##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:metaseqR2.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings metaseqR2_1.21.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/metaseqR2.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘metaseqR2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘metaseqR2’ version ‘1.21.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 46 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ‘metaseqR2’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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 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
getUcscUtr: no visible binding for global variable ‘customDir’
Undefined global functions or variables:
  customDir
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  metaseqr2.Rd: render
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
read2count    11.087  2.935  16.831
statNoiseq     6.490  1.062   7.551
metaseqr2      5.321  0.872   7.096
getAnnotation  2.117  0.298   5.238
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/metaseqR2.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL metaseqR2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘metaseqR2’ ...
** this is package ‘metaseqR2’ version ‘1.21.2’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c pval.c -o pval.o
pval.c: In function ‘add_from_both_sides’:
pval.c:26:11: warning: unused variable ‘esttotalperlength’ [-Wunused-variable]
   26 |    double esttotalperlength = total/2;
      |           ^~~~~~~~~~~~~~~~~
gcc -std=gnu2x -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o metaseqR2.so pval.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-metaseqR2/00new/metaseqR2/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (metaseqR2)

R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 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.

> BiocGenerics:::testPackage("metaseqR2")

Attaching package: 'generics'

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, 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


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

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


Attaching package: 'limma'

The following object is masked from 'package:DESeq2':

    plotMA

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

    plotMA

locfit 1.5-9.12 	 2025-03-05

Attaching package: 'metaseqR2'

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

    readTargets


Downsampling counts...
Estimating initial dispersion population...
Estimating dispersions using log-likelihood...

Running simulations... This procedure requires time... Please wait...Using Ensembl host https://jan2024.archive.ensembl.org

2025-10-24 01:19:45: Data processing started...

Read counts file: imported custom data frame
Conditions: G1, G2
Samples to include: G1_rep1, G1_rep2, G1_rep3, G2_rep1, G2_rep2, G2_rep3
Samples to exclude: none
Requested contrasts: G1_vs_G2
Annotation: embedded
Organism: mm10
Reference source: ensembl
Count type: gene
Analysis preset: all_basic
Transcriptional level: gene
Exon filters: none applied
Gene filters: none applied
Filter application: postnorm
Normalization algorithm: edaseq
Normalization arguments: 
  within.which: loess
  between.which: full
Statistical algorithm(s): edger, limma
Statistical arguments: 
  edger: classic, 5, 10, movingave, NULL, grid, 11, c(-6, 6), NULL, CoxReid, 10000, NULL, auto, NULL, NULL, NULL, NULL, 0.125, NULL, auto, chisq, TRUE, FALSE, c(0.05, 0.1)
  limma: none
Meta-analysis method: simes
Multiple testing correction: BH
Logarithmic transformation offset: 1
Analysis preset: all_basic
Quality control plots: 
Figure format: png
Output directory: /tmp/RtmpRoiCHZ
Output data: annotation, p_value, adj_p_value, meta_p_value, adj_meta_p_value, fold_change
Output scale(s): natural, log2
Output values: normalized
Loading gene annotation...
Saving gene model to /tmp/RtmpRoiCHZ/data/gene_model.RData
Removing genes with zero counts in all samples...
Normalizing with: edaseq
Running statistical tests with: edger
  Contrast: G1_vs_G2
Running statistical tests with: limma
  Contrast: G1_vs_G2
Performing meta-analysis with simes
Building output files...
  Contrast: G1_vs_G2
    Adding non-filtered data...
      binding annotation...
      binding p-values...
      binding FDRs...
      binding meta p-values...
      binding adjusted meta p-values...
      binding natural normalized fold changes...
      binding log2 normalized fold changes...
    Writing output...

2025-10-24 01:19:45: Data processing finished!


Total processing time: 00 seconds


Estimating AUFC weights... Please wait...
Processing edger
Processing limma

Retrieving edger
Retrieving limma

2025-10-24 01:19:47: Data processing started...

Read counts file: imported custom data frame
Conditions: e14.5, adult_8_weeks
Samples to include: e14.5_1, e14.5_2, a8w_1, a8w_2
Samples to exclude: none
Requested contrasts: adult_8_weeks_vs_e14.5
Library sizes: 
  e14.5_1: 3102907
  e14.5_2: 2067905
  a8w_1: 3742059
  a8w_2: 4403954
Annotation: embedded
Organism: mm9
Reference source: ensembl
Count type: gene
Analysis preset: medium_basic
Transcriptional level: gene
Exon filters: minActiveExons
  minActiveExons: 
    exonsPerGene: 5
    minExons: 2
    frac: 0.2
Gene filters: length, avgReads, expression, biotype
  length: 
    length: 500
  avgReads: 
    averagePerBp: 100
    quantile: 0.25
  expression: 
    median: TRUE
    mean: FALSE
    quantile: NA
    known: NA
    custom: NA
  biotype: 
    pseudogene: FALSE
    snRNA: FALSE
    protein_coding: FALSE
    antisense: FALSE
    miRNA: FALSE
    lincRNA: FALSE
    snoRNA: FALSE
    processed_transcript: FALSE
    misc_RNA: FALSE
    rRNA: TRUE
    sense_overlapping: FALSE
    sense_intronic: FALSE
    polymorphic_pseudogene: FALSE
    non_coding: FALSE
    three_prime_overlapping_ncrna: FALSE
    IG_C_gene: FALSE
    IG_J_gene: FALSE
    IG_D_gene: FALSE
    IG_V_gene: FALSE
    ncrna_host: FALSE
Filter application: postnorm
Normalization algorithm: edger
Normalization arguments: 
  method: TMM
  logratioTrim: 0.3
  sumTrim: 0.05
  doWeighting: TRUE
  Acutoff: -1e+10
  p: 0.75
Statistical algorithm(s): edger, limma
Statistical arguments: 
  edger: classic, 5, 10, movingave, NULL, grid, 11, c(-6, 6), NULL, CoxReid, 10000, NULL, auto, NULL, NULL, NULL, NULL, 0.125, NULL, auto, chisq, TRUE, FALSE, c(0.05, 0.1)
  limma: none
Meta-analysis method: simes
Multiple testing correction: BH
p-value threshold: 0.05
Logarithmic transformation offset: 1
Analysis preset: medium_basic
Quality control plots: mds
Figure format: png
Output directory: /tmp/RtmpRoiCHZ
Output data: annotation, p_value, adj_p_value, meta_p_value, adj_meta_p_value, fold_change
Output scale(s): natural, log2
Output values: normalized
Loading gene annotation...
Saving gene model to /tmp/RtmpRoiCHZ/data/gene_model.RData
Removing genes with zero counts in all samples...
Normalizing with: edger
Applying gene filter length...
  Threshold below which ignored: 500
Applying gene filter avgReads...
  Threshold below which ignored: 0.0659629215631332
Applying gene filter expression...
  Threshold below which ignored: 68
Applying gene filter biotype...
  Biotypes ignored: rRNA
2106 genes filtered out
1681 genes remain after filtering
Running statistical tests with: edger
  Contrast: adult_8_weeks_vs_e14.5
  Contrast adult_8_weeks_vs_e14.5: found 906 genes
Running statistical tests with: limma
  Contrast: adult_8_weeks_vs_e14.5
  Contrast adult_8_weeks_vs_e14.5: found 912 genes
Performing meta-analysis with simes
Building output files...
  Contrast: adult_8_weeks_vs_e14.5
    Adding non-filtered data...
      binding annotation...
      binding p-values...
      binding FDRs...
      binding meta p-values...
      binding adjusted meta p-values...
      binding natural normalized fold changes...
      binding log2 normalized fold changes...
    Writing output...
    Adding filtered data...
      binding annotation...
      binding p-values...
      binding FDRs...
      binding meta p-values...
      binding adjusted meta p-values...
      binding natural normalized fold changes...
      binding log2 normalized fold changes...
    Writing output...
    Adding report data...
      binding annotation...
      binding meta p-values...
      binding adjusted meta p-values...
      binding log2 normalized fold changes...
      binding normalized mean counts...
      binding normalized mean counts...
Creating quality control graphs...
Plotting in png format...
  Plotting mds...
  Importing mds...
Writing plot database in /tmp/RtmpRoiCHZ/data/reportdb.js
Creating HTML report...
Compressing figures...  adding: tmp/RtmpRoiCHZ/plots/qc/mds.png (deflated 44%)

Downloading required JavaScript libraries...trying URL 'https://raw.github.com/HubSpot/pace/v1.0.0/pace.min.js'
Content type 'text/plain; charset=utf-8' length 12363 bytes (12 KB)
==================================================
downloaded 12 KB

trying URL 'https://code.highcharts.com/highcharts.js'
downloaded 272 KB

trying URL 'https://code.highcharts.com/highcharts-more.js'
downloaded 96 KB

trying URL 'https://code.highcharts.com/modules/exporting.js'
downloaded 26 KB

trying URL 'https://code.highcharts.com/modules/offline-exporting.js'
downloaded 5942 bytes

trying URL 'https://code.highcharts.com/modules/export-data.js'
downloaded 13 KB

trying URL 'https://unpkg.com/dexie@2.0.4/dist/dexie.min.js'
Content type 'text/javascript; charset=utf-8' length 56670 bytes (55 KB)
==================================================
downloaded 55 KB



processing file: metaseqr2_report.Rmd
output file: metaseqr2_report.knit.md

/usr/bin/pandoc +RTS -K512m -RTS metaseqr2_report.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpRoiCHZ/index.html --lua-filter /home/biocbuild/bbs-3.22-bioc/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.22-bioc/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua +RTS -K2048m -RTS --variable 'material:true' --variable 'lightbox:true' --variable 'thumbnails:true' --variable 'gallery:true' --variable 'cards:true' --variable bs3=TRUE --standalone --section-divs --table-of-contents --toc-depth 1 --template /home/biocbuild/bbs-3.22-bioc/R/site-library/rmdformats/templates/material/material.html --highlight-style kate --variable theme=bootstrap --include-in-header /tmp/RtmpRoiCHZ/rmarkdown-str9cc2b5b5e2de6.html 

Output created: /tmp/RtmpRoiCHZ/index.html


2025-10-24 01:19:54: Data processing finished!


Total processing time: 06 seconds



RUNIT TEST PROTOCOL -- Fri Oct 24 01:19:54 2025 
*********************************************** 
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
metaseqR2 RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 
There were 50 or more warnings (use warnings() to see the first 50)
> 
> proc.time()
   user  system elapsed 
 30.891   2.441  36.269