############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:recount3.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings recount3_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/recount3.Rcheck’ * using R version 4.2.3 (2023-03-15) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘recount3/DESCRIPTION’ ... OK * this is package ‘recount3’ version ‘1.8.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘recount3’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘recount3-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: available_projects > ### Title: List available projects in recount3 > ### Aliases: available_projects > > ### ** Examples > > > ## Find all the human projects > human_projects <- available_projects() 2023-04-10 22:12:22 caching file sra.recount_project.MD.gz. 2023-04-10 22:12:23 caching file gtex.recount_project.MD.gz. 2023-04-10 22:12:23 caching file tcga.recount_project.MD.gz. > > ## Explore the results > dim(human_projects) [1] 8742 6 > head(human_projects) project organism file_source project_home project_type n_samples 1 SRP107565 human sra data_sources/sra data_sources 216 2 SRP149665 human sra data_sources/sra data_sources 4 3 SRP017465 human sra data_sources/sra data_sources 23 4 SRP119165 human sra data_sources/sra data_sources 6 5 SRP133965 human sra data_sources/sra data_sources 12 6 SRP096765 human sra data_sources/sra data_sources 7 > > ## How many are from a data source vs a compilation? > table(human_projects$project_type, useNA = "ifany") data_sources 8742 > > ## What are the unique file sources? > table( + human_projects$file_source[human_projects$project_type == "data_sources"] + ) gtex sra tcga 32 8677 33 > > ## Note that big projects are broken up to make them easier to access > ## For example, GTEx and TCGA are broken up by tissue > head(subset(human_projects, file_source == "gtex")) project organism file_source project_home project_type 8678 ADIPOSE_TISSUE human gtex data_sources/gtex data_sources 8679 MUSCLE human gtex data_sources/gtex data_sources 8680 BLOOD_VESSEL human gtex data_sources/gtex data_sources 8681 HEART human gtex data_sources/gtex data_sources 8682 OVARY human gtex data_sources/gtex data_sources 8683 UTERUS human gtex data_sources/gtex data_sources n_samples 8678 1293 8679 881 8680 1398 8681 942 8682 195 8683 159 > head(subset(human_projects, file_source == "tcga")) project organism file_source project_home project_type n_samples 8710 ACC human tcga data_sources/tcga data_sources 79 8711 BLCA human tcga data_sources/tcga data_sources 433 8712 BRCA human tcga data_sources/tcga data_sources 1256 8713 CESC human tcga data_sources/tcga data_sources 309 8714 CHOL human tcga data_sources/tcga data_sources 45 8715 COAD human tcga data_sources/tcga data_sources 546 > > ## Find all the mouse projects > mouse_projects <- available_projects(organism = "mouse") 2023-04-10 22:12:29 caching file sra.recount_project.MD.gz. > > ## Explore the results > dim(mouse_projects) [1] 10088 6 > head(mouse_projects) project organism file_source project_home project_type n_samples 1 SRP170963 mouse sra data_sources/sra data_sources 368 2 SRP045763 mouse sra data_sources/sra data_sources 22 3 DRP005463 mouse sra data_sources/sra data_sources 12 4 SRP172863 mouse sra data_sources/sra data_sources 8 5 SRP186363 mouse sra data_sources/sra data_sources 13 6 SRP101363 mouse sra data_sources/sra data_sources 22 > > ## How many are from a data source vs a compilation? > table(mouse_projects$project_type, useNA = "ifany") data_sources 10088 > > ## What are the unique file sources? > table( + mouse_projects$file_source[mouse_projects$project_type == "data_sources"] + ) sra 10088 > > ## Use with a custom recount3_url: > available_projects( + recount3_url = "http://snaptron.cs.jhu.edu/data/temp/recount3test", + available_homes = "data_sources/sra" + ) Warning: The 'url' does not exist or is not available. Error in file(file, "rt") : invalid 'description' argument Calls: available_projects ... available_samples -> lapply -> FUN -> read.table -> file Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: 4. └─recount3::locate_url(...) 5. ├─base::match.arg(project_home) 6. │ └─base::eval(formal.args[[as.character(substitute(arg))]], envir = sys.frame(sysP)) 7. │ └─base::eval(formal.args[[as.character(substitute(arg))]], envir = sys.frame(sysP)) 8. └─recount3::project_homes(organism = organism, recount3_url = recount3_url) ── Error ('test-recount3_cache_rm.R:4:1'): (code run outside of `test_that()`) ── Error in `BiocFileCache::bfcrpath(temp_bfc_rm, test_url)`: not all 'rnames' found or unique. Backtrace: ▆ 1. ├─BiocFileCache::bfcrpath(temp_bfc_rm, test_url) at test-recount3_cache_rm.R:4:0 2. └─BiocFileCache::bfcrpath(temp_bfc_rm, test_url) [ FAIL 2 | WARN 3 | SKIP 0 | PASS 50 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 ERRORs See ‘/Users/biocbuild/bbs-3.16-bioc/meat/recount3.Rcheck/00check.log’ for details.