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This page was generated on 2025-09-30 12:04 -0400 (Tue, 30 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4843
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4631
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4575
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4576
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 2035/2337HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SNPhood 1.39.0  (landing page)
Christian Arnold
Snapshot Date: 2025-09-29 13:45 -0400 (Mon, 29 Sep 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 nebbiolo2

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: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:SNPhood.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings SNPhood_1.39.0.tar.gz
StartedAt: 2025-09-30 04:41:18 -0400 (Tue, 30 Sep 2025)
EndedAt: 2025-09-30 04:55:06 -0400 (Tue, 30 Sep 2025)
EllapsedTime: 827.7 seconds
RetCode: 0
Status:   OK  
CheckDir: SNPhood.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:SNPhood.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings SNPhood_1.39.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/SNPhood.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... 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                  108.567  4.638 113.354
plotAllelicBiasResults           42.345  0.107  30.819
plotAndSummarizeAllelicBiasTest  40.238  0.147  28.444
plotFDRResults                   39.755  0.573  29.300
testForAllelicBiases             37.975  0.931  28.874
annotationBins2                  10.619  0.004  10.625
associateGenotypes                5.716  0.004   5.720
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/SNPhood.Rcheck/00check.log’
for details.


Installation output

SNPhood.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL SNPhood
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-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
analyzeSNPhood108.567 4.638113.354
annotation-methods0.2000.0190.219
annotationBins0.1150.0190.135
annotationBins210.619 0.00410.625
annotationDatasets0.1130.0060.119
annotationReadGroups0.1270.0000.127
annotationRegions0.1290.0000.129
associateGenotypes5.7160.0045.720
bins-methods0.1160.0300.146
changeObjectIntegrityChecking0.1400.0190.158
collectFiles0.0300.0000.031
convertToAllelicFractions0.2100.0000.209
counts-method0.2060.0090.215
datasets-methods0.1220.0000.123
deleteDatasets1.2610.0251.286
deleteReadGroups0.1660.0070.173
deleteRegions1.4600.0221.481
enrichment-methods0.1470.0150.161
getDefaultParameterList0.0010.0000.000
mergeReadGroups0.1890.0320.221
parameters-methods0.1300.0330.163
plotAllelicBiasResults42.345 0.10730.819
plotAllelicBiasResultsOverview1.1440.0561.201
plotAndCalculateCorrelationDatasets1.3890.0111.401
plotAndCalculateWeakAndStrongGenotype0.6390.0270.667
plotAndClusterMatrix0.5940.0110.606
plotAndSummarizeAllelicBiasTest40.238 0.14728.444
plotBinCounts1.6860.0231.710
plotClusterAverage0.7850.0250.809
plotFDRResults39.755 0.57329.300
plotGenotypesPerCluster0.5200.0360.557
plotGenotypesPerSNP0.4140.0100.424
plotRegionCounts2.0620.0382.099
readGroups-methods0.1130.0000.113
regions-methods0.1390.0110.151
renameBins0.1440.0030.148
renameDatasets0.1850.0220.207
renameReadGroups0.1330.0170.150
renameRegions3.2640.0653.329
results1.4730.9662.438
testForAllelicBiases37.975 0.93128.874