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This page was generated on 2024-06-11 14:41 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4522
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4468
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: 2024-06-09 14:00 -0400 (Sun, 09 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
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for QSutils on palomino3

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: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:QSutils.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings QSutils_1.22.0.tar.gz
StartedAt: 2024-06-10 09:06:40 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 09:11:17 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 277.0 seconds
RetCode: 0
Status:   OK  
CheckDir: QSutils.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:QSutils.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings QSutils_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/QSutils.Rcheck'
* using R version 4.4.0 (2024-04-24 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 '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 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
  'F:/biocbuild/bbs-3.19-bioc/meat/QSutils.Rcheck/00check.log'
for details.


Installation output

QSutils.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL QSutils
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/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
Collapse0.110.050.16
ConsSeq0.040.000.03
CorrectGapsAndNs0.010.000.01
DBrule0.060.000.07
DNA.dist0.020.000.01
DSFT0.010.000.02
Diverge0.020.000.01
DottedAlignment0.020.000.02
FAD0.010.000.01
FreqMat0.000.000.02
GenerateVars000
GenotypeStandards_A-H.fas0.000.010.01
GetInfProfile0.010.000.02
GetQSData0.610.030.64
GetRandomSeq000
GiniSimpson000
HCq000
Hill000
IntersectStrandHpls0.100.010.25
MutationFreq0.760.040.80
MutsTbl0.020.000.02
NucleotideDiversity000
PolyDist0.020.000.02
Rao0.010.000.01
ReadAmplSeqs0.020.000.03
Renyi000
ReportVariants0.020.000.02
SegSites0.010.000.01
Shannon000
SortByMutations0.250.010.27
SummaryMuts0.020.000.01
TotalMutations0.010.000.02
Toy.GapsAndNs.fna0.030.000.03
ToyData_10_50_1000.fna0.030.010.05
ToyData_FWReads.fna0.070.000.06
ToyData_RVReads.fna0.060.000.07
UniqueMutations0.000.020.01
Unknown-Genotype.fna0.000.000.02
fn.ab000
geom.series0.000.010.01