Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-06-11 15:41 -0400 (Tue, 11 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
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 1816/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
scanMiR 1.11.0 (landing page) Pierre-Luc Germain
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the scanMiR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scanMiR.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: scanMiR |
Version: 1.11.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:scanMiR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings scanMiR_1.11.0.tar.gz |
StartedAt: 2024-06-10 08:56:48 -0400 (Mon, 10 Jun 2024) |
EndedAt: 2024-06-10 09:03:06 -0400 (Mon, 10 Jun 2024) |
EllapsedTime: 378.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: scanMiR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:scanMiR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings scanMiR_1.11.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/scanMiR.Rcheck' * using R version 4.4.0 RC (2024-04-16 r86468 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 'scanMiR/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'scanMiR' 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 'scanMiR' 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 ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. * 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .aggregateSiteInfo: no visible binding for global variable 'ORF' .aggregateSiteInfo: no visible global function definition for '.' .aggregateSiteInfo: no visible binding for global variable 'ORF.canonical' .aggregateSiteInfo: no visible binding for global variable 'ORF.nonCanonical' .aggregateSiteInfo: no visible binding for global variable '..cols' .aggregate_miRNA: no visible binding for global variable 'ORF' .aggregate_miRNA: no visible binding for global variable 'log_kd' .aggregate_miRNA: no visible binding for global variable 'orf.length' .aggregate_miRNA: no visible binding for global variable 'utr.length' .aggregate_miRNA: no visible binding for global variable 'utr_score' .aggregate_miRNA: no visible binding for global variable 'orf_score' dummyKdData: no visible binding for global variable 'SampleKdModel' plotKdModel: no visible binding for global variable 'seed' plotKdModel: no visible binding for global variable 'log_kd' viewTargetAlignment: no visible binding for global variable 'x' viewTargetAlignment: no visible binding for global variable 'y' viewTargetAlignment: no visible binding for global variable 'label' Undefined global functions or variables: . ..cols ORF ORF.canonical ORF.nonCanonical SampleKdModel label log_kd orf.length orf_score seed utr.length utr_score x y * checking Rd files ... NOTE checkRd: (-1) plotKdModel.Rd:28: Lost braces 28 | [seqLogo]{https://bioconductor.org/packages/release/bioc/html/seqLogo.html} | ^ * 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 contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... 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: 3 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/scanMiR.Rcheck/00check.log' for details.
scanMiR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL scanMiR ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'scanMiR' ... ** using staged installation ** R ** data ** 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 (scanMiR)
scanMiR.Rcheck/tests/testthat.Rout
R version 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 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(scanMiR) > > test_check("scanMiR") [ FAIL 0 | WARN 18 | SKIP 0 | PASS 76 ] [ FAIL 0 | WARN 18 | SKIP 0 | PASS 76 ] > > proc.time() user system elapsed 9.73 9.07 18.82
scanMiR.Rcheck/scanMiR-Ex.timings
name | user | system | elapsed | |
KdModel | 0 | 0 | 0 | |
KdModelList-methods | 0.02 | 0.00 | 0.02 | |
KdModelList | 0 | 0 | 0 | |
SampleKdModel | 0.02 | 0.00 | 0.02 | |
aggregateMatches | 0.5 | 0.0 | 0.5 | |
assignKdType | 0.05 | 0.01 | 0.06 | |
conservation | 0 | 0 | 0 | |
dummyKdData | 0 | 0 | 0 | |
findSeedMatches | 0.33 | 0.00 | 0.32 | |
get3pAlignment | 0.01 | 0.00 | 0.02 | |
get8merRange | 0 | 0 | 0 | |
getKdModel | 0.20 | 0.01 | 0.22 | |
getKmers | 0 | 0 | 0 | |
getMatchTypes | 0 | 0 | 0 | |
getRandomSeq | 0 | 0 | 0 | |
getSeed8mers | 0 | 0 | 0 | |
plotKdModel | 0.22 | 0.06 | 0.30 | |
removeOverlappingRanges | 0.28 | 1.40 | 1.81 | |
viewTargetAlignment | 0.69 | 0.01 | 0.71 | |