Back to Multiple platform build/check report for BioC 3.19:   simplified   long
ABCDEFGHIJKLMNOPQRSTU[V]WXYZ

This page was generated on 2024-06-11 14:44 -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 2252/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
VariantTools 1.46.0  (landing page)
Michael Lawrence
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/VariantTools
git_branch: RELEASE_3_19
git_last_commit: 4376907
git_last_commit_date: 2024-04-30 10:29:25 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for VariantTools on kjohnson3

To the developers/maintainers of the VariantTools package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/VariantTools.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: VariantTools
Version: 1.46.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:VariantTools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings VariantTools_1.46.0.tar.gz
StartedAt: 2024-06-11 09:19:34 -0400 (Tue, 11 Jun 2024)
EndedAt: 2024-06-11 09:28:42 -0400 (Tue, 11 Jun 2024)
EllapsedTime: 548.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: VariantTools.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:VariantTools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings VariantTools_1.46.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/VariantTools.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-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 Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘VariantTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘VariantTools’ version ‘1.46.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘VariantTools’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   5.4Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... NOTE
Problems with news in ‘NEWS’:
  Cannot process chunk/lines:
    Initial release
    (start date: 12 September, 2012)
* 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 ... WARNING
Missing or unexported object: ‘GenomicRanges::genome’
Unexported objects imported by ':::' calls:
  ‘BiocGenerics:::testPackage’ ‘IRanges:::unlist_as_integer’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
LowerFrequencyInOtherFilter : <anonymous>: no visible binding for
  global variable ‘control.alt.depth’
LowerFrequencyInOtherFilter : <anonymous>: no visible binding for
  global variable ‘control.total.depth’
ReadPositionTTestFilter : <anonymous>: no visible binding for global
  variable ‘read.pos.mean’
ReadPositionTTestFilter : <anonymous>: no visible binding for global
  variable ‘read.pos.mean.ref’
ReadPositionTTestFilter : <anonymous>: no visible binding for global
  variable ‘read.pos.var’
ReadPositionTTestFilter : <anonymous>: no visible binding for global
  variable ‘read.pos.var.ref’
ReadPositionTTestFilter : <anonymous>: no visible global function
  definition for ‘rawDepth’
StrandFETFilter : <anonymous>: no visible binding for global variable
  ‘count.plus.ref’
StrandFETFilter : <anonymous>: no visible binding for global variable
  ‘count.minus.ref’
StrandFETFilter : <anonymous>: no visible binding for global variable
  ‘count.plus’
StrandFETFilter : <anonymous>: no visible binding for global variable
  ‘count.minus’
calculateConcordanceMatrix: no visible binding for global variable ‘x’
caseControlFET: no visible binding for global variable
  ‘control.alt.depth’
caseControlFET: no visible binding for global variable
  ‘control.total.depth’
variantGR2Vcf: no visible global function definition for
  ‘variantGRangesIsDeprecated’
variantGR2Vcf: no visible global function definition for
  ‘makeVRangesFromVariantGRanges’
callVariants,GenomicRanges: no visible global function definition for
  ‘variantGRangesIsDeprecated’
callVariants,GenomicRanges: no visible global function definition for
  ‘variantGRangesToVRanges’
Undefined global functions or variables:
  control.alt.depth control.total.depth count.minus count.minus.ref
  count.plus count.plus.ref makeVRangesFromVariantGRanges rawDepth
  read.pos.mean read.pos.mean.ref read.pos.var read.pos.var.ref
  variantGRangesIsDeprecated variantGRangesToVRanges x
* checking Rd files ... WARNING
checkRd: (-1) callVariants.Rd:48: Lost braces
    48 |   \code{...}{Arguments for \code{VariantCallingFilters}, listed below.}
       |             ^
./man/tallyVariants.Rd: non-ASCII input and no declared encoding
problem found in ‘tallyVariants.Rd’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... NOTE
The following directories should probably not be installed:
  ‘fig’

Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                             user system elapsed
callGenotypes              80.395 13.645  93.056
callSampleSpecificVariants  6.855  2.855   5.415
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘VariantTools_unit_tests.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: 2 WARNINGs, 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/VariantTools.Rcheck/00check.log’
for details.


Installation output

VariantTools.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL VariantTools
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘VariantTools’ ...
** 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 (VariantTools)

Tests output

VariantTools.Rcheck/tests/VariantTools_unit_tests.Rout


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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.

> ##require("VariantTools") || stop("unable to load VariantTools package")
> ##VariantTools:::.test()
> 
> proc.time()
   user  system elapsed 
  0.183   0.076   0.383 

Example timings

VariantTools.Rcheck/VariantTools-Ex.timings

nameusersystemelapsed
FilterConstructors1.1980.0671.648
annnotateWithControlDepth1.8700.0362.492
callGenotypes80.39513.64593.056
callSampleSpecificVariants6.8552.8555.415
callVariants3.3481.4192.949
callWildtype0.3130.0490.461
pileupVariants0.2160.1820.533
postFilterVariants0.3230.0530.518
qaVariants0.2290.0380.347
tallyVariants3.1901.4462.476
variantGR2Vcf0.0010.0000.000
vignette0.0110.0060.021