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This page was generated on 2021-10-15 15:05:45 -0400 (Fri, 15 Oct 2021).

BUILD results for metaseqR2 on nebbiolo1

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raw results

Package 1093/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
metaseqR2 1.4.14  (landing page)
Panagiotis Moulos
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/metaseqR2
git_branch: RELEASE_3_13
git_last_commit: 1690bc0
git_last_commit_date: 2021-10-13 12:29:04 -0400 (Wed, 13 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    ERROR  skipped
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  YES
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: metaseqR2
Version: 1.4.14
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data metaseqR2
StartedAt: 2021-10-14 07:41:13 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 07:48:22 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 428.9 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data metaseqR2
###
##############################################################################
##############################################################################


* checking for file ‘metaseqR2/DESCRIPTION’ ... OK
* preparing ‘metaseqR2’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘metaseqr2-annotation.Rmd’ using rmarkdown
Loading required package: DESeq2
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, 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 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: limma

Attaching package: 'limma'

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

    plotMA

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

    plotMA

Loading required package: locfit
locfit 1.5-9.4 	 2020-03-24
Loading required package: splines

Attaching package: 'metaseqR2'

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

    readTargets

Warning in loadAnnotation(genome = "mm10", refdb = "refseq", level = "gene",  :
  The requested annotation does not seem to exist in the database! It will be loaded on the fly.
Consider importing it by using buildAnnotationDatabase.
Warning in .local(conn, statement, ...) :
  Unsigned INTEGER in col 1 imported as numeric
Warning in .local(conn, statement, ...) :
  Unsigned INTEGER in col 2 imported as numeric
trying URL 'http://hgdownload.cse.ucsc.edu/goldenPath/eboVir3/database/ncbiGene.txt.gz'
Content type 'application/x-gzip' length 238 bytes
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trying URL 'http://hgdownload.cse.ucsc.edu/goldenPath/eboVir3/database/chromInfo.txt.gz'
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trying URL 'http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/genePredToGtf'
Content type 'unknown' length 38689208 bytes (36.9 MB)
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Warning in buildCustomAnnotation(gtfFile = gtfFile, metadata = list(organism = "eboVir3_test",  :
  A version should be provided with metadata! Using today...
--- finished re-building ‘metaseqr2-annotation.Rmd’

--- re-building ‘metaseqr2-statistics.Rmd’ using rmarkdown
Warning: call dbDisconnect() when finished working with a connection
  adding: tmp/RtmpeP07h5/test1/plots/qc/correlation_correlogram.png (deflated 2%)
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  adding: tmp/RtmpeP07h5/test1/plots/statistics/de_heatmap_adult_8_weeks_vs_e14.5_asis.png (deflated 9%)
  adding: tmp/RtmpeP07h5/test1/plots/statistics/de_heatmap_adult_8_weeks_vs_e14.5_zscore.png (deflated 7%)
  adding: tmp/RtmpeP07h5/test1/plots/statistics/mastat_plot_adult_8_weeks_vs_e14.5.png (deflated 6%)
  adding: tmp/RtmpeP07h5/test1/plots/statistics/volcano_plot_adult_8_weeks_vs_e14.5.png (deflated 9%)
  adding: tmp/RtmpeP07h5/test1/plots/qc/correlation_correlogram.pdf (deflated 4%)
  adding: tmp/RtmpeP07h5/test1/plots/qc/correlation_heatmap.pdf (deflated 26%)
  adding: tmp/RtmpeP07h5/test1/plots/qc/correlation_pairs.pdf (deflated 4%)
  adding: tmp/RtmpeP07h5/test1/plots/qc/filtered_genes.pdf (deflated 7%)
  adding: tmp/RtmpeP07h5/test1/plots/qc/mds.pdf (deflated 12%)
  adding: tmp/RtmpeP07h5/test1/plots/normalization/boxplot_normalized.pdf (deflated 12%)
  adding: tmp/RtmpeP07h5/test1/plots/normalization/boxplot_raw.pdf (deflated 12%)
  adding: tmp/RtmpeP07h5/test1/plots/normalization/gcbias_normalized.pdf (deflated 4%)
  adding: tmp/RtmpeP07h5/test1/plots/normalization/gcbias_raw.pdf (deflated 4%)
  adding: tmp/RtmpeP07h5/test1/plots/normalization/lengthbias_normalized.pdf (deflated 1%)
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  adding: tmp/RtmpeP07h5/test1/plots/normalization/meandiff_normalized_adult_8_weeks_a8w_1_a8w_2.pdf (deflated 20%)
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  adding: tmp/RtmpeP07h5/test1/plots/normalization/meandiff_raw_adult_8_weeks_a8w_1_a8w_2.pdf (deflated 20%)
  adding: tmp/RtmpeP07h5/test1/plots/normalization/meandiff_raw_e14.5_e14.5_1_e14.5_2.pdf (deflated 20%)
  adding: tmp/RtmpeP07h5/test1/plots/normalization/meanvar_normalized.pdf (deflated 43%)
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  adding: tmp/RtmpeP07h5/test1/plots/statistics/volcano_plot_adult_8_weeks_vs_e14.5.pdf (deflated 2%)
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)
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trying URL 'https://unpkg.com/dexie@2.0.4/dist/dexie.min.js'
downloaded 55 KB

Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: Specifying width/height in layout() is now deprecated.
Please specify in ggplotly() or plot_ly()
Warning in fix_not_all_unique(rownames(x)) :
  Not all the values are unique - manually added prefix numbers
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: Specifying width/height in layout() is now deprecated.
Please specify in ggplotly() or plot_ly()
Warning in fix_not_all_unique(rownames(x)) :
  Not all the values are unique - manually added prefix numbers
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: Specifying width/height in layout() is now deprecated.
Please specify in ggplotly() or plot_ly()

2021-10-14 07:45:28: 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_normal
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: prenorm
Normalization algorithm: edaseq
Normalization arguments: 
  within.which: loess
  between.which: full
Statistical algorithm(s): deseq, edger
Statistical arguments: 
  deseq: blind, fit-only, local
  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)
Meta-analysis method: fisher
Multiple testing correction: BH
p-value threshold: 0.05
Logarithmic transformation offset: 1
Analysis preset: medium_normal
Quality control plots: mds, filtered, correl, pairwise, boxplot, gcbias, lengthbias, meandiff, meanvar, deheatmap, volcano, mastat
Figure format: png, pdf
Output directory: /tmp/RtmpeP07h5/test2
Output data: annotation, p_value, adj_p_value, meta_p_value, adj_meta_p_value, fold_change, stats, counts
Output scale(s): natural, log2
Output values: normalized
Output statistics: mean, sd, cv

Loading gene annotation...
Saving gene model to /tmp/RtmpeP07h5/test2/data/gene_model.RData
Removing genes with zero counts in all samples...
Prefiltering normalization with: edaseq
Applying gene filter length...
  Threshold below which ignored: 500
Applying gene filter avgReads...
  Threshold below which ignored: 0.0707638509084404
Applying gene filter expression...
  Threshold below which ignored: 67
Applying gene filter biotype...
  Biotypes ignored: rRNA
Normalizing with: edaseq
2107 genes filtered out
1680 genes remain after filtering
Running statistical tests with: deseq
  Contrast: adult_8_weeks_vs_e14.5
  Contrast adult_8_weeks_vs_e14.5: found 334 genes
Running statistical tests with: edger
  Contrast: adult_8_weeks_vs_e14.5
  Contrast adult_8_weeks_vs_e14.5: found 1083 genes
Performing meta-analysis with fisher
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...
      binding normalized mean counts...
      binding normalized count sds...
      binding normalized count CVs...
      binding normalized mean counts...
      binding normalized count sds...
      binding normalized count CVs...
      binding all normalized counts for adult_8_weeks...
      binding all normalized counts for e14.5...
    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...
      binding normalized mean counts...
      binding normalized count sds...
      binding normalized count CVs...
      binding normalized mean counts...
      binding normalized count sds...
      binding normalized count CVs...
      binding all normalized counts for adult_8_weeks...
      binding all normalized counts for e14.5...
    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...
  Plotting correl...
  Plotting pairwise...
  Plotting boxplot...
  Plotting gcbias...
  Plotting lengthbias...
  Plotting meandiff...
  Plotting meanvar...
  Plotting boxplot...
  Plotting gcbias...
  Plotting lengthbias...
  Plotting meandiff...
  Plotting meanvar...
  Plotting deheatmap...
  Contrast: adult_8_weeks_vs_e14.5
  Plotting volcano...
  Contrast: adult_8_weeks_vs_e14.5
  Plotting mastat...
  Contrast: adult_8_weeks_vs_e14.5
  Plotting filtered...
Plotting in pdf format...
  Plotting mds...
  Plotting correl...
  Plotting pairwise...
  Plotting boxplot...
  Plotting gcbias...
  Plotting lengthbias...
  Plotting meandiff...
  Plotting meanvar...
  Plotting boxplot...
  Plotting gcbias...
  Plotting lengthbias...
  Plotting meandiff...
  Plotting meanvar...
  Plotting deheatmap...
  Contrast: adult_8_weeks_vs_e14.5
  Plotting volcano...
  Contrast: adult_8_weeks_vs_e14.5
  Plotting mastat...
  Contrast: adult_8_weeks_vs_e14.5
  Plotting filtered...
  Importing mds...
  Importing pairwise...
  Importing filtered...
  Importing boxplot...
  Importing gcbias...
  Importing lengthbias...
  Importing meandif...
  Importing meanvar...
  Importing volcano
    adult_8_weeks_vs_e14.5 adult_8_weeks_vs_e14.5
  Importing mastat
    adult_8_weeks_vs_e14.5 adult_8_weeks_vs_e14.5
Writing plot database in /tmp/RtmpeP07h5/test2/data/reportdb.js
Creating HTML report...
Compressing figures...  adding: tmp/RtmpeP07h5/test2/plots/qc/correlation_correlogram.png (deflated 2%)
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  adding: tmp/RtmpeP07h5/test2/plots/normalization/meanvar_raw.png (deflated 8%)
  adding: tmp/RtmpeP07h5/test2/plots/statistics/de_heatmap_adult_8_weeks_vs_e14.5_asis.png (deflated 8%)
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  adding: tmp/RtmpeP07h5/test2/plots/qc/correlation_correlogram.pdf (deflated 4%)
  adding: tmp/RtmpeP07h5/test2/plots/qc/correlation_heatmap.pdf (deflated 26%)
  adding: tmp/RtmpeP07h5/test2/plots/qc/correlation_pairs.pdf (deflated 4%)
  adding: tmp/RtmpeP07h5/test2/plots/qc/filtered_genes.pdf (deflated 7%)
  adding: tmp/RtmpeP07h5/test2/plots/qc/mds.pdf (deflated 12%)
  adding: tmp/RtmpeP07h5/test2/plots/normalization/boxplot_normalized.pdf (deflated 8%)
  adding: tmp/RtmpeP07h5/test2/plots/normalization/boxplot_raw.pdf (deflated 12%)
  adding: tmp/RtmpeP07h5/test2/plots/normalization/gcbias_normalized.pdf (deflated 5%)
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  adding: tmp/RtmpeP07h5/test2/plots/normalization/meanvar_normalized.pdf (deflated 43%)
  adding: tmp/RtmpeP07h5/test2/plots/normalization/meanvar_raw.pdf (deflated 38%)
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  adding: tmp/RtmpeP07h5/test2/plots/statistics/de_heatmap_adult_8_weeks_vs_e14.5_zscore.pdf (deflated 8%)
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  adding: tmp/RtmpeP07h5/test2/plots/statistics/volcano_plot_adult_8_weeks_vs_e14.5.pdf (deflated 2%)

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processing file: metaseqr2_report.Rmd
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
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Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: Specifying width/height in layout() is now deprecated.
Please specify in ggplotly() or plot_ly()
Warning in fix_not_all_unique(rownames(x)) :
  Not all the values are unique - manually added prefix numbers
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
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Warning: Specifying width/height in layout() is now deprecated.
Please specify in ggplotly() or plot_ly()
Warning in fix_not_all_unique(rownames(x)) :
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Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
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Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: Specifying width/height in layout() is now deprecated.
Please specify in ggplotly() or plot_ly()
output file: metaseqr2_report.knit.md

Output created: /tmp/RtmpeP07h5/test2/index.html


2021-10-14 07:46:01: Data processing finished!


Total processing time: 33 seconds


2021-10-14 07:46:01: 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_normal
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: edaseq
Normalization arguments: 
  within.which: loess
  between.which: full
Statistical algorithm(s): deseq, edger
Statistical arguments: 
  deseq: blind, fit-only, local
  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)
Meta-analysis method: fisher
Multiple testing correction: BH
p-value threshold: 0.05
Logarithmic transformation offset: 1
Analysis preset: medium_normal
Quality control plots: mds, filtered, correl, pairwise, boxplot, gcbias, lengthbias, meandiff, meanvar, deheatmap, volcano, mastat
Figure format: png, pdf
Output directory: /tmp/RtmpeP07h5/test3
Output data: annotation, p_value, adj_p_value, meta_p_value, adj_meta_p_value, fold_change, stats, counts
Output scale(s): natural, log2
Output values: normalized
Output statistics: mean, sd, cv

Loading gene annotation...
Saving gene model to /tmp/RtmpeP07h5/test3/data/gene_model.RData
Removing genes with zero counts in all samples...
Normalizing with: edaseq
Applying gene filter length...
  Threshold below which ignored: 500
Applying gene filter avgReads...
  Threshold below which ignored: 0.0707638509084404
Applying gene filter expression...
  Threshold below which ignored: 67
Applying gene filter biotype...
  Biotypes ignored: rRNA
2107 genes filtered out
1680 genes remain after filtering
Running statistical tests with: deseq
  Contrast: adult_8_weeks_vs_e14.5
  Contrast adult_8_weeks_vs_e14.5: found 334 genes
Running statistical tests with: edger
  Contrast: adult_8_weeks_vs_e14.5
  Contrast adult_8_weeks_vs_e14.5: found 1083 genes
Performing meta-analysis with fisher
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...
      binding normalized mean counts...
      binding normalized count sds...
      binding normalized count CVs...
      binding normalized mean counts...
      binding normalized count sds...
      binding normalized count CVs...
      binding all normalized counts for adult_8_weeks...
      binding all normalized counts for e14.5...
    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...
      binding normalized mean counts...
      binding normalized count sds...
      binding normalized count CVs...
      binding normalized mean counts...
      binding normalized count sds...
      binding normalized count CVs...
      binding all normalized counts for adult_8_weeks...
      binding all normalized counts for e14.5...
    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...
  Plotting correl...
  Plotting pairwise...
  Plotting boxplot...
  Plotting gcbias...
  Plotting lengthbias...
  Plotting meandiff...
  Plotting meanvar...
  Plotting boxplot...
  Plotting gcbias...
  Plotting lengthbias...
  Plotting meandiff...
  Plotting meanvar...
  Plotting deheatmap...
  Contrast: adult_8_weeks_vs_e14.5
  Plotting volcano...
  Contrast: adult_8_weeks_vs_e14.5
  Plotting mastat...
  Contrast: adult_8_weeks_vs_e14.5
  Plotting filtered...
Plotting in pdf format...
  Plotting mds...
  Plotting correl...
  Plotting pairwise...
  Plotting boxplot...
  Plotting gcbias...
  Plotting lengthbias...
  Plotting meandiff...
  Plotting meanvar...
  Plotting boxplot...
  Plotting gcbias...
  Plotting lengthbias...
  Plotting meandiff...
  Plotting meanvar...
  Plotting deheatmap...
  Contrast: adult_8_weeks_vs_e14.5
  Plotting volcano...
  Contrast: adult_8_weeks_vs_e14.5
  Plotting mastat...
  Contrast: adult_8_weeks_vs_e14.5
  Plotting filtered...
  Importing mds...
  Importing pairwise...
  Importing filtered...
  Importing boxplot...
  Importing gcbias...
  Importing lengthbias...
  Importing meandif...
  Importing meanvar...
  Importing volcano
    adult_8_weeks_vs_e14.5 adult_8_weeks_vs_e14.5
  Importing mastat
    adult_8_weeks_vs_e14.5 adult_8_weeks_vs_e14.5
Writing plot database in /tmp/RtmpeP07h5/test3/data/reportdb.js
Creating HTML report...
Compressing figures...  adding: tmp/RtmpeP07h5/test3/plots/qc/correlation_correlogram.png (deflated 2%)
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  adding: tmp/RtmpeP07h5/test3/plots/qc/correlation_correlogram.pdf (deflated 4%)
  adding: tmp/RtmpeP07h5/test3/plots/qc/correlation_heatmap.pdf (deflated 26%)
  adding: tmp/RtmpeP07h5/test3/plots/qc/correlation_pairs.pdf (deflated 4%)
  adding: tmp/RtmpeP07h5/test3/plots/qc/filtered_genes.pdf (deflated 7%)
  adding: tmp/RtmpeP07h5/test3/plots/qc/mds.pdf (deflated 12%)
  adding: tmp/RtmpeP07h5/test3/plots/normalization/boxplot_normalized.pdf (deflated 12%)
  adding: tmp/RtmpeP07h5/test3/plots/normalization/boxplot_raw.pdf (deflated 12%)
  adding: tmp/RtmpeP07h5/test3/plots/normalization/gcbias_normalized.pdf (deflated 4%)
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  adding: tmp/RtmpeP07h5/test3/plots/normalization/meanvar_raw.pdf (deflated 38%)
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  adding: tmp/RtmpeP07h5/test3/plots/statistics/de_heatmap_adult_8_weeks_vs_e14.5_zscore.pdf (deflated 8%)
  adding: tmp/RtmpeP07h5/test3/plots/statistics/mastat_plot_adult_8_weeks_vs_e14.5.pdf (deflated 5%)
  adding: tmp/RtmpeP07h5/test3/plots/statistics/volcano_plot_adult_8_weeks_vs_e14.5.pdf (deflated 2%)

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trying URL 'http://jvenn.toulouse.inra.fr/app/js/jvenn.min.js'
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trying URL 'https://unpkg.com/dexie@2.0.4/dist/dexie.min.js'
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processing file: metaseqr2_report.Rmd
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: Specifying width/height in layout() is now deprecated.
Please specify in ggplotly() or plot_ly()
Warning in fix_not_all_unique(rownames(x)) :
  Not all the values are unique - manually added prefix numbers
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: Specifying width/height in layout() is now deprecated.
Please specify in ggplotly() or plot_ly()
Warning in fix_not_all_unique(rownames(x)) :
  Not all the values are unique - manually added prefix numbers
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: Specifying width/height in layout() is now deprecated.
Please specify in ggplotly() or plot_ly()
output file: metaseqr2_report.knit.md

Output created: /tmp/RtmpeP07h5/test3/index.html


2021-10-14 07:46:37: Data processing finished!


Total processing time: 36 seconds


2021-10-14 07:46:37: 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: 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: fisher
Multiple testing correction: BH
p-value threshold: 0.05
Logarithmic transformation offset: 1
Analysis preset: medium_basic
Quality control plots: mds, filtered, correl, pairwise, boxplot, gcbias, lengthbias, meandiff, meanvar, deheatmap, volcano, mastat
Figure format: png
Output directory: /tmp/RtmpeP07h5/test4
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/RtmpeP07h5/test4/data/gene_model.RData
Removing genes with zero counts in all samples...
Normalizing with: edaseq
Applying gene filter length...
  Threshold below which ignored: 500
Applying gene filter avgReads...
  Threshold below which ignored: 0.0707638509084404
Applying gene filter expression...
  Threshold below which ignored: 67
Applying gene filter biotype...
  Biotypes ignored: rRNA
2107 genes filtered out
1680 genes remain after filtering
Running statistical tests with: edger
  Contrast: adult_8_weeks_vs_e14.5
  Contrast adult_8_weeks_vs_e14.5: found 1083 genes
Running statistical tests with: limma
  Contrast: adult_8_weeks_vs_e14.5
  Contrast adult_8_weeks_vs_e14.5: found 1084 genes
Performing meta-analysis with fisher
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...
  Plotting correl...
  Plotting pairwise...
  Plotting boxplot...
  Plotting gcbias...
  Plotting lengthbias...
  Plotting meandiff...
  Plotting meanvar...
  Plotting boxplot...
  Plotting gcbias...
  Plotting lengthbias...
  Plotting meandiff...
  Plotting meanvar...
  Plotting deheatmap...
  Contrast: adult_8_weeks_vs_e14.5
  Plotting volcano...
  Contrast: adult_8_weeks_vs_e14.5
  Plotting mastat...
  Contrast: adult_8_weeks_vs_e14.5
  Plotting filtered...
  Importing mds...
  Importing pairwise...
  Importing filtered...
  Importing boxplot...
  Importing gcbias...
  Importing lengthbias...
  Importing meandif...
  Importing meanvar...
  Importing volcano
    adult_8_weeks_vs_e14.5 adult_8_weeks_vs_e14.5
  Importing mastat
    adult_8_weeks_vs_e14.5 adult_8_weeks_vs_e14.5
Writing plot database in /tmp/RtmpeP07h5/test4/data/reportdb.js
Creating HTML report...
Compressing figures...  adding: tmp/RtmpeP07h5/test4/plots/qc/correlation_correlogram.png (deflated 2%)
  adding: tmp/RtmpeP07h5/test4/plots/qc/correlation_heatmap.png (deflated 13%)
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processing file: metaseqr2_report.Rmd
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
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Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
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Warning in fix_not_all_unique(rownames(x)) :
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Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
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Warning: Specifying width/height in layout() is now deprecated.
Please specify in ggplotly() or plot_ly()
Warning in fix_not_all_unique(rownames(x)) :
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output file: metaseqr2_report.knit.md

Output created: /tmp/RtmpeP07h5/test4/index.html


2021-10-14 07:47:06: Data processing finished!


Total processing time: 29 seconds


Downsampling counts...
Estimating initial dispersion population...
Estimating dispersions using log-likelihood...
Warning in log(mu * phi/(1 + mu * phi)) : NaNs produced
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Warning in log(mu * phi/(1 + mu * phi)) : NaNs produced
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Warning in log(mu * phi/(1 + mu * phi)) : NaNs produced
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Warning in log(mu * phi/(1 + mu * phi)) : NaNs produced
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Warning in log(mu * phi/(1 + mu * phi)) : NaNs produced
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Warning in log(mu * phi/(1 + mu * phi)) : NaNs produced
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Warning in log(mu * phi/(1 + mu * phi)) : NaNs produced
Warning in optimize(mlfo, c(x$h - 0.01, x$h + 0.01), y = x$y, tol = eps) :
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Warning in log(mu * phi/(1 + mu * phi)) : NaNs produced
Warning in optimize(mlfo, c(x$h - 0.01, x$h + 0.01), y = x$y, tol = eps) :
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Warning in log(mu * phi/(1 + mu * phi)) : NaNs produced
Warning in optimize(mlfo, c(x$h - 0.01, x$h + 0.01), y = x$y, tol = eps) :
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Warning in log(mu * phi/(1 + mu * phi)) : NaNs produced
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Warning in log(mu * phi/(1 + mu * phi)) : NaNs produced
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Warning in log(mu * phi/(1 + mu * phi)) : NaNs produced
Warning in optimize(mlfo, c(x$h - 0.01, x$h + 0.01), y = x$y, tol = eps) :
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Warning in log(mu * phi/(1 + mu * phi)) : NaNs produced
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Warning in optimize(mlfo, c(x$h - 0.01, x$h + 0.01), y = x$y, tol = eps) :
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Running simulations... This procedure requires time... Please wait...Using Ensembl host https://nov2020.archive.ensembl.org
Ensembl site unresponsive, trying asia mirror
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Error: processing vignette 'metaseqr2-statistics.Rmd' failed with diagnostics:
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--- failed re-building ‘metaseqr2-statistics.Rmd’

SUMMARY: processing the following file failed:
  ‘metaseqr2-statistics.Rmd’

Error: Vignette re-building failed.
Execution halted