Back to Multiple platform build/check report for BioC 3.19:   simplified   long
ABCDEFGHIJKLMNOP[Q]RSTUVWXYZ

This page was generated on 2024-07-12 17:41 -0400 (Fri, 12 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4741
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4483
merida1macOS 12.7.4 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4512
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4461
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 1649/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
QSutils 1.22.0  (landing page)
Mercedes Guerrero-Murillo
Snapshot Date: 2024-07-10 14:00 -0400 (Wed, 10 Jul 2024)
git_url: https://git.bioconductor.org/packages/QSutils
git_branch: RELEASE_3_19
git_last_commit: e5e3765
git_last_commit_date: 2024-04-30 11:10:22 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for QSutils on merida1

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.

raw results


Summary

Package: QSutils
Version: 1.22.0
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_1.22.0.tar.gz
StartedAt: 2024-07-11 09:54:23 -0400 (Thu, 11 Jul 2024)
EndedAt: 2024-07-11 09:57:38 -0400 (Thu, 11 Jul 2024)
EllapsedTime: 194.3 seconds
RetCode: 0
Status:   OK  
CheckDir: QSutils.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/QSutils.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 12.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘QSutils/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘QSutils’ version ‘1.22.0’
* 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-3.19-bioc/meat/QSutils.Rcheck/00check.log’
for details.


Installation output

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)

Tests output


Example timings

QSutils.Rcheck/QSutils-Ex.timings

nameusersystemelapsed
Collapse0.2820.0400.685
ConsSeq0.0530.0090.212
CorrectGapsAndNs0.0130.0030.016
DBrule0.1020.0160.678
DNA.dist0.0160.0060.025
DSFT0.0090.0020.011
Diverge0.0050.0010.007
DottedAlignment0.0190.0050.025
FAD0.0150.0040.018
FreqMat0.0420.0150.060
GenerateVars0.0080.0030.014
GenotypeStandards_A-H.fas0.0130.0030.018
GetInfProfile0.0470.0120.063
GetQSData0.7600.0590.889
GetRandomSeq0.0010.0010.000
GiniSimpson0.0010.0000.002
HCq0.0110.0030.015
Hill0.0090.0030.012
IntersectStrandHpls0.1550.0080.175
MutationFreq0.5560.0280.617
MutsTbl0.0410.0090.056
NucleotideDiversity0.0150.0030.018
PolyDist0.0640.0040.078
Rao0.0290.0040.038
ReadAmplSeqs0.0640.0040.076
Renyi0.0070.0030.010
ReportVariants0.0360.0030.043
SegSites0.0250.0020.029
Shannon0.0010.0010.002
SortByMutations0.5920.0290.685
SummaryMuts0.0400.0030.047
TotalMutations0.0370.0010.042
Toy.GapsAndNs.fna0.1140.0070.130
ToyData_10_50_1000.fna0.0620.0040.074
ToyData_FWReads.fna0.1450.0070.156
ToyData_RVReads.fna0.1440.0080.155
UniqueMutations0.0240.0020.029
Unknown-Genotype.fna0.0220.0040.033
fn.ab0.0080.0040.012
geom.series0.0070.0000.008