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This page was generated on 2025-10-18 12:06 -0400 (Sat, 18 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4887
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4677
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4622
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4632
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 2050/2353HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SNPhood 1.39.0  (landing page)
Christian Arnold
Snapshot Date: 2025-10-17 13:45 -0400 (Fri, 17 Oct 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 12.7.6 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: 2025-10-17 22:16:10 -0400 (Fri, 17 Oct 2025)
EndedAt: 2025-10-17 22:20:13 -0400 (Fri, 17 Oct 2025)
EllapsedTime: 242.7 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 (2025-09-10 r88807)
* 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                  40.108  0.811  41.172
plotAllelicBiasResults          11.610  0.241  12.458
plotAndSummarizeAllelicBiasTest 11.217  0.106  11.731
plotFDRResults                  10.801  0.125  11.239
testForAllelicBiases            10.657  0.181  11.344
* 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
analyzeSNPhood40.108 0.81141.172
annotation-methods0.0730.0210.093
annotationBins0.0480.0120.060
annotationBins24.8150.0134.829
annotationDatasets0.0460.0100.055
annotationReadGroups0.0510.0140.065
annotationRegions0.0520.0140.066
associateGenotypes1.8380.0851.954
bins-methods0.0470.0170.064
changeObjectIntegrityChecking0.0580.0140.074
collectFiles0.0110.0000.011
convertToAllelicFractions0.0780.0220.101
counts-method0.0800.0110.092
datasets-methods0.0530.0120.065
deleteDatasets0.5170.0130.543
deleteReadGroups0.0600.0070.067
deleteRegions0.4960.0100.515
enrichment-methods0.0530.0080.061
getDefaultParameterList000
mergeReadGroups0.0660.0150.080
parameters-methods0.0500.0080.061
plotAllelicBiasResults11.610 0.24112.458
plotAllelicBiasResultsOverview0.3700.0120.385
plotAndCalculateCorrelationDatasets0.5610.0110.590
plotAndCalculateWeakAndStrongGenotype0.2400.0250.278
plotAndClusterMatrix0.1950.0170.218
plotAndSummarizeAllelicBiasTest11.217 0.10611.731
plotBinCounts0.5210.0170.548
plotClusterAverage0.2420.0130.267
plotFDRResults10.801 0.12511.239
plotGenotypesPerCluster0.1710.0140.192
plotGenotypesPerSNP0.1440.0110.157
plotRegionCounts0.6130.0140.647
readGroups-methods0.0500.0160.068
regions-methods0.0820.0300.111
renameBins0.0510.0080.062
renameDatasets0.0560.0140.069
renameReadGroups0.0510.0060.057
renameRegions1.1490.0341.192
results0.7662.5363.360
testForAllelicBiases10.657 0.18111.344