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This page was generated on 2024-06-18 17:58 -0400 (Tue, 18 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4758
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4492
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4464
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4464
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: 2024-06-16 14:00 -0400 (Sun, 16 Jun 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
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
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 nebbiolo1

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: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:QSutils.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings QSutils_1.22.0.tar.gz
StartedAt: 2024-06-17 02:45:00 -0400 (Mon, 17 Jun 2024)
EndedAt: 2024-06-17 02:47:12 -0400 (Mon, 17 Jun 2024)
EllapsedTime: 132.3 seconds
RetCode: 0
Status:   OK  
CheckDir: QSutils.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:QSutils.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings QSutils_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/QSutils.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/QSutils.Rcheck/00check.log’
for details.


Installation output

QSutils.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL QSutils
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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
Collapse0.1110.0280.139
ConsSeq0.0180.0040.022
CorrectGapsAndNs0.0030.0030.006
DBrule0.0320.0160.048
DNA.dist0.0030.0050.009
DSFT0.0040.0020.006
Diverge0.0030.0000.003
DottedAlignment0.0070.0030.010
FAD0.0070.0010.007
FreqMat0.0060.0100.017
GenerateVars0.0000.0040.003
GenotypeStandards_A-H.fas0.0060.0020.006
GetInfProfile0.0140.0040.018
GetQSData0.3620.0120.375
GetRandomSeq0.0010.0000.001
GiniSimpson0.0000.0000.001
HCq0.0030.0030.006
Hill0.0040.0000.004
IntersectStrandHpls0.0590.0080.069
MutationFreq0.2720.0040.277
MutsTbl0.0110.0040.016
NucleotideDiversity0.0060.0000.006
PolyDist0.0210.0000.021
Rao0.0120.0000.013
ReadAmplSeqs0.0240.0000.025
Renyi0.0040.0000.005
ReportVariants0.0140.0000.015
SegSites0.0080.0000.009
Shannon0.0010.0000.001
SortByMutations0.2690.0040.273
SummaryMuts0.0150.0000.015
TotalMutations0.0140.0000.014
Toy.GapsAndNs.fna0.0400.0070.047
ToyData_10_50_1000.fna0.0230.0010.023
ToyData_FWReads.fna0.0560.0000.055
ToyData_RVReads.fna0.0560.0040.059
UniqueMutations0.0090.0000.009
Unknown-Genotype.fna0.0090.0000.008
fn.ab0.0040.0000.004
geom.series0.0020.0000.002