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 11:41 -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 1829/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
scanMiRApp 1.11.0 (landing page) Pierre-Luc Germain
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the scanMiRApp package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scanMiRApp.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: scanMiRApp |
Version: 1.11.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:scanMiRApp.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings scanMiRApp_1.11.0.tar.gz |
StartedAt: 2024-08-16 04:41:19 -0400 (Fri, 16 Aug 2024) |
EndedAt: 2024-08-16 04:47:14 -0400 (Fri, 16 Aug 2024) |
EllapsedTime: 355.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: scanMiRApp.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:scanMiRApp.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings scanMiRApp_1.11.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/scanMiRApp.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 'scanMiRApp/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'scanMiRApp' version '1.11.0' * 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 'scanMiRApp' 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 ':::' calls which should be '::': 'BSgenome.Hsapiens.UCSC.hg38:::BSgenome.Hsapiens.UCSC.hg38' 'BSgenome.Mmusculus.UCSC.mm10:::BSgenome.Mmusculus.UCSC.mm10' 'BSgenome.Mmusculus.UCSC.mm39:::BSgenome.Mmusculus.UCSC.mm39' 'BSgenome.Rnorvegicus.UCSC.rn6:::BSgenome.Rnorvegicus.UCSC.rn6' 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 ... NOTE .fakeAnno: no visible binding for global variable 'SampleTranscript' .fakeAnno: no visible binding for global variable 'SampleKdModel' plotSitesOnUTR: no visible binding for global variable 'logKd' plotSitesOnUTR: no visible binding for global variable 'note' plotSitesOnUTR: no visible binding for global variable 'type' Undefined global functions or variables: SampleKdModel SampleTranscript logKd note 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 ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking files in 'vignettes' ... OK * checking examples ... OK * 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: 2 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/scanMiRApp.Rcheck/00check.log' for details.
scanMiRApp.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL scanMiRApp ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'scanMiRApp' ... ** 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 (scanMiRApp)
scanMiRApp.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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(scanMiRApp) Loading required package: scanMiR > > test_check("scanMiRApp") Loading annotation Extracting transcripts Scanning with 1 thread(s) Loading annotation Extracting transcripts Scanning with 1 thread(s) Prepare miRNA model Get Transcript Sequence Scan Prepare miRNA model Get Transcript Sequence Scan [ FAIL 0 | WARN 1 | SKIP 2 | PASS 13 ] ══ Skipped tests (2) ═══════════════════════════════════════════════════════════ • On CRAN (1): 'test-shiny.R:10:3' • empty test (1): 'test-utils.R:46:1' [ FAIL 0 | WARN 1 | SKIP 2 | PASS 13 ] > > proc.time() user system elapsed 23.40 1.40 25.23
scanMiRApp.Rcheck/scanMiRApp-Ex.timings
name | user | system | elapsed | |
IndexedFst-class | 0.05 | 0.02 | 0.06 | |
ScanMiRAnno | 1.06 | 0.11 | 1.17 | |
enrichedMirTxPairs | 0.85 | 0.01 | 0.86 | |
getTranscriptSequence | 1.84 | 0.10 | 1.94 | |
plotSitesOnUTR | 3.23 | 0.03 | 3.28 | |
runFullScan | 1.18 | 0.04 | 1.22 | |
save-load-IndexedFst | 0.01 | 0.00 | 0.02 | |
scanMiRApp | 0 | 0 | 0 | |
scanMiRserver | 0.61 | 0.00 | 0.61 | |
scanMiRui | 0.27 | 0.08 | 0.51 | |