Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:46 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 814/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GenomicDataCommons 1.31.0 (landing page) Sean Davis
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: GenomicDataCommons |
Version: 1.31.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:GenomicDataCommons.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings GenomicDataCommons_1.31.0.tar.gz |
StartedAt: 2024-12-24 07:01:27 -0000 (Tue, 24 Dec 2024) |
EndedAt: 2024-12-24 07:03:58 -0000 (Tue, 24 Dec 2024) |
EllapsedTime: 150.1 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: GenomicDataCommons.Rcheck |
Warnings: 5 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:GenomicDataCommons.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings GenomicDataCommons_1.31.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/GenomicDataCommons.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GenomicDataCommons/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘GenomicDataCommons’ version ‘1.31.0’ * 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 ... WARNING Found the following significant warnings: Warning: program compiled against libxml 212 using older 211 See ‘/home/biocbuild/bbs-3.21-bioc/meat/GenomicDataCommons.Rcheck/00install.out’ for details. * 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 ...Warning: program compiled against libxml 212 using older 211 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 ... NOTE Warning: program compiled against libxml 212 using older 211 A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start. Probably some imports need to be declared in the NAMESPACE file. * 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 Warning: program compiled against libxml 212 using older 211 * checking S3 generic/method consistency ... WARNING Warning: program compiled against libxml 212 using older 211 See section ‘Generic functions and methods’ in the ‘Writing R Extensions’ manual. * checking replacement functions ... WARNING Warning: program compiled against libxml 212 using older 211 The argument of a replacement function which corresponds to the right hand side must be named ‘value’. * checking foreign function calls ... NOTE Warning: program compiled against libxml 212 using older 211 See chapter ‘System and foreign language interfaces’ in the ‘Writing R Extensions’ manual. * checking R code for possible problems ... NOTE Warning: program compiled against libxml 212 using older 211 * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Warning: program compiled against libxml 212 using older 211 All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... WARNING Warning: program compiled against libxml 212 using older 211 Warning: program compiled against libxml 212 using older 211 Warning: program compiled against libxml 212 using older 211 * checking Rd \usage sections ... NOTE Warning: program compiled against libxml 212 using older 211 The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking R/sysdata.rda ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed filtering 0.565 0.016 7.487 aggregations 0.106 0.008 5.088 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 5 WARNINGs, 5 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/GenomicDataCommons.Rcheck/00check.log’ for details.
GenomicDataCommons.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL GenomicDataCommons ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘GenomicDataCommons’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Warning: program compiled against libxml 212 using older 211 ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: program compiled against libxml 212 using older 211 ** testing if installed package can be loaded from final location Warning: program compiled against libxml 212 using older 211 ** testing if installed package keeps a record of temporary installation path * DONE (GenomicDataCommons)
GenomicDataCommons.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-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) Warning: program compiled against libxml 212 using older 211 Attaching package: 'GenomicDataCommons' The following object is masked from 'package:stats': filter > > test_check("GenomicDataCommons") [ FAIL 0 | WARN 1 | SKIP 0 | PASS 46 ] [ FAIL 0 | WARN 1 | SKIP 0 | PASS 46 ] > > proc.time() user system elapsed 6.131 0.529 19.043
GenomicDataCommons.Rcheck/GenomicDataCommons-Ex.timings
name | user | system | elapsed | |
aggregations | 0.106 | 0.008 | 5.088 | |
available_expand | 0.020 | 0.000 | 0.438 | |
available_fields | 0.040 | 0.000 | 0.677 | |
available_values | 0.043 | 0.000 | 0.848 | |
constants | 0.001 | 0.000 | 0.001 | |
count | 0.078 | 0.000 | 1.191 | |
default_fields | 0.042 | 0.000 | 0.680 | |
entity_name | 0.052 | 0.001 | 0.691 | |
expand | 0.103 | 0.000 | 1.394 | |
faceting | 0.069 | 0.000 | 0.734 | |
field_description | 0.186 | 0.007 | 2.132 | |
filtering | 0.565 | 0.016 | 7.487 | |
gdc_cache | 0.001 | 0.000 | 0.001 | |
gdc_client | 0.004 | 0.000 | 0.004 | |
gdc_clinical | 0.606 | 0.028 | 2.539 | |
gdc_token | 0.000 | 0.000 | 0.001 | |
gdcdata | 0.24 | 0.00 | 2.06 | |
grep_fields | 0.023 | 0.003 | 0.243 | |
id_field | 0.039 | 0.000 | 0.262 | |
ids | 0.225 | 0.001 | 2.416 | |
manifest | 0.115 | 0.004 | 0.814 | |
mapping | 0.017 | 0.000 | 0.229 | |
query | 0.092 | 0.000 | 1.736 | |
readDNAcopy | 0.300 | 0.011 | 0.311 | |
readHTSeqFile | 0.071 | 0.004 | 0.075 | |
response | 0.049 | 0.004 | 0.531 | |
results | 0.052 | 0.000 | 0.523 | |
results_all | 0.069 | 0.000 | 1.203 | |
select | 0.103 | 0.000 | 1.821 | |
slicing | 0 | 0 | 0 | |
status | 0.013 | 0.000 | 0.247 | |
transfer | 0 | 0 | 0 | |
write_manifest | 0.131 | 0.000 | 0.876 | |