############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data weitrix ### ############################################################################## ############################################################################## * checking for file ‘weitrix/DESCRIPTION’ ... OK * preparing ‘weitrix’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘V1_overview.Rmd’ using rmarkdown --- finished re-building ‘V1_overview.Rmd’ --- re-building ‘V2_tail_length.Rmd’ using rmarkdown ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ── ✔ ggplot2 3.3.6 ✔ purrr 0.3.4 ✔ tibble 3.1.7 ✔ dplyr 1.0.9 ✔ tidyr 1.2.0 ✔ stringr 1.4.0 ✔ readr 2.1.2 ✔ forcats 0.5.1 ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ── ✖ dplyr::filter() masks stats::filter() ✖ dplyr::lag() masks stats::lag() Loading required package: AnnotationDbi Loading required package: stats4 Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following object is masked from 'package:limma': plotMA The following objects are masked from 'package:dplyr': combine, intersect, setdiff, union 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 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")'. Loading required package: IRanges Loading required package: S4Vectors Attaching package: 'S4Vectors' The following objects are masked from 'package:dplyr': first, rename The following object is masked from 'package:tidyr': expand The following objects are masked from 'package:base': I, expand.grid, unname Attaching package: 'IRanges' The following objects are masked from 'package:dplyr': collapse, desc, slice The following object is masked from 'package:purrr': reduce Attaching package: 'AnnotationDbi' The following object is masked from 'package:dplyr': select Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'matrixStats' The following objects are masked from 'package:Biobase': anyMissing, rowMedians The following object is masked from 'package:dplyr': count 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 The following object is masked from 'package:Biobase': rowMedians Loading required package: GenomicRanges Loading required package: GenomeInfoDb Rows: 6532 Columns: 21 ── Column specification ──────────────────────────────────────────────────────── Delimiter: "," chr (1): Feature dbl (20): WT-tpre, WT-t0m, WT-t15m, WT-t30m, WT-t45m, WT-t60m, WT-t75m, WT-t... ℹ Use `spec()` to retrieve the full column specification for this data. ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. Rows: 6532 Columns: 21 ── Column specification ──────────────────────────────────────────────────────── Delimiter: "," chr (1): Feature dbl (20): WT-tpre, WT-t0m, WT-t15m, WT-t30m, WT-t45m, WT-t60m, WT-t75m, WT-t... ℹ Use `spec()` to retrieve the full column specification for this data. ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. 'select()' returned 1:1 mapping between keys and columns Finding 6 components Iter 1 R^2=0.42751 1.0sec Iter 2 R^2=0.54354 0.8sec Iter 3 R^2=0.57327 0.9sec Iter 4 R^2=0.58677 0.9sec Iter 5 R^2=0.59221 0.8sec Iter 1 R^2=0.46766 0.8sec Iter 2 R^2=0.53970 0.9sec Iter 3 R^2=0.56648 0.9sec Iter 4 R^2=0.58017 0.9sec Iter 5 R^2=0.58710 0.9sec Iter 1 R^2=0.43957 0.9sec Iter 2 R^2=0.53486 0.9sec Iter 3 R^2=0.56369 0.8sec Iter 4 R^2=0.58320 0.9sec Iter 5 R^2=0.59613 0.9sec Iter 1 R^2=0.60305 0.8sec Iter 2 R^2=0.60611 0.9sec Iter 3 R^2=0.60743 0.8sec Iter 4 R^2=0.60807 0.9sec Iter 5 R^2=0.60841 0.9sec Iter 10 R^2=0.60886 0.8sec Finding 5 components Iter 1 R^2=0.54325 0.8sec Iter 2 R^2=0.55061 0.7sec Iter 3 R^2=0.55611 0.8sec Iter 4 R^2=0.55948 0.8sec Iter 5 R^2=0.56129 0.7sec Iter 1 R^2=0.53721 0.7sec Iter 2 R^2=0.54722 0.8sec Iter 3 R^2=0.55463 0.7sec Iter 4 R^2=0.55835 0.8sec Iter 5 R^2=0.56000 0.8sec Iter 1 R^2=0.54335 0.8sec Iter 2 R^2=0.55168 0.8sec Iter 3 R^2=0.55765 0.8sec Iter 4 R^2=0.56079 1.5sec Iter 5 R^2=0.56218 0.7sec Iter 1 R^2=0.56277 0.6sec Iter 2 R^2=0.56303 0.6sec Iter 3 R^2=0.56316 0.7sec Iter 4 R^2=0.56322 0.7sec Iter 5 R^2=0.56325 0.6sec Finding 4 components Iter 1 R^2=0.49239 0.6sec Iter 2 R^2=0.50166 0.6sec Iter 3 R^2=0.50543 0.6sec Iter 4 R^2=0.50751 0.6sec Iter 5 R^2=0.50869 0.6sec Iter 1 R^2=0.50024 0.6sec Iter 2 R^2=0.50291 0.6sec Iter 3 R^2=0.50370 0.6sec Iter 4 R^2=0.50408 0.6sec Iter 5 R^2=0.50429 0.6sec Iter 1 R^2=0.49031 0.6sec Iter 2 R^2=0.50163 0.6sec Iter 3 R^2=0.50295 0.6sec Iter 4 R^2=0.50340 0.6sec Iter 5 R^2=0.50368 0.6sec Iter 1 R^2=0.50936 0.6sec Iter 2 R^2=0.50974 0.6sec Iter 3 R^2=0.50996 0.6sec Iter 4 R^2=0.51009 0.6sec Iter 5 R^2=0.51016 0.6sec Finding 3 components Iter 1 R^2=0.42432 0.6sec Iter 2 R^2=0.42804 0.6sec Iter 3 R^2=0.43249 0.6sec Iter 4 R^2=0.43711 0.6sec Iter 5 R^2=0.44104 0.5sec Iter 1 R^2=0.44346 0.6sec Iter 2 R^2=0.44856 0.6sec Iter 3 R^2=0.44894 0.6sec Iter 4 R^2=0.44902 0.6sec Iter 5 R^2=0.44907 0.6sec Iter 1 R^2=0.43886 0.6sec Iter 2 R^2=0.44018 0.6sec Iter 3 R^2=0.44137 0.6sec Iter 4 R^2=0.44248 0.5sec Iter 5 R^2=0.44347 0.6sec Iter 1 R^2=0.44910 0.5sec Iter 2 R^2=0.44912 0.6sec Iter 3 R^2=0.44914 0.6sec Iter 4 R^2=0.44915 0.6sec Iter 5 R^2=0.44917 0.5sec Finding 2 components Iter 1 R^2=0.37189 0.5sec Iter 2 R^2=0.37275 0.5sec Iter 3 R^2=0.37314 0.5sec Iter 4 R^2=0.37340 0.6sec Iter 5 R^2=0.37360 0.5sec Iter 1 R^2=0.36737 0.5sec Iter 2 R^2=0.37249 0.5sec Iter 3 R^2=0.37325 0.5sec Iter 4 R^2=0.37351 0.5sec Iter 5 R^2=0.37369 0.5sec Iter 1 R^2=0.31689 0.5sec Iter 2 R^2=0.35156 0.5sec Iter 3 R^2=0.35682 0.5sec Iter 4 R^2=0.35840 0.5sec Iter 5 R^2=0.35999 0.5sec Iter 1 R^2=0.37382 0.5sec Iter 2 R^2=0.37392 0.5sec Iter 3 R^2=0.37400 0.5sec Iter 4 R^2=0.37406 0.5sec Iter 5 R^2=0.37411 0.5sec Iter 10 R^2=0.37423 0.5sec Finding 1 components Iter 1 R^2=0.28154 0.5sec Iter 2 R^2=0.28245 0.4sec Iter 3 R^2=0.28254 0.5sec Iter 4 R^2=0.28255 0.5sec Iter 5 R^2=0.28255 0.5sec Iter 1 R^2=0.23781 0.5sec Iter 2 R^2=0.27594 0.5sec Iter 3 R^2=0.28177 0.5sec Iter 4 R^2=0.28246 0.4sec Iter 5 R^2=0.28254 0.5sec Iter 1 R^2=0.14387 0.5sec Iter 2 R^2=0.24127 0.5sec Iter 3 R^2=0.27715 0.5sec Iter 4 R^2=0.28194 0.5sec Iter 5 R^2=0.28248 0.5sec Iter 1 R^2=0.28255 0.5sec Iter 2 R^2=0.28255 0.4sec Iter 3 R^2=0.28255 0.5sec Iter 4 R^2=0.28255 0.5sec Iter 5 R^2=0.28255 0.4sec --- finished re-building ‘V2_tail_length.Rmd’ --- re-building ‘V3_shift.Rmd’ using rmarkdown Attaching package: 'reshape2' The following object is masked from 'package:tidyr': smiths Rows: 4053 Columns: 6 ── Column specification ──────────────────────────────────────────────────────── Delimiter: "," chr (4): name, chromosome, relation, gene_name dbl (2): strand, pos ℹ Use `spec()` to retrieve the full column specification for this data. ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. Rows: 4053 Columns: 21 ── Column specification ──────────────────────────────────────────────────────── Delimiter: "," chr (1): name dbl (20): WT-tpre, WT-t0m, WT-t15m, WT-t30m, WT-t45m, WT-t60m, WT-t75m, WT-t... ℹ Use `spec()` to retrieve the full column specification for this data. ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. Rows: 1805 Columns: 4 ── Column specification ──────────────────────────────────────────────────────── Delimiter: "," chr (4): name, symbol, biotype, product ℹ Use `spec()` to retrieve the full column specification for this data. ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. Finding 6 components Iter 1 R^2=0.72563 0.3sec Iter 2 R^2=0.83978 0.3sec Iter 3 R^2=0.85744 0.4sec Iter 4 R^2=0.86144 0.3sec Iter 5 R^2=0.86317 0.3sec Iter 1 R^2=0.71776 0.3sec Iter 2 R^2=0.82352 0.3sec Iter 3 R^2=0.85252 0.3sec Iter 4 R^2=0.86117 0.3sec Iter 5 R^2=0.86347 0.3sec Iter 1 R^2=0.67471 0.3sec Iter 2 R^2=0.82470 0.3sec Iter 3 R^2=0.84671 0.3sec Iter 4 R^2=0.85793 0.3sec Iter 5 R^2=0.86275 0.3sec Iter 1 R^2=0.86425 0.3sec Iter 2 R^2=0.86458 0.3sec Iter 3 R^2=0.86474 0.3sec Iter 4 R^2=0.86481 0.3sec Iter 5 R^2=0.86485 0.3sec Finding 5 components Iter 1 R^2=0.81900 0.2sec Iter 2 R^2=0.83113 0.2sec Iter 3 R^2=0.83625 0.3sec Iter 4 R^2=0.83808 0.2sec Iter 5 R^2=0.83887 0.3sec Iter 1 R^2=0.82722 0.2sec Iter 2 R^2=0.83664 0.2sec Iter 3 R^2=0.83995 0.3sec Iter 4 R^2=0.84124 0.2sec Iter 5 R^2=0.84182 0.3sec Iter 1 R^2=0.80691 0.2sec Iter 2 R^2=0.81842 0.2sec Iter 3 R^2=0.82467 0.3sec Iter 4 R^2=0.82833 0.2sec Iter 5 R^2=0.83154 0.3sec Iter 1 R^2=0.84211 0.2sec Iter 2 R^2=0.84226 0.2sec Iter 3 R^2=0.84235 0.3sec Iter 4 R^2=0.84241 0.2sec Iter 5 R^2=0.84245 0.3sec Iter 10 R^2=0.84253 0.3sec Finding 4 components Iter 1 R^2=0.79773 0.2sec Iter 2 R^2=0.80746 0.3sec Iter 3 R^2=0.81042 0.2sec Iter 4 R^2=0.81256 0.3sec Iter 5 R^2=0.81420 0.2sec Iter 1 R^2=0.80835 0.2sec Iter 2 R^2=0.81404 0.3sec Iter 3 R^2=0.81590 0.2sec Iter 4 R^2=0.81643 0.2sec Iter 5 R^2=0.81658 0.3sec Iter 1 R^2=0.71705 0.2sec Iter 2 R^2=0.79636 0.3sec Iter 3 R^2=0.80982 0.2sec Iter 4 R^2=0.81467 0.2sec Iter 5 R^2=0.81606 0.3sec Iter 1 R^2=0.81663 0.2sec Iter 2 R^2=0.81665 0.3sec Iter 3 R^2=0.81665 0.2sec Iter 4 R^2=0.81666 0.2sec Iter 5 R^2=0.81666 0.3sec Finding 3 components Iter 1 R^2=0.73231 0.2sec Iter 2 R^2=0.74384 0.3sec Iter 3 R^2=0.75323 0.2sec Iter 4 R^2=0.76248 0.2sec Iter 5 R^2=0.76938 0.3sec Iter 1 R^2=0.76565 0.2sec Iter 2 R^2=0.77440 0.2sec Iter 3 R^2=0.77545 0.3sec Iter 4 R^2=0.77589 0.2sec Iter 5 R^2=0.77609 0.2sec Iter 1 R^2=0.73669 0.2sec Iter 2 R^2=0.76725 0.3sec Iter 3 R^2=0.77222 0.2sec Iter 4 R^2=0.77450 0.2sec Iter 5 R^2=0.77550 0.3sec Iter 1 R^2=0.77619 0.2sec Iter 2 R^2=0.77623 0.2sec Iter 3 R^2=0.77625 0.3sec Iter 4 R^2=0.77626 0.2sec Iter 5 R^2=0.77626 0.2sec Finding 2 components Iter 1 R^2=0.70180 0.2sec Iter 2 R^2=0.71601 0.3sec Iter 3 R^2=0.71654 0.2sec Iter 4 R^2=0.71674 0.2sec Iter 5 R^2=0.71685 0.2sec Iter 1 R^2=0.67533 0.2sec Iter 2 R^2=0.71124 0.2sec Iter 3 R^2=0.71363 0.2sec Iter 4 R^2=0.71499 0.2sec Iter 5 R^2=0.71585 0.2sec Iter 1 R^2=0.66233 0.2sec Iter 2 R^2=0.71014 0.2sec Iter 3 R^2=0.71336 0.2sec Iter 4 R^2=0.71487 0.2sec Iter 5 R^2=0.71578 0.2sec Iter 1 R^2=0.71690 0.2sec Iter 2 R^2=0.71694 0.2sec Iter 3 R^2=0.71695 0.2sec Iter 4 R^2=0.71696 0.2sec Iter 5 R^2=0.71697 0.2sec Finding 1 components Iter 1 R^2=0.63303 0.2sec Iter 2 R^2=0.63666 0.2sec Iter 3 R^2=0.63703 0.2sec Iter 4 R^2=0.63707 0.2sec Iter 5 R^2=0.63708 0.2sec Iter 1 R^2=0.63305 0.2sec Iter 2 R^2=0.63663 0.3sec Iter 3 R^2=0.63703 0.2sec Iter 4 R^2=0.63707 0.2sec Iter 5 R^2=0.63708 0.2sec Iter 1 R^2=0.40937 0.2sec Iter 2 R^2=0.62647 0.2sec Iter 3 R^2=0.63587 0.2sec Iter 4 R^2=0.63694 0.2sec Iter 5 R^2=0.63706 0.2sec Iter 1 R^2=0.63708 0.2sec Iter 2 R^2=0.63708 0.2sec Iter 3 R^2=0.63708 0.2sec Iter 4 R^2=0.63708 0.2sec Iter 5 R^2=0.63708 0.2sec --- finished re-building ‘V3_shift.Rmd’ --- re-building ‘V4_airway.Rmd’ using rmarkdown Loading required package: grid ======================================== ComplexHeatmap version 2.13.0 Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/ Github page: https://github.com/jokergoo/ComplexHeatmap Documentation: http://jokergoo.github.io/ComplexHeatmap-reference If you use it in published research, please cite: Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics 2016. The new InteractiveComplexHeatmap package can directly export static complex heatmaps into an interactive Shiny app with zero effort. Have a try! This message can be suppressed by: suppressPackageStartupMessages(library(ComplexHeatmap)) ======================================== Quitting from lines 25-40 (V4_airway.Rmd) Error: processing vignette 'V4_airway.Rmd' failed with diagnostics: there is no package called 'EnsDb.Hsapiens.v86' --- failed re-building ‘V4_airway.Rmd’ --- re-building ‘V5_slam_seq.Rmd’ using rmarkdown Rows: 22281 Columns: 28 ── Column specification ──────────────────────────────────────────────────────── Delimiter: "," chr (1): gene dbl (27): no_s4U_Rep_1, no_s4U_Rep_2, no_s4U_Rep_3, 24h_s4U_Rep_1, 24h_s4U_R... ℹ Use `spec()` to retrieve the full column specification for this data. ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. Rows: 22281 Columns: 28 ── Column specification ──────────────────────────────────────────────────────── Delimiter: "," chr (1): gene dbl (27): no_s4U_Rep_1, no_s4U_Rep_2, no_s4U_Rep_3, 24h_s4U_Rep_1, 24h_s4U_R... ℹ Use `spec()` to retrieve the full column specification for this data. ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. Iter 1 R^2=0.75864 1.4sec Iter 2 R^2=0.94304 1.3sec Iter 3 R^2=0.94335 1.9sec Iter 4 R^2=0.94337 1.3sec Iter 5 R^2=0.94337 1.2sec --- finished re-building ‘V5_slam_seq.Rmd’ SUMMARY: processing the following file failed: ‘V4_airway.Rmd’ Error: Vignette re-building failed. Execution halted