Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-09-24 22:54 -0400 (Tue, 24 Sep 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4760 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4497 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4526 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4475 |
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 |
Package 830/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GenomicDataCommons 1.28.0 (landing page) Sean Davis
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
To the developers/maintainers of the GenomicDataCommons package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GenomicDataCommons.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: GenomicDataCommons |
Version: 1.28.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:GenomicDataCommons.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings GenomicDataCommons_1.28.0.tar.gz |
StartedAt: 2024-09-22 23:30:32 -0400 (Sun, 22 Sep 2024) |
EndedAt: 2024-09-22 23:33:03 -0400 (Sun, 22 Sep 2024) |
EllapsedTime: 150.3 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: GenomicDataCommons.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:GenomicDataCommons.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings GenomicDataCommons_1.28.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/GenomicDataCommons.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘GenomicDataCommons/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘GenomicDataCommons’ version ‘1.28.0’ * 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 ‘GenomicDataCommons’ 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 code 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 ... 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 R/sysdata.rda ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * 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: > > test_check("GenomicDataCommons") [ FAIL 1 | WARN 1 | SKIP 0 | PASS 45 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test_clinical.R:16:5'): clinical data is structured properly ────── all(vapply(clinical_data, nrow, integer(1L)) >= sizen) is not TRUE `actual`: FALSE `expected`: TRUE [ FAIL 1 | WARN 1 | SKIP 0 | PASS 45 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR See ‘/home/biocbuild/bbs-3.19-bioc/meat/GenomicDataCommons.Rcheck/00check.log’ for details.
GenomicDataCommons.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL GenomicDataCommons ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘GenomicDataCommons’ ... ** 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 (GenomicDataCommons)
GenomicDataCommons.Rcheck/tests/testthat.Rout.fail
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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(GenomicDataCommons) Loading required package: magrittr Attaching package: 'magrittr' The following objects are masked from 'package:testthat': equals, is_less_than, not Attaching package: 'GenomicDataCommons' The following object is masked from 'package:stats': filter > > test_check("GenomicDataCommons") [ FAIL 1 | WARN 1 | SKIP 0 | PASS 45 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test_clinical.R:16:5'): clinical data is structured properly ────── all(vapply(clinical_data, nrow, integer(1L)) >= sizen) is not TRUE `actual`: FALSE `expected`: TRUE [ FAIL 1 | WARN 1 | SKIP 0 | PASS 45 ] Error: Test failures Execution halted
GenomicDataCommons.Rcheck/GenomicDataCommons-Ex.timings
name | user | system | elapsed | |
GDC-defunct | 0.124 | 0.015 | 0.429 | |
aggregations | 0.037 | 0.003 | 0.547 | |
available_expand | 0.018 | 0.000 | 0.073 | |
available_fields | 0.038 | 0.000 | 0.126 | |
available_values | 0.041 | 0.000 | 0.501 | |
constants | 0.000 | 0.001 | 0.002 | |
count | 0.071 | 0.002 | 0.249 | |
default_fields | 0.038 | 0.000 | 0.121 | |
entity_name | 0.071 | 0.000 | 0.178 | |
expand | 0.110 | 0.004 | 0.295 | |
faceting | 0.073 | 0.016 | 0.205 | |
field_description | 0.177 | 0.016 | 0.405 | |
filtering | 0.485 | 0.037 | 1.505 | |
gdc_cache | 0.001 | 0.000 | 0.002 | |
gdc_client | 0.003 | 0.000 | 0.004 | |
gdc_clinical | 0.460 | 0.004 | 0.841 | |
gdc_token | 0.001 | 0.000 | 0.000 | |
gdcdata | 0.208 | 0.007 | 0.579 | |
grep_fields | 0.024 | 0.000 | 0.053 | |
id_field | 0.028 | 0.000 | 0.067 | |
ids | 0.216 | 0.012 | 0.753 | |
manifest | 0.159 | 0.003 | 0.319 | |
mapping | 0.013 | 0.002 | 0.043 | |
query | 0.069 | 0.005 | 0.148 | |
readDNAcopy | 0.214 | 0.023 | 0.247 | |
readHTSeqFile | 0.051 | 0.004 | 0.053 | |
response | 0.041 | 0.000 | 0.141 | |
results | 0.044 | 0.000 | 0.147 | |
results_all | 0.068 | 0.004 | 0.259 | |
select | 0.160 | 0.009 | 0.417 | |
slicing | 0.000 | 0.000 | 0.001 | |
status | 0.010 | 0.000 | 0.044 | |
transfer | 0.000 | 0.000 | 0.001 | |
write_manifest | 0.091 | 0.000 | 0.295 | |