R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library("testthat")
> library("mosdef")

> 
> test_check("mosdef")
Loading required package: S4Vectors
Loading required package: stats4
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, saveRDS, setdiff, table,
    tapply, union, unique, unsplit, which.max, which.min


Attaching package: 'S4Vectors'

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

    findMatches

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

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")'.


Attaching package: 'Biobase'

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

    rowMedians

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

    anyMissing, rowMedians

Loading required package: graph
Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: SparseM

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.

Attaching package: 'topGO'

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

    members


using counts and average transcript lengths from tximeta
'select()' returned 1:many mapping between keys and columns
estimating size factors
using 'avgTxLength' from assays(dds), correcting for library size
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
'select()' returned 1:many mapping between keys and columns
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
Your dataset has 1024 DE genes.
You selected 400 (39.06%) genes for the enrichment analysis.
You are analyzing up_and_down-regulated genes in the `res_de` container

Your dataset has 500 DE genes.
You selected 400 (80.00%) genes for the enrichment analysis.

'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
Your dataset has 652 DE genes.
You selected 652 (100.00%) genes for the enrichment analysis.
You are analyzing up-regulated genes in the `res_de` container

'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
Your dataset has 372 DE genes.
You selected 372 (100.00%) genes for the enrichment analysis.
You are analyzing down-regulated genes in the `res_de` container

Your dataset has 1024 DE genes.
You selected 400 (39.06%) genes for the enrichment analysis.
You are analyzing up_and_down-regulated genes in the `res_de` container

Can't find hg38/ensGene length data in genLenDataBase...
Found the annotation package, TxDb.Hsapiens.UCSC.hg38.knownGene
Trying to get the gene lengths from it.
Loading required package: GenomicFeatures

Attaching package: 'GenomicFeatures'

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

    genes

Fetching GO annotations...
For 3702 genes, we could not find any categories. These genes will be excluded.
To force their use, please run with use_genes_without_cat=TRUE (see documentation).
This was the default behavior for version 1.15.1 and earlier.
Calculating the p-values...
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
Your dataset has 500 DE genes.
You selected 400 (80.00%) genes for the enrichment analysis.

Can't find hg38/ensGene length data in genLenDataBase...
Found the annotation package, TxDb.Hsapiens.UCSC.hg38.knownGene
Trying to get the gene lengths from it.
Fetching GO annotations...
For 3702 genes, we could not find any categories. These genes will be excluded.
To force their use, please run with use_genes_without_cat=TRUE (see documentation).
This was the default behavior for version 1.15.1 and earlier.
Calculating the p-values...
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
Your dataset has 652 DE genes.
You selected 652 (100.00%) genes for the enrichment analysis.
You are analyzing up-regulated genes in the `res_de` container

Can't find hg38/ensGene length data in genLenDataBase...
Found the annotation package, TxDb.Hsapiens.UCSC.hg38.knownGene
Trying to get the gene lengths from it.
Fetching GO annotations...
For 3702 genes, we could not find any categories. These genes will be excluded.
To force their use, please run with use_genes_without_cat=TRUE (see documentation).
This was the default behavior for version 1.15.1 and earlier.
Calculating the p-values...
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
Your dataset has 372 DE genes.
You selected 372 (100.00%) genes for the enrichment analysis.
You are analyzing down-regulated genes in the `res_de` container

Can't find hg38/ensGene length data in genLenDataBase...
Found the annotation package, TxDb.Hsapiens.UCSC.hg38.knownGene
Trying to get the gene lengths from it.
Fetching GO annotations...
For 3702 genes, we could not find any categories. These genes will be excluded.
To force their use, please run with use_genes_without_cat=TRUE (see documentation).
This was the default behavior for version 1.15.1 and earlier.
Calculating the p-values...
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
Your dataset has 1024 DE genes.
You selected 400 (39.06%) genes for the enrichment analysis.
You are analyzing up_and_down-regulated genes in the `res_de` container

6125 GO terms were analyzed. Not all of them are significantly enriched.
We suggest further subsetting the output list by for example: 
using a pvalue cutoff in the column: 
'p.value_elim'.
Your dataset has 500 DE genes.
You selected 400 (80.00%) genes for the enrichment analysis.

6130 GO terms were analyzed. Not all of them are significantly enriched.
We suggest further subsetting the output list by for example: 
using a pvalue cutoff in the column: 
'p.value_elim'.
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
Your dataset has 652 DE genes.
You selected 652 (100.00%) genes for the enrichment analysis.
You are analyzing up-regulated genes in the `res_de` container

6125 GO terms were analyzed. Not all of them are significantly enriched.
We suggest further subsetting the output list by for example: 
using a pvalue cutoff in the column: 
'p.value_elim'.
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
Your dataset has 372 DE genes.
You selected 372 (100.00%) genes for the enrichment analysis.
You are analyzing down-regulated genes in the `res_de` container

6125 GO terms were analyzed. Not all of them are significantly enriched.
We suggest further subsetting the output list by for example: 
using a pvalue cutoff in the column: 
'p.value_elim'.
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
Your dataset has 1024 DE genes.
You selected 1024 (100.00%) genes for the enrichment analysis.
You are analyzing up_and_down-regulated genes in the `res_de` container

6125 GO terms were analyzed. Not all of them are significantly enriched.
We suggest further subsetting the output list by for example: 
using a pvalue cutoff in the column: 
'p.value_elim'.
[ FAIL 0 | WARN 9 | SKIP 0 | PASS 14 ]

[ FAIL 0 | WARN 9 | SKIP 0 | PASS 14 ]
> 
> proc.time()
   user  system elapsed 
750.221  39.293 805.924 

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no mosdef_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-longtests/meat/mosdef.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘mosdef/DESCRIPTION’ ... OK
* this is package ‘mosdef’ version ‘1.2.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘mosdef’ can be installed ... OK
* checking installed package size ... OK
* checking package 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 ... 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 ... SKIPPED
* 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’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-bioc-longtests/meat/mosdef.Rcheck/00check.log’
for details.

* installing *source* package ‘mosdef’ ...
** 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 (mosdef)