############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data TCGAbiolinks ### ############################################################################## ############################################################################## * checking for file ‘TCGAbiolinks/DESCRIPTION’ ... OK * preparing ‘TCGAbiolinks’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘analysis.Rmd’ using rmarkdown ℹ Loading TCGAbiolinks Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'matrixStats' The following objects are masked from 'package:TCGAbiolinks': count, rowRanges 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:TCGAbiolinks': IQR, mad, sd, var, xtabs 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:base': I, expand.grid, unname Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:TCGAbiolinks': 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 The following object is masked from 'package:TCGAbiolinks': content Attaching package: 'dplyr' The following object is masked from 'package:Biobase': combine The following objects are masked from 'package:GenomicRanges': intersect, setdiff, union The following object is masked from 'package:GenomeInfoDb': intersect The following objects are masked from 'package:IRanges': collapse, desc, intersect, setdiff, slice, union The following objects are masked from 'package:S4Vectors': first, intersect, rename, setdiff, setequal, union The following objects are masked from 'package:BiocGenerics': combine, intersect, setdiff, union The following object is masked from 'package:matrixStats': count The following objects are masked from 'package:TCGAbiolinks': count, filter, lag, summarize The following object is masked from 'package:testthat': matches The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union --- finished re-building ‘analysis.Rmd’ --- re-building ‘casestudy.Rmd’ using rmarkdown --- finished re-building ‘casestudy.Rmd’ --- re-building ‘classifiers.Rmd’ using rmarkdown --- finished re-building ‘classifiers.Rmd’ --- re-building ‘clinical.Rmd’ using rmarkdown -------------------------------------- o GDCquery: Searching in GDC database -------------------------------------- Genome of reference: hg38 -------------------------------------------- oo Accessing GDC. This might take a while... -------------------------------------------- ooo Project: TCGA-ACC -------------------- oo Filtering results -------------------- ooo By data.format ooo By data.type ---------------- oo Checking data ---------------- ooo Checking if there are duplicated cases Warning: There are more than one file for the same case. Please verify query results. You can use the command View(getResults(query)) in rstudio ooo Checking if there are results for the query ------------------- o Preparing output ------------------- Downloading data for project TCGA-ACC GDCdownload will download 7 files. A total of 160.95 KB Downloading as: Thu_Jul__7_06_31_30_2022.tar.gz New names: • `metastatic_tumor_site` -> `metastatic_tumor_site...38` • `metastatic_tumor_site` -> `metastatic_tumor_site...39` -------------------------------------- o GDCquery: Searching in GDC database -------------------------------------- Genome of reference: hg38 -------------------------------------------- oo Accessing GDC. This might take a while... -------------------------------------------- ooo Project: TCGA-ACC -------------------- oo Filtering results -------------------- ooo By data.format ooo By data.type ooo By file.type ---------------- oo Checking data ---------------- ooo Checking if there are duplicated cases ooo Checking if there are results for the query ------------------- o Preparing output ------------------- Downloading data for project TCGA-ACC Of the 1 files for download 1 already exist. All samples have been already downloaded -------------------------------------- o GDCquery: Searching in GDC database -------------------------------------- Genome of reference: hg38 -------------------------------------------- oo Accessing GDC. This might take a while... -------------------------------------------- ooo Project: TCGA-BRCA -------------------- oo Filtering results -------------------- ooo By data.format ooo By data.type ---------------- oo Checking data ---------------- ooo Checking if there are duplicated cases Warning: There are more than one file for the same case. Please verify query results. You can use the command View(getResults(query)) in rstudio ooo Checking if there are results for the query ------------------- o Preparing output ------------------- Downloading data for project TCGA-BRCA GDCdownload will download 9 files. A total of 3.585413 MB Downloading as: Thu_Jul__7_06_32_16_2022.tar.gz -------------------------------------- o GDCquery: Searching in GDC database -------------------------------------- Genome of reference: hg38 -------------------------------------------- oo Accessing GDC. This might take a while... -------------------------------------------- ooo Project: TCGA-BRCA -------------------- oo Filtering results -------------------- ooo By data.format ooo By data.type ---------------- oo Checking data ---------------- ooo Checking if there are duplicated cases Warning: There are more than one file for the same case. Please verify query results. You can use the command View(getResults(query)) in rstudio ooo Checking if there are results for the query ------------------- o Preparing output ------------------- Downloading data for project TCGA-BRCA GDCdownload will download 10 files. A total of 7.705475 MB Downloading as: Thu_Jul__7_06_33_26_2022.tar.gz Warning: One or more parsing issues, see `problems()` for details -------------------------------------- o GDCquery: Searching in GDC database -------------------------------------- Genome of reference: hg38 -------------------------------------------- oo Accessing GDC. This might take a while... -------------------------------------------- ooo Project: TCGA-COAD -------------------- oo Filtering results -------------------- ooo By file.type ooo By barcode ---------------- oo Checking data ---------------- ooo Checking if there are duplicated cases Warning: There are more than one file for the same case. Please verify query results. You can use the command View(getResults(query)) in rstudio ooo Checking if there are results for the query ------------------- o Preparing output ------------------- Downloading data for project TCGA-COAD GDCdownload will download 3 files. A total of 148.797 KB Downloading as: Thu_Jul__7_06_35_07_2022.tar.gz To get the following information please change the clinical.info argument => new_tumor_events: new_tumor_event => drugs: drug => follow_ups: follow_up => radiations: radiation Parsing follow up version: follow_up_v1.0 Adding stage event information Warning: `funs()` was deprecated in dplyr 0.8.0. Please use a list of either functions or lambdas: # Simple named list: list(mean = mean, median = median) # Auto named with `tibble::lst()`: tibble::lst(mean, median) # Using lambdas list(~ mean(., trim = .2), ~ median(., na.rm = TRUE)) This warning is displayed once every 8 hours. Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated. -------------------------------------- o GDCquery: Searching in GDC database -------------------------------------- Genome of reference: hg19 -------------------------------------------- oo Accessing GDC. This might take a while... -------------------------------------------- ooo Project: TCGA-COAD -------------------- oo Filtering results -------------------- ooo By data.type ooo By barcode ---------------- oo Checking data ---------------- ooo Checking if there are duplicated cases Warning: There are more than one file for the same case. Please verify query results. You can use the command View(getResults(query)) in rstudio ooo Checking if there are results for the query ------------------- o Preparing output ------------------- -------------------------------------- o GDCquery: Searching in GDC database -------------------------------------- Genome of reference: hg38 -------------------------------------------- oo Accessing GDC. This might take a while... -------------------------------------------- ooo Project: TCGA-OV -------------------- oo Filtering results -------------------- ooo By data.type ---------------- oo Checking data ---------------- ooo Checking if there are duplicated cases Warning: There are more than one file for the same case. Please verify query results. You can use the command View(getResults(query)) in rstudio ooo Checking if there are results for the query ------------------- o Preparing output ------------------- -------------------------------------- o GDCquery: Searching in GDC database -------------------------------------- Genome of reference: hg38 -------------------------------------------- oo Accessing GDC. This might take a while... -------------------------------------------- ooo Project: TCGA-COAD -------------------- oo Filtering results -------------------- ooo By experimental.strategy ooo By data.type ooo By barcode ---------------- oo Checking data ---------------- ooo Checking if there are duplicated cases ooo Checking if there are results for the query ------------------- o Preparing output ------------------- -------------------------------------- o GDCquery: Searching in GDC database -------------------------------------- Genome of reference: hg19 -------------------------------------------- oo Accessing GDC. This might take a while... -------------------------------------------- ooo Project: TCGA-COAD -------------------- oo Filtering results -------------------- ooo By data.type ooo By barcode ---------------- oo Checking data ---------------- ooo Checking if there are duplicated cases ooo Checking if there are results for the query ------------------- o Preparing output ------------------- -------------------------------------- o GDCquery: Searching in GDC database -------------------------------------- Genome of reference: hg19 -------------------------------------------- oo Accessing GDC. This might take a while... -------------------------------------------- ooo Project: TCGA-COAD -------------------- oo Filtering results -------------------- ooo By data.type ooo By barcode ---------------- oo Checking data ---------------- ooo Checking if there are duplicated cases ooo Checking if there are results for the query ------------------- o Preparing output ------------------- -------------------------------------- o GDCquery: Searching in GDC database -------------------------------------- Genome of reference: hg19 -------------------------------------------- oo Accessing GDC. This might take a while... -------------------------------------------- ooo Project: TCGA-COAD -------------------- oo Filtering results -------------------- ooo By data.type ooo By file.type ---------------- oo Checking data ---------------- ooo Checking if there are duplicated cases Warning: There are more than one file for the same case. Please verify query results. You can use the command View(getResults(query)) in rstudio ooo Checking if there are results for the query ------------------- o Preparing output ------------------- --- finished re-building ‘clinical.Rmd’ --- re-building ‘download_prepare.Rmd’ using rmarkdown --- finished re-building ‘download_prepare.Rmd’ --- re-building ‘extension.Rmd’ using rmarkdown --- finished re-building ‘extension.Rmd’ --- re-building ‘gui.Rmd’ using rmarkdown --- finished re-building ‘gui.Rmd’ --- re-building ‘index.Rmd’ using rmarkdown --- finished re-building ‘index.Rmd’ --- re-building ‘mutation.Rmd’ using rmarkdown -------------------------------------- o GDCquery: Searching in GDC database -------------------------------------- Genome of reference: hg19 -------------------------------------------- oo Accessing GDC. This might take a while... -------------------------------------------- ooo Project: TCGA-CHOL -------------------- oo Filtering results -------------------- ooo By access ooo By data.type ---------------- oo Checking data ---------------- ooo Checking if there are duplicated cases Warning: There are more than one file for the same case. Please verify query results. You can use the command View(getResults(query)) in rstudio ooo Checking if there are results for the query ------------------- o Preparing output ------------------- Quitting from lines 143-146 (mutation.Rmd) Error: processing vignette 'mutation.Rmd' failed with diagnostics: there is no package called 'maftools' --- failed re-building ‘mutation.Rmd’ --- re-building ‘query.Rmd’ using rmarkdown -------------------------------------- o GDCquery: Searching in GDC database -------------------------------------- Genome of reference: hg38 -------------------------------------------- oo Accessing GDC. This might take a while... -------------------------------------------- ooo Project: TCGA-GBM ooo Project: TCGA-LGG -------------------- oo Filtering results -------------------- ooo By platform ooo By sample.type ---------------- oo Checking data ---------------- ooo Checking if there are duplicated cases Warning: There are more than one file for the same case. Please verify query results. You can use the command View(getResults(query)) in rstudio ooo Checking if there are results for the query ------------------- o Preparing output ------------------- -------------------------------------- o GDCquery: Searching in GDC database -------------------------------------- Genome of reference: hg38 -------------------------------------------- oo Accessing GDC. This might take a while... -------------------------------------------- ooo Project: TCGA-ACC -------------------- oo Filtering results -------------------- ooo By data.format ooo By data.type ooo By workflow.type ---------------- oo Checking data ---------------- ooo Checking if there are duplicated cases ooo Checking if there are results for the query ------------------- o Preparing output ------------------- -------------------------------------- o GDCquery: Searching in GDC database -------------------------------------- Genome of reference: hg38 -------------------------------------------- oo Accessing GDC. This might take a while... -------------------------------------------- ooo Project: TCGA-ACC -------------------- oo Filtering results -------------------- ooo By data.format ooo By data.type ooo By workflow.type ---------------- oo Checking data ---------------- ooo Checking if there are duplicated cases ooo Checking if there are results for the query ------------------- o Preparing output ------------------- -------------------------------------- o GDCquery: Searching in GDC database -------------------------------------- Genome of reference: hg38 -------------------------------------------- oo Accessing GDC. This might take a while... -------------------------------------------- ooo Project: TCGA-ACC -------------------- oo Filtering results -------------------- ooo By data.format ooo By data.type ooo By workflow.type ---------------- oo Checking data ---------------- ooo Checking if there are duplicated cases ooo Checking if there are results for the query ------------------- o Preparing output ------------------- -------------------------------------- o GDCquery: Searching in GDC database -------------------------------------- Genome of reference: hg38 -------------------------------------------- oo Accessing GDC. This might take a while... -------------------------------------------- ooo Project: TCGA-ACC -------------------- oo Filtering results -------------------- ooo By data.format ooo By data.type ooo By workflow.type ---------------- oo Checking data ---------------- ooo Checking if there are duplicated cases ooo Checking if there are results for the query ------------------- o Preparing output ------------------- -------------------------------------- o GDCquery: Searching in GDC database -------------------------------------- Genome of reference: hg38 -------------------------------------------- oo Accessing GDC. This might take a while... -------------------------------------------- ooo Project: TCGA-ACC -------------------- oo Filtering results -------------------- ooo By data.format ooo By data.type ooo By workflow.type ---------------- oo Checking data ---------------- ooo Checking if there are duplicated cases ooo Checking if there are results for the query ------------------- o Preparing output ------------------- -------------------------------------- o GDCquery: Searching in GDC database -------------------------------------- Genome of reference: hg19 -------------------------------------------- oo Accessing GDC. This might take a while... -------------------------------------------- ooo Project: TCGA-GBM -------------------- oo Filtering results -------------------- ooo By platform ---------------- oo Checking data ---------------- ooo Checking if there are duplicated cases ooo Checking if there are results for the query ------------------- o Preparing output ------------------- -------------------------------------- o GDCquery: Searching in GDC database -------------------------------------- Genome of reference: hg19 -------------------------------------------- oo Accessing GDC. This might take a while... -------------------------------------------- ooo Project: TCGA-GBM -------------------- oo Filtering results -------------------- ooo By platform ooo By experimental.strategy ooo By data.type ooo By file.type ooo By barcode ---------------- oo Checking data ---------------- ooo Checking if there are duplicated cases ooo Checking if there are results for the query ------------------- o Preparing output ------------------- Rows: 47 Columns: 4 ── Column specification ──────────────────────────────────────────────────────── Delimiter: "\t" chr (3): id, filename, md5 dbl (1): size 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. Accessing information for project: TCGA-ACC --- finished re-building ‘query.Rmd’ --- re-building ‘stemness_score.Rmd’ using rmarkdown Quitting from lines 52-83 (stemness_score.Rmd) Error: processing vignette 'stemness_score.Rmd' failed with diagnostics: EDASeq package is needed for this function to work. Please install it. --- failed re-building ‘stemness_score.Rmd’ --- re-building ‘subtypes.Rmd’ using rmarkdown --- finished re-building ‘subtypes.Rmd’ SUMMARY: processing the following files failed: ‘mutation.Rmd’ ‘stemness_score.Rmd’ Error: Vignette re-building failed. Execution halted