Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-16 11:42 -0400 (Fri, 16 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4420 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4413 |
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 2188/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Ularcirc 1.23.0 (landing page) David Humphreys
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the Ularcirc package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Ularcirc.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: Ularcirc |
Version: 1.23.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Ularcirc.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings Ularcirc_1.23.0.tar.gz |
StartedAt: 2024-08-16 06:07:34 -0400 (Fri, 16 Aug 2024) |
EndedAt: 2024-08-16 06:09:33 -0400 (Fri, 16 Aug 2024) |
EllapsedTime: 118.4 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: Ularcirc.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Ularcirc.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings Ularcirc_1.23.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/Ularcirc.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'Ularcirc/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'Ularcirc' version '1.23.0' * 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 whether package 'Ularcirc' 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 dependencies in R code ... NOTE Namespaces in Imports field not imported from: 'DT' 'GenomeInfoDb' 'GenomeInfoDbData' 'Organism.dplyr' 'ggplot2' 'ggrepel' 'mirbase.db' 'moments' 'shinyFiles' 'shinydashboard' 'shinyjs' 'yaml' All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE FilterChimericJuncs: no visible global function definition for 'Filter_by_Data_Set' FilterChimericJuncs: no visible binding for global variable 'strandDonor' FilterChimericJuncs: no visible binding for global variable 'startDonor' FilterChimericJuncs: no visible binding for global variable 'startAcceptor' Junction_Sequence_from_Genome: no visible global function definition for 'extractGenomeSequence' SelectUniqueJunctions : filtersteps: no visible global function definition for '.' SelectUniqueJunctions : filtersteps: no visible binding for global variable 'type' SelectUniqueJunctions: no visible binding for global variable 'BSjuncName' SelectUniqueJunctions: no visible binding for global variable 'JuncType' SelectUniqueJunctions: no visible binding for global variable 'strandDonor' loadSTAR_chimeric: no visible binding for global variable '..returnColIdx' Undefined global functions or variables: . ..returnColIdx BSjuncName Filter_by_Data_Set JuncType extractGenomeSequence startAcceptor startDonor strandDonor type * 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 ... WARNING Undocumented arguments in Rd file 'Junction_Sequence_from_Genome.Rd' 'SelectUniqueJunct_Value' Documented arguments not in \usage in Rd file 'Junction_Sequence_from_Genome.Rd': 'SelectUniqueJunct_value' Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual. * 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 Compatible_Annotation_DBs 10.02 0.69 10.77 * 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: 1 WARNING, 2 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/Ularcirc.Rcheck/00check.log' for details.
Ularcirc.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL Ularcirc ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'Ularcirc' ... ** 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 (Ularcirc)
Ularcirc.Rcheck/Ularcirc-Ex.timings
name | user | system | elapsed | |
BSJ_details | 0 | 0 | 0 | |
Compatible_Annotation_DBs | 10.02 | 0.69 | 10.77 | |
FilterChimericJuncs | 1.27 | 0.67 | 2.79 | |
Ularcirc | 0 | 0 | 0 | |
bsj_fastq_generate | 0.08 | 0.00 | 0.07 | |
bsj_to_circRNA_sequence | 2.75 | 0.15 | 2.91 | |
chimericStats | 0.34 | 0.63 | 1.73 | |
plot_AllJunctions | 2.86 | 0.19 | 3.11 | |