############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data glmSparseNet ### ############################################################################## ############################################################################## * checking for file ‘glmSparseNet/DESCRIPTION’ ... OK * preparing ‘glmSparseNet’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘example_brca_logistic.Rmd’ using rmarkdown Attaching package: 'dplyr' The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union Loading required package: MultiAssayExperiment Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'matrixStats' 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 Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Attaching package: 'BiocGenerics' 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: S4Vectors Attaching package: 'S4Vectors' The following objects are masked from 'package:dplyr': first, rename The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Attaching package: 'IRanges' The following objects are masked from 'package:dplyr': collapse, desc, slice Loading required package: GenomeInfoDb 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 Attaching package: 'TCGAutils' The following object is masked from 'package:MultiAssayExperiment': splitAssays Loading required package: Matrix Attaching package: 'Matrix' The following object is masked from 'package:S4Vectors': expand Loading required package: glmnet Loaded glmnet 4.1-3 snapshotDate(): 2021-10-19 Working on: BRCA_RNASeq2GeneNorm-20160128 see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation loading from cache Working on: BRCA_colData-20160128 see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation loading from cache Working on: BRCA_metadata-20160128 see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation loading from cache Working on: BRCA_sampleMap-20160128 see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation loading from cache harmonizing input: removing 13161 sampleMap rows not in names(experiments) removing 5 colData rownames not in sampleMap 'primary' Quitting from lines 133-134 (example_brca_logistic.Rmd) Error: processing vignette 'example_brca_logistic.Rmd' failed with diagnostics: Problem while computing `..1 = value > 0`. Caused by error: ! object 'value' not found --- failed re-building ‘example_brca_logistic.Rmd’ --- re-building ‘example_brca_protein-protein-interactions_survival.Rmd’ using rmarkdown Loading required package: grid Warning: Problem while computing `Days.to.Last.Contact = as.integer(Days.to.Date.of.Last.Contact)`. ℹ NAs introduced by coercion Warning in gsub("~m", msg, message, fixed = TRUE) : argument 'replacement' has length > 1 and only the first element will be used --- finished re-building ‘example_brca_protein-protein-interactions_survival.Rmd’ --- re-building ‘example_brca_survival.Rmd’ using rmarkdown Warning: Problem while computing `Days.to.Last.Contact = as.integer(Days.to.Date.of.Last.Contact)`. ℹ NAs introduced by coercion Quitting from lines 164-165 (example_brca_survival.Rmd) Error: processing vignette 'example_brca_survival.Rmd' failed with diagnostics: Problem while computing `..1 = value > 0`. Caused by error: ! object 'value' not found --- failed re-building ‘example_brca_survival.Rmd’ --- re-building ‘example_prad_survival.Rmd’ using rmarkdown Quitting from lines 161-162 (example_prad_survival.Rmd) Error: processing vignette 'example_prad_survival.Rmd' failed with diagnostics: Problem while computing `..1 = value > 0`. Caused by error: ! object 'value' not found --- failed re-building ‘example_prad_survival.Rmd’ --- re-building ‘example_skcm_survival.Rmd’ using rmarkdown Warning: Problem while computing `time = max(days_to_last_followup, days_to_death, na.rm = TRUE)`. ℹ no non-missing arguments to max; returning -Inf ℹ The warning occurred in row 122. Warning: Problem while computing `time = max(days_to_last_followup, days_to_death, na.rm = TRUE)`. ℹ no non-missing arguments to max; returning -Inf ℹ The warning occurred in row 123. Warning: Problem while computing `time = max(days_to_last_followup, days_to_death, na.rm = TRUE)`. ℹ no non-missing arguments to max; returning -Inf ℹ The warning occurred in row 138. Warning: Problem while computing `time = max(days_to_last_followup, days_to_death, na.rm = TRUE)`. ℹ no non-missing arguments to max; returning -Inf ℹ The warning occurred in row 162. Warning: Problem while computing `time = max(days_to_last_followup, days_to_death, na.rm = TRUE)`. ℹ no non-missing arguments to max; returning -Inf ℹ The warning occurred in row 332. Warning: Problem while computing `time = max(days_to_last_followup, days_to_death, na.rm = TRUE)`. ℹ no non-missing arguments to max; returning -Inf ℹ The warning occurred in row 376. Warning: Problem while computing `time = max(days_to_last_followup, days_to_death, na.rm = TRUE)`. ℹ no non-missing arguments to max; returning -Inf ℹ The warning occurred in row 400. Warning: Problem while computing `time = max(days_to_last_followup, days_to_death, na.rm = TRUE)`. ℹ no non-missing arguments to max; returning -Inf ℹ The warning occurred in row 414. Warning: Problem while computing `time = max(days_to_last_followup, days_to_death, na.rm = TRUE)`. ℹ no non-missing arguments to max; returning -Inf ℹ The warning occurred in row 438. Warning: Problem while computing `time = max(days_to_last_followup, days_to_death, na.rm = TRUE)`. ℹ no non-missing arguments to max; returning -Inf ℹ The warning occurred in row 122. Warning: Problem while computing `time = max(days_to_last_followup, days_to_death, na.rm = TRUE)`. ℹ no non-missing arguments to max; returning -Inf ℹ The warning occurred in row 123. Warning: Problem while computing `time = max(days_to_last_followup, days_to_death, na.rm = TRUE)`. ℹ no non-missing arguments to max; returning -Inf ℹ The warning occurred in row 138. Warning: Problem while computing `time = max(days_to_last_followup, days_to_death, na.rm = TRUE)`. ℹ no non-missing arguments to max; returning -Inf ℹ The warning occurred in row 162. Warning: Problem while computing `time = max(days_to_last_followup, days_to_death, na.rm = TRUE)`. ℹ no non-missing arguments to max; returning -Inf ℹ The warning occurred in row 332. Warning: Problem while computing `time = max(days_to_last_followup, days_to_death, na.rm = TRUE)`. ℹ no non-missing arguments to max; returning -Inf ℹ The warning occurred in row 376. Warning: Problem while computing `time = max(days_to_last_followup, days_to_death, na.rm = TRUE)`. ℹ no non-missing arguments to max; returning -Inf ℹ The warning occurred in row 400. Warning: Problem while computing `time = max(days_to_last_followup, days_to_death, na.rm = TRUE)`. ℹ no non-missing arguments to max; returning -Inf ℹ The warning occurred in row 414. Warning: Problem while computing `time = max(days_to_last_followup, days_to_death, na.rm = TRUE)`. ℹ no non-missing arguments to max; returning -Inf ℹ The warning occurred in row 438. Quitting from lines 170-171 (example_skcm_survival.Rmd) Error: processing vignette 'example_skcm_survival.Rmd' failed with diagnostics: Problem while computing `..1 = value > 0`. Caused by error: ! object 'value' not found --- failed re-building ‘example_skcm_survival.Rmd’ --- re-building ‘separate2GroupsCox.Rmd’ using rmarkdown --- finished re-building ‘separate2GroupsCox.Rmd’ SUMMARY: processing the following files failed: ‘example_brca_logistic.Rmd’ ‘example_brca_survival.Rmd’ ‘example_prad_survival.Rmd’ ‘example_skcm_survival.Rmd’ Error: Vignette re-building failed. Execution halted