Back to Build/check report for BioC 3.16 annotations |
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This page was generated on 2023-04-12 06:00:10 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
To the developers/maintainers of the GenomicState package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 20/36 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||||
GenomicState 0.99.15 (landing page) Leonardo Collado-Torres
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | ERROR | ||||||||
Package: GenomicState |
Version: 0.99.15 |
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:GenomicState.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings GenomicState_0.99.15.tar.gz |
StartedAt: 2023-04-12 03:04:43 -0400 (Wed, 12 Apr 2023) |
EndedAt: 2023-04-12 03:10:09 -0400 (Wed, 12 Apr 2023) |
EllapsedTime: 325.8 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: GenomicState.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:GenomicState.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings GenomicState_0.99.15.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.16-data-annotation/meat/GenomicState.Rcheck’ * using R version 4.2.3 (2023-03-15) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * checking for file ‘GenomicState/DESCRIPTION’ ... OK * this is package ‘GenomicState’ version ‘0.99.15’ * 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 ‘GenomicState’ 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 loading without being on the library search path ... OK * checking dependencies in R code ... NOTE Unexported objects imported by ':::' calls: ‘GenomicFeatures:::.prepareGFFMetadata’ ‘GenomicFeatures:::.tidy_seqinfo’ See the note in ?`:::` about the use of this operator. * 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 ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed gencode_annotated_genes 25.397 0.728 26.127 GenomicStateHub 17.738 0.676 18.941 gencode_genomic_state 9.844 0.168 10.012 * 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: Backtrace: ▆ 1. └─GenomicState::gencode_txdb("31", "hg19", chrs = "chr21") at test-gencode.R:1:0 2. ├─rtracklayer::import(gtf_file) 3. └─rtracklayer::import(gtf_file) 4. ├─BiocIO::import(FileForFormat(con), ...) 5. └─BiocIO::import(FileForFormat(con), ...) 6. ├─BiocIO::import(con, ...) 7. └─rtracklayer::import(con, ...) 8. └─rtracklayer (local) .local(con, format, text, ...) 9. └─utils::download.file(resource(con), destfile) [ FAIL 1 | WARN 1 | SKIP 0 | PASS 0 ] 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 ... ‘GenomicState.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 1 NOTE See ‘/home/biocbuild/bbs-3.16-data-annotation/meat/GenomicState.Rcheck/00check.log’ for details.
GenomicState.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL GenomicState ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’ * installing *source* package ‘GenomicState’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (GenomicState)
GenomicState.Rcheck/tests/testthat.Rout.fail
R version 4.2.3 (2023-03-15) -- "Shortstop Beagle" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(GenomicState) Loading required package: AnnotationHub Loading required package: BiocGenerics Attaching package: 'BiocGenerics' 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, aperm, 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: BiocFileCache Loading required package: dbplyr > > test_check("GenomicState") trying URL 'ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_31/GRCh37_mapping/gencode.v31lift37.annotation.gtf.gz' [ FAIL 1 | WARN 1 | SKIP 0 | PASS 0 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-gencode.R:1:1'): (code run outside of `test_that()`) ─────────── Error in `download.file(resource(con), destfile)`: cannot open URL 'ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_31/GRCh37_mapping/gencode.v31lift37.annotation.gtf.gz' Backtrace: ▆ 1. └─GenomicState::gencode_txdb("31", "hg19", chrs = "chr21") at test-gencode.R:1:0 2. ├─rtracklayer::import(gtf_file) 3. └─rtracklayer::import(gtf_file) 4. ├─BiocIO::import(FileForFormat(con), ...) 5. └─BiocIO::import(FileForFormat(con), ...) 6. ├─BiocIO::import(con, ...) 7. └─rtracklayer::import(con, ...) 8. └─rtracklayer (local) .local(con, format, text, ...) 9. └─utils::download.file(resource(con), destfile) [ FAIL 1 | WARN 1 | SKIP 0 | PASS 0 ] Error: Test failures Execution halted
GenomicState.Rcheck/GenomicState-Ex.timings
name | user | system | elapsed | |
GenomicStateHub | 17.738 | 0.676 | 18.941 | |
gencode_annotated_genes | 25.397 | 0.728 | 26.127 | |
gencode_genomic_state | 9.844 | 0.168 | 10.012 | |
gencode_txdb | 0.448 | 0.004 | 0.452 | |
local_metadata | 0.009 | 0.000 | 0.009 | |