Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1634/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
QSutils 1.24.0 (landing page) Mercedes Guerrero-Murillo
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the QSutils package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/QSutils.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: QSutils |
Version: 1.24.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:QSutils.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings QSutils_1.24.0.tar.gz |
StartedAt: 2024-12-20 08:03:47 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 08:06:32 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 165.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: QSutils.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:QSutils.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings QSutils_1.24.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/QSutils.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘QSutils/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘QSutils’ version ‘1.24.0’ * 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 ‘QSutils’ 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 ... NOTE Problems with news in ‘NEWS’: Cannot process chunk/lines: CHANGES IN VERSION 0.99.8 Internal changes: - QSutils review correction: · Add exports to NAMESPACE Cannot process chunk/lines: CHANGES IN VERSION 0.99.4,5, and 7 Internal changes: - QSutils review correction: · fn.ab function correction Cannot process chunk/lines: CHANGES IN VERSION 0.99.3 Internal changes: - QSutils review correction: · Vignette: add chunk names · R Change class -> is() · R hide helper functions · R join more than one function in one file · R vectorize some apply · R Change fn.ab.1,fn.ab.2 and fn.ab.3 -> fn.ab with 3 agruments in fn Cannot process chunk/lines: CHANGES IN VERSION 0.99.2 Internal changes: - Biocheck NOTEs correction: · Change sapply()->vapply() · Change 1:... -> seq_len() Cannot process chunk/lines: CHANGES IN VERSION 0.99.1 Internal changes: - Correction of WARNINGS and ERRORS with Biocheck: · Collapse() example ERROR. · Change class == -> is() or !is() · Update R version dependency from 3.4.0 to 3.5. · Correct -> 'VignetteIndexEntry{VignetteTitle}' in QSUtils-Alignment.Rmd * 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 ... 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 files in ‘vignettes’ ... OK * checking examples ... 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 ‘/Users/biocbuild/bbs-3.20-bioc/meat/QSutils.Rcheck/00check.log’ for details.
QSutils.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL QSutils ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘QSutils’ ... ** 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 (QSutils)
QSutils.Rcheck/QSutils-Ex.timings
name | user | system | elapsed | |
Collapse | 0.283 | 0.039 | 0.328 | |
ConsSeq | 0.052 | 0.008 | 0.061 | |
CorrectGapsAndNs | 0.013 | 0.004 | 0.016 | |
DBrule | 0.102 | 0.013 | 0.119 | |
DNA.dist | 0.015 | 0.005 | 0.020 | |
DSFT | 0.008 | 0.001 | 0.010 | |
Diverge | 0.005 | 0.001 | 0.006 | |
DottedAlignment | 0.017 | 0.004 | 0.022 | |
FAD | 0.013 | 0.003 | 0.016 | |
FreqMat | 0.038 | 0.014 | 0.054 | |
GenerateVars | 0.008 | 0.003 | 0.013 | |
GenotypeStandards_A-H.fas | 0.013 | 0.003 | 0.016 | |
GetInfProfile | 0.045 | 0.010 | 0.056 | |
GetQSData | 0.728 | 0.072 | 0.827 | |
GetRandomSeq | 0.001 | 0.001 | 0.001 | |
GiniSimpson | 0.001 | 0.000 | 0.002 | |
HCq | 0.009 | 0.003 | 0.011 | |
Hill | 0.008 | 0.003 | 0.011 | |
IntersectStrandHpls | 0.151 | 0.007 | 0.169 | |
MutationFreq | 0.530 | 0.033 | 0.569 | |
MutsTbl | 0.037 | 0.009 | 0.047 | |
NucleotideDiversity | 0.014 | 0.001 | 0.016 | |
PolyDist | 0.059 | 0.003 | 0.063 | |
Rao | 0.028 | 0.003 | 0.031 | |
ReadAmplSeqs | 0.057 | 0.004 | 0.062 | |
Renyi | 0.008 | 0.003 | 0.010 | |
ReportVariants | 0.033 | 0.002 | 0.035 | |
SegSites | 0.021 | 0.002 | 0.024 | |
Shannon | 0.002 | 0.001 | 0.002 | |
SortByMutations | 0.573 | 0.055 | 0.635 | |
SummaryMuts | 0.037 | 0.003 | 0.040 | |
TotalMutations | 0.039 | 0.002 | 0.041 | |
Toy.GapsAndNs.fna | 0.109 | 0.007 | 0.117 | |
ToyData_10_50_1000.fna | 0.060 | 0.007 | 0.067 | |
ToyData_FWReads.fna | 0.142 | 0.011 | 0.154 | |
ToyData_RVReads.fna | 0.144 | 0.007 | 0.158 | |
UniqueMutations | 0.024 | 0.001 | 0.026 | |
Unknown-Genotype.fna | 0.021 | 0.002 | 0.022 | |
fn.ab | 0.008 | 0.003 | 0.011 | |
geom.series | 0.007 | 0.001 | 0.008 | |