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This page was generated on 2025-08-26 12:06 -0400 (Tue, 26 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4821
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4610
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4553
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4539
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 2021/2319HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SNPhood 1.39.0  (landing page)
Christian Arnold
Snapshot Date: 2025-08-25 13:45 -0400 (Mon, 25 Aug 2025)
git_url: https://git.bioconductor.org/packages/SNPhood
git_branch: devel
git_last_commit: 79a2c60
git_last_commit_date: 2025-04-15 10:56:04 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  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 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for SNPhood on kjohnson3

To the developers/maintainers of the SNPhood package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SNPhood.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: SNPhood
Version: 1.39.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SNPhood.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SNPhood_1.39.0.tar.gz
StartedAt: 2025-08-25 21:40:57 -0400 (Mon, 25 Aug 2025)
EndedAt: 2025-08-25 21:44:48 -0400 (Mon, 25 Aug 2025)
EllapsedTime: 231.6 seconds
RetCode: 0
Status:   OK  
CheckDir: SNPhood.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SNPhood.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SNPhood_1.39.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/SNPhood.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SNPhood/DESCRIPTION’ ... OK
* this is package ‘SNPhood’ version ‘1.39.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘SNPhood’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
BugReports field is not a suitable URL but contains an email address:
   use the Contact field instead
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* 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 whether startup messages can be suppressed ... 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 ... NOTE
.calcBinomTestVector: no visible binding for global variable ‘pp’
Undefined global functions or variables:
  pp
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  analyzeSNPhood.Rd: BamFile-class, BamFileList-class
  collectFiles.Rd: BamFile-class, BamFileList-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                  user system elapsed
analyzeSNPhood                  38.800  0.854  39.797
plotAllelicBiasResults          10.826  0.194  11.065
plotFDRResults                  10.793  0.130  11.533
testForAllelicBiases            10.780  0.132  11.320
plotAndSummarizeAllelicBiasTest 10.265  0.142  10.687
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/SNPhood.Rcheck/00check.log’
for details.


Installation output

SNPhood.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘SNPhood’ ...
** this is package ‘SNPhood’ version ‘1.39.0’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (SNPhood)

Tests output


Example timings

SNPhood.Rcheck/SNPhood-Ex.timings

nameusersystemelapsed
analyzeSNPhood38.800 0.85439.797
annotation-methods0.0740.0260.100
annotationBins0.0510.0040.055
annotationBins24.6110.0094.625
annotationDatasets0.0470.0040.051
annotationReadGroups0.4510.0100.462
annotationRegions0.0540.0040.059
associateGenotypes1.7360.0321.770
bins-methods0.0490.0050.054
changeObjectIntegrityChecking0.4680.0230.491
collectFiles0.0100.0010.011
convertToAllelicFractions0.0620.0030.065
counts-method0.4820.0090.491
datasets-methods0.0480.0060.055
deleteDatasets0.0550.0060.060
deleteReadGroups0.0520.0040.058
deleteRegions0.4670.0110.478
enrichment-methods0.0560.0040.060
getDefaultParameterList000
mergeReadGroups0.0670.0070.073
parameters-methods0.0490.0070.056
plotAllelicBiasResults10.826 0.19411.065
plotAllelicBiasResultsOverview0.2730.0040.278
plotAndCalculateCorrelationDatasets0.5590.0240.601
plotAndCalculateWeakAndStrongGenotype0.6780.0160.693
plotAndClusterMatrix0.1880.0110.204
plotAndSummarizeAllelicBiasTest10.265 0.14210.687
plotBinCounts0.3740.0060.380
plotClusterAverage0.1630.0050.168
plotFDRResults10.793 0.13011.533
plotGenotypesPerCluster0.1340.0060.140
plotGenotypesPerSNP0.1160.0070.124
plotRegionCounts0.5160.0120.532
readGroups-methods0.0490.0080.056
regions-methods0.0650.0110.076
renameBins0.0550.0050.060
renameDatasets0.5030.0180.524
renameReadGroups0.0460.0050.052
renameRegions0.6400.0280.674
results0.7302.3993.156
testForAllelicBiases10.780 0.13211.320