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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data weitrix
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* 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
