############################################################################## ############################################################################## ### ### 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 ================================================== downloaded 238 bytes trying URL 'http://hgdownload.cse.ucsc.edu/goldenPath/eboVir3/database/chromInfo.txt.gz' Content type 'application/x-gzip' length 71 bytes ================================================== downloaded 71 bytes trying URL 'http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/genePredToGtf' Content type 'unknown' length 38689208 bytes (36.9 MB) ================================================== downloaded 36.9 MB Warning in buildCustomAnnotation(gtfFile = gtfFile, metadata = list(organism = "eboVir3_test", : A version should be provided with metadata! 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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( = FALSE)` is deprecated. Please use `guides( = "none")` instead. Warning: `guides( = FALSE)` is deprecated. Please use `guides( = "none")` instead. Warning: `guides( = FALSE)` is deprecated. Please use `guides( = "none")` instead. Warning: `guides( = FALSE)` is deprecated. Please use `guides( = "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... 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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( = FALSE)` is deprecated. Please use `guides( = "none")` instead. Warning: `guides( = FALSE)` is deprecated. Please use `guides( = "none")` instead. Warning: `guides( = FALSE)` is deprecated. Please use `guides( = "none")` instead. Warning: `guides( = FALSE)` is deprecated. Please use `guides( = "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... 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Please use `guides( = "none")` instead. Warning: `guides( = FALSE)` is deprecated. Please use `guides( = "none")` instead. Warning: `guides( = FALSE)` is deprecated. Please use `guides( = "none")` instead. Warning: `guides( = FALSE)` is deprecated. Please use `guides( = "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( = FALSE)` is deprecated. Please use `guides( = "none")` instead. Warning: `guides( = FALSE)` is deprecated. Please use `guides( = "none")` instead. Warning: `guides( = FALSE)` is deprecated. Please use `guides( = "none")` instead. Warning: `guides( = FALSE)` is deprecated. Please use `guides( = "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( = FALSE)` is deprecated. Please use `guides( = "none")` instead. Warning: `guides( = FALSE)` is deprecated. Please use `guides( = "none")` instead. Warning: `guides( = FALSE)` is deprecated. Please use `guides( = "none")` instead. Warning: `guides( = FALSE)` is deprecated. Please use `guides( = "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... 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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( = FALSE)` is deprecated. Please use `guides( = "none")` instead. Warning: `guides( = FALSE)` is deprecated. Please use `guides( = "none")` instead. Warning: `guides( = FALSE)` is deprecated. Please use `guides( = "none")` instead. Warning: `guides( = FALSE)` is deprecated. Please use `guides( = "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/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 Warning in optimize(mlfo, c(x$h - 0.01, x$h + 0.01), y = x$y, tol = eps) : NA/Inf replaced by maximum positive value Warning in log(mu * phi/(1 + mu * phi)) : NaNs produced Warning in optimize(mlfo, c(x$h - 0.01, x$h + 0.01), y = x$y, tol = eps) : NA/Inf replaced by maximum positive value 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$y, tol = eps) : NA/Inf replaced by maximum positive value Warning in log(mu * phi/(1 + mu * phi)) : NaNs produced Warning in optimize(mlfo, c(x$h - 0.01, x$h + 0.01), y = x$y, tol = eps) : NA/Inf replaced by maximum positive value 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$y, tol = eps) : NA/Inf replaced by maximum positive value Warning in log(mu * phi/(1 + mu * phi)) : NaNs produced Warning in optimize(mlfo, c(x$h - 0.01, x$h + 0.01), y = x$y, tol = eps) : NA/Inf replaced by maximum positive value 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$y, tol = eps) : NA/Inf replaced by maximum positive value Warning in log(mu * phi/(1 + mu * phi)) : NaNs produced Warning in optimize(mlfo, c(x$h - 0.01, x$h + 0.01), y = x$y, tol = eps) : NA/Inf replaced by maximum positive value 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$y, tol = eps) : NA/Inf replaced by maximum positive value Warning in log(mu * phi/(1 + mu * phi)) : NaNs produced Warning in optimize(mlfo, c(x$h - 0.01, x$h + 0.01), y = x$y, tol = eps) : NA/Inf replaced by maximum positive value 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$y, tol = eps) : NA/Inf replaced by maximum positive value Warning in log(mu * phi/(1 + mu * phi)) : NaNs produced Warning in optimize(mlfo, c(x$h - 0.01, x$h + 0.01), y = x$y, tol = eps) : NA/Inf replaced by maximum positive value 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$y, tol = eps) : NA/Inf replaced by maximum positive value Warning in log(mu * phi/(1 + mu * phi)) : NaNs produced Warning in optimize(mlfo, c(x$h - 0.01, x$h + 0.01), y = x$y, tol = eps) : NA/Inf replaced by maximum positive value 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$y, tol = eps) : NA/Inf replaced by maximum positive value Warning in log(mu * phi/(1 + mu * phi)) : NaNs produced Warning in optimize(mlfo, c(x$h - 0.01, x$h + 0.01), y = x$y, tol = eps) : NA/Inf replaced by maximum positive value 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$y, tol = eps) : NA/Inf replaced by maximum positive value Warning in log(mu * phi/(1 + mu * phi)) : NaNs produced Warning in optimize(mlfo, c(x$h - 0.01, x$h + 0.01), y = x$y, tol = eps) : NA/Inf replaced by maximum positive value 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$y, tol = eps) : NA/Inf replaced by maximum positive value Warning in log(mu * phi/(1 + mu * phi)) : NaNs produced Warning in optimize(mlfo, c(x$h - 0.01, x$h + 0.01), y = x$y, tol = eps) : NA/Inf replaced by maximum positive value 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$y, tol = eps) : NA/Inf replaced by maximum positive value Warning in log(mu * phi/(1 + mu * phi)) : NaNs produced Warning in optimize(mlfo, c(x$h - 0.01, x$h + 0.01), y = x$y, tol = eps) : NA/Inf replaced by maximum positive value 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$y, tol = eps) : NA/Inf replaced by maximum positive value Warning in log(mu * phi/(1 + mu * phi)) : NaNs produced Warning in optimize(mlfo, c(x$h - 0.01, x$h + 0.01), y = x$y, tol = eps) : NA/Inf replaced by maximum positive value 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$y, tol = eps) : NA/Inf replaced by maximum positive value Warning in log(mu * phi/(1 + mu * phi)) : NaNs produced Warning in optimize(mlfo, c(x$h - 0.01, x$h + 0.01), y = x$y, tol = eps) : NA/Inf replaced by maximum positive value 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$y, tol = eps) : NA/Inf replaced by maximum positive value Warning in log(mu * phi/(1 + mu * phi)) : NaNs produced Warning in optimize(mlfo, c(x$h - 0.01, x$h + 0.01), y = x$y, tol = eps) : NA/Inf replaced by maximum positive value 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$y, tol = eps) : NA/Inf replaced by maximum positive value Warning in log(mu * phi/(1 + mu * phi)) : NaNs produced Warning in optimize(mlfo, c(x$h - 0.01, x$h + 0.01), y = x$y, tol = eps) : NA/Inf replaced by maximum positive value 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) : NA/Inf replaced by maximum positive value Running simulations... This procedure requires time... Please wait...Using Ensembl host https://nov2020.archive.ensembl.org Ensembl site unresponsive, trying asia mirror Quitting from lines 437-445 (metaseqr2-statistics.Rmd) Error: processing vignette 'metaseqr2-statistics.Rmd' failed with diagnostics: Internal Server Error (HTTP 500). --- failed re-building ‘metaseqr2-statistics.Rmd’ SUMMARY: processing the following file failed: ‘metaseqr2-statistics.Rmd’ Error: Vignette re-building failed. Execution halted