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This page was generated on 2024-03-27 11:36:00 -0400 (Wed, 27 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4667
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4403
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4426
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1214/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
metaseqR2 1.14.0  (landing page)
Panagiotis Moulos
Snapshot Date: 2024-03-25 14:05:07 -0400 (Mon, 25 Mar 2024)
git_url: https://git.bioconductor.org/packages/metaseqR2
git_branch: RELEASE_3_18
git_last_commit: c5496b0
git_last_commit_date: 2023-10-24 11:22:10 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for metaseqR2 on nebbiolo2


To the developers/maintainers of the metaseqR2 package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/metaseqR2.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: metaseqR2
Version: 1.14.0
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:metaseqR2.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings metaseqR2_1.14.0.tar.gz
StartedAt: 2024-03-25 23:52:20 -0400 (Mon, 25 Mar 2024)
EndedAt: 2024-03-26 00:08:12 -0400 (Tue, 26 Mar 2024)
EllapsedTime: 952.2 seconds
RetCode: 0
Status:   OK  
CheckDir: metaseqR2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:metaseqR2.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings metaseqR2_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/metaseqR2.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* 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 ‘metaseqR2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘metaseqR2’ version ‘1.14.0’
* 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 ‘metaseqR2’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* 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 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 ... 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 ... 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 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 9.013  1.801  14.529
statNoiseq 6.515  0.383   6.897
metaseqr2  5.077  0.661  12.041
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘metaseqr2-annotation.Rmd’ using ‘UTF-8’... OK
  ‘metaseqr2-statistics.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/metaseqR2.Rcheck/00check.log’
for details.



Installation output

metaseqR2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL metaseqR2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘metaseqR2’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -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 -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o metaseqR2.so pval.o -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.18-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)

Tests output

metaseqR2.Rcheck/tests/runTests.Rout


R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-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("metaseqR2")

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


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 1.5-9.9 	 2024-03-01

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://nov2020.archive.ensembl.org

2024-03-26 00:00:37: 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/RtmpSQa0ln
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/RtmpSQa0ln/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...

2024-03-26 00:00:38: Data processing finished!


Total processing time: 00 seconds


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

Retrieving edger
Retrieving limma

2024-03-26 00:00:40: 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/RtmpSQa0ln
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/RtmpSQa0ln/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 911 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/RtmpSQa0ln/data/reportdb.js
Creating HTML report...
Compressing figures...  adding: tmp/RtmpSQa0ln/plots/qc/mds.png (deflated 52%)

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 268 KB

trying URL 'https://code.highcharts.com/highcharts-more.js'
downloaded 92 KB

trying URL 'https://code.highcharts.com/modules/exporting.js'
downloaded 19 KB

trying URL 'https://code.highcharts.com/modules/offline-exporting.js'
downloaded 9681 bytes

trying URL 'https://code.highcharts.com/modules/export-data.js'
downloaded 12 KB

trying URL 'http://jvenn.toulouse.inrae.fr/app/js/canvas2svg.js'
Content type 'text/javascript' length 35122 bytes (34 KB)
==================================================
downloaded 34 KB

trying URL 'http://jvenn.toulouse.inrae.fr/app/js/jvenn.min.js'
Content type 'text/javascript' length 100524 bytes (98 KB)
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downloaded 98 KB

trying URL 'https://unpkg.com/dexie@2.0.4/dist/dexie.min.js'
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/RtmpSQa0ln/index.html --lua-filter /home/biocbuild/bbs-3.18-bioc/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.18-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-3.18-bioc/R/site-library/rmdformats/templates/material/material.html --highlight-style kate --variable theme=bootstrap --include-in-header /tmp/RtmpSQa0ln/rmarkdown-str28336131dcefb2.html 

Output created: /tmp/RtmpSQa0ln/index.html


2024-03-26 00:00:50: Data processing finished!


Total processing time: 10 seconds



RUNIT TEST PROTOCOL -- Tue Mar 26 00:00:50 2024 
*********************************************** 
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 
 27.125   2.382  37.222 

Example timings

metaseqR2.Rcheck/metaseqR2-Ex.timings

nameusersystemelapsed
buildAnnotationDatabase000
buildCustomAnnotation4.4190.3164.735
combineBonferroni0.0010.0000.000
combineHarmonic0.0010.0000.001
combineMaxp000
combineMinp000
combineSimes0.0010.0000.000
combineWeight000
createSignalTracks1.0580.0611.157
diagplotAvgFtd0.0470.0000.047
diagplotBoxplot0.6370.0040.640
diagplotCor0.1430.0040.147
diagplotDeHeatmap0.7480.0040.751
diagplotEdaseq0.4100.0200.429
diagplotFiltered0.0210.0040.024
diagplotFtd0.0170.0000.017
diagplotMds0.2730.0000.273
diagplotNoiseq0.4390.0120.451
diagplotPairs0.8640.0120.875
diagplotRoc0.0170.0080.025
diagplotVenn0.1740.0040.178
diagplotVolcano2.6110.1802.792
downsampleCounts0.1990.0000.199
estimateAufcWeights0.9300.0041.035
estimateSimParams0.7300.0240.772
getAnnotation0.9420.0884.865
getDefaults0.0000.0000.001
getInstalledAnnotations0.0010.0000.001
getWeights000
importCustomAnnotation0.8160.0680.884
loadAnnotation0.0020.0000.002
makeSimDataSd0.7990.1400.977
makeSimDataTcc0.0000.0000.001
metaTest0.0100.0000.029
metaseqr2 5.077 0.66112.041
metaseqrPlot0.5370.0200.558
normalizeAbsseq0.6180.0760.694
normalizeDeseq0.1520.0040.156
normalizeDeseq20.5680.0440.613
normalizeDss0.2550.0150.271
normalizeEdaseq0.3770.0010.377
normalizeEdger0.1090.0030.112
normalizeNbpseq0.1150.0200.135
normalizeNoiseq0.1460.0010.146
read2count 9.013 1.80114.529
readTargets0.0200.0040.024
statAbsseq1.2440.1041.350
statDeseq0.9650.0150.982
statDeseq23.3750.1363.512
statDss0.6710.0160.688
statEdger0.5200.0000.519
statLimma0.2470.0040.252
statNbpseq0.9350.0120.947
statNoiseq6.5150.3836.897