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This page was generated on 2025-10-16 11:41 -0400 (Thu, 16 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.6 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.7.5 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4586
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 2037/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SNPhood 1.38.0  (landing page)
Christian Arnold
Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025)
git_url: https://git.bioconductor.org/packages/SNPhood
git_branch: RELEASE_3_21
git_last_commit: a7144d2
git_last_commit_date: 2025-04-15 10:56:04 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.7.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for SNPhood on kunpeng2

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: SNPhood
Version: 1.38.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:SNPhood.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings SNPhood_1.38.0.tar.gz
StartedAt: 2025-10-14 14:28:59 -0000 (Tue, 14 Oct 2025)
EndedAt: 2025-10-14 14:44:07 -0000 (Tue, 14 Oct 2025)
EllapsedTime: 908.0 seconds
RetCode: 0
Status:   OK  
CheckDir: SNPhood.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:SNPhood.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings SNPhood_1.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/SNPhood.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SNPhood/DESCRIPTION’ ... OK
* this is package ‘SNPhood’ version ‘1.38.0’
* 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                  144.334  2.027 174.027
plotAllelicBiasResults           43.312  0.162  47.257
plotAndSummarizeAllelicBiasTest  39.695  0.152  42.062
plotFDRResults                   39.487  0.227  42.909
testForAllelicBiases             38.631  0.011  45.284
annotationBins2                  11.694  0.003  13.095
associateGenotypes                8.090  0.060   9.030
* 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
  ‘/home/biocbuild/bbs-3.21-bioc/meat/SNPhood.Rcheck/00check.log’
for details.


Installation output

SNPhood.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL SNPhood
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘SNPhood’ ...
** this is package ‘SNPhood’ version ‘1.38.0’
** 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
analyzeSNPhood144.334 2.027174.027
annotation-methods0.3460.0080.355
annotationBins0.2190.0120.231
annotationBins211.694 0.00313.095
annotationDatasets0.2150.0000.216
annotationReadGroups0.2260.0000.226
annotationRegions0.2410.0120.318
associateGenotypes8.090.069.03
bins-methods0.2180.0120.235
changeObjectIntegrityChecking0.2550.0040.259
collectFiles0.0370.0000.038
convertToAllelicFractions0.3220.0080.331
counts-method0.3550.0040.376
datasets-methods0.2310.0120.351
deleteDatasets1.3800.0081.514
deleteReadGroups0.2640.0110.275
deleteRegions1.4070.0001.569
enrichment-methods0.2450.0120.256
getDefaultParameterList0.0010.0000.001
mergeReadGroups0.3160.0000.439
parameters-methods0.2330.0120.245
plotAllelicBiasResults43.312 0.16247.257
plotAllelicBiasResultsOverview1.7270.0271.911
plotAndCalculateCorrelationDatasets1.5980.0161.769
plotAndCalculateWeakAndStrongGenotype0.9070.0360.973
plotAndClusterMatrix0.8490.0160.946
plotAndSummarizeAllelicBiasTest39.695 0.15242.062
plotBinCounts2.5470.0123.121
plotClusterAverage1.2520.0321.332
plotFDRResults39.487 0.22742.909
plotGenotypesPerCluster0.7820.0121.003
plotGenotypesPerSNP0.6480.0160.666
plotRegionCounts3.0560.0154.334
readGroups-methods0.2220.0000.223
regions-methods0.2740.0000.273
renameBins0.2340.0040.348
renameDatasets1.4250.0521.522
renameReadGroups0.2260.0040.230
renameRegions3.1320.0043.249
results1.7341.2403.654
testForAllelicBiases38.631 0.01145.284