",
                 "purple", "lightblue", "maroon"))
  Docs: function(ora, plotly = FALSE, pattern = NULL, cutoff = 0.05,
                 lines = TRUE, colors = c("darkgray", "purple",
                 "lightblue"))
  Argument names in code not in docs:
    paired
  Mismatches in argument names (first 3):
    Position: 2 Code: pattern Docs: plotly
    Position: 3 Code: paired Docs: pattern
    Position: 4 Code: plotly Docs: cutoff
  Mismatches in argument default values:
    Name: 'colors' Code: c("darkgray", "purple", "lightblue", "maroon") Docs: c("darkgray", "purple", "lightblue")

* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in documentation object 'plot_ora':
  ‘paired’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
paired_diff    19.212  0.112  19.370
prepare_msigdb 10.768  0.195  10.998
* 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 ...
  ‘User-Guide.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/pairedGSEA.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL pairedGSEA
###
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* installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’
* installing *source* package ‘pairedGSEA’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (pairedGSEA)

R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> suppressPackageStartupMessages(library("pairedGSEA"))
> data("example_se", "example_ora_results", "example_diff_result", package = "pairedGSEA")
> test_check("pairedGSEA")
Running Example
Preparing metadata
Running SVA
No significant surrogate variables

Found 0 surrogate variables
Running DESeq2
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
Stored DESeqDataSet in results/Example_dds.RDS
Extracting results
Stored differential expression results in results/Example_expression_results.RDS
Initiating DEXSeq
Creating DEXSeqDataSet
converting counts to integer mode
Stored DEXSeqDataSet in results/Example_dxd.RDS

Running DEXSeq -- This might take a while
Stored differential splicing results in results/Example_splicing_results.RDS
Example is analysed.
Aggregating p values
Stored gene pvalue aggregation in results/Example_aggregated_pvals.RDS
Done.
No significant surrogate variables
converting counts to integer mode
No significant surrogate variables
converting counts to integer mode
No significant surrogate variables
OBS: your design will be overwritten to: ~source
No significant surrogate variables
converting counts to integer mode
No significant surrogate variables
converting counts to integer mode
converting counts to integer mode
converting counts to integer mode
Running SVA
Number of significant surrogate variables is:  2 
Iteration (out of 5 ):1  2  3  4  5  
Found 2 surrogate variables
Redefining DESeq2 design formula

Running over-representation analyses
Joining result
Running over-representation analyses
Running over-representation analyses
Joining result
Storing fora results
Stored ORA on differential analysis results in results/test_ora.RDS
Running over-representation analyses
Storing fora results
Stored ORA on only DESeq2 results in results/test_ora.RDS
Running 
Preparing metadata

Removing 0 rows with a summed count lower than 10
Removing 108 rows with counts in less than 2 samples.

Running SVA
Number of significant surrogate variables is:  2 
Iteration (out of 5 ):1  2  3  4  5  
Found 2 surrogate variables
Redefining DESeq2 design formula

Running limma+voom
Total number of exons:  5503 
Total number of genes:  955 
Number of genes with 1 exon:  142 
Mean number of exons in a gene:  6 
Max number of exons in a gene:  36 
Aggregating p values
Done.
Running over-representation analyses
Joining result
converting counts to integer mode
converting counts to integer mode

Removing 1 rows with a summed count lower than 30
Removing 1 rows with counts in less than 2 samples.


Removing 0 rows with a summed count lower than 1
Removing 1 rows with counts in less than 2 samples.

Stored results in results/test_result.RDS
Stored results in results/test_result.csv
Stored results in results/test_result.xlsx
Stored results in results/test_result.rdata
Stored results in results/test_result.tsv
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 140 ]
> 
> proc.time()
   user  system elapsed 
174.370   2.501 177.212