| Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-28 12:05 -0400 (Tue, 28 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4901 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4691 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4637 |
| 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 2058/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SNPhood 1.39.0 (landing page) Christian Arnold
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | |||||||||
|
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. |
| 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: 2025-10-27 22:10:15 -0400 (Mon, 27 Oct 2025) |
| EndedAt: 2025-10-27 22:14:10 -0400 (Mon, 27 Oct 2025) |
| EllapsedTime: 234.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SNPhood.Rcheck |
| Warnings: 0 |
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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
###
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* 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 39.634 0.785 40.825
plotAndSummarizeAllelicBiasTest 11.146 0.134 11.337
plotAllelicBiasResults 11.031 0.174 11.229
plotFDRResults 10.607 0.129 10.754
testForAllelicBiases 10.388 0.173 10.570
* 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.
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)
SNPhood.Rcheck/SNPhood-Ex.timings
| name | user | system | elapsed | |
| analyzeSNPhood | 39.634 | 0.785 | 40.825 | |
| annotation-methods | 0.072 | 0.019 | 0.091 | |
| annotationBins | 0.045 | 0.016 | 0.062 | |
| annotationBins2 | 4.331 | 0.013 | 4.343 | |
| annotationDatasets | 0.045 | 0.011 | 0.056 | |
| annotationReadGroups | 0.048 | 0.006 | 0.054 | |
| annotationRegions | 0.051 | 0.009 | 0.059 | |
| associateGenotypes | 1.783 | 0.078 | 1.864 | |
| bins-methods | 0.046 | 0.011 | 0.058 | |
| changeObjectIntegrityChecking | 0.055 | 0.010 | 0.065 | |
| collectFiles | 0.010 | 0.001 | 0.011 | |
| convertToAllelicFractions | 0.076 | 0.018 | 0.095 | |
| counts-method | 0.077 | 0.012 | 0.089 | |
| datasets-methods | 0.051 | 0.012 | 0.063 | |
| deleteDatasets | 0.488 | 0.016 | 0.503 | |
| deleteReadGroups | 0.058 | 0.011 | 0.068 | |
| deleteRegions | 0.496 | 0.009 | 0.505 | |
| enrichment-methods | 0.051 | 0.006 | 0.057 | |
| getDefaultParameterList | 0.000 | 0.001 | 0.001 | |
| mergeReadGroups | 0.063 | 0.010 | 0.074 | |
| parameters-methods | 0.049 | 0.013 | 0.063 | |
| plotAllelicBiasResults | 11.031 | 0.174 | 11.229 | |
| plotAllelicBiasResultsOverview | 0.350 | 0.008 | 0.358 | |
| plotAndCalculateCorrelationDatasets | 0.519 | 0.010 | 0.529 | |
| plotAndCalculateWeakAndStrongGenotype | 0.243 | 0.033 | 0.277 | |
| plotAndClusterMatrix | 0.198 | 0.019 | 0.216 | |
| plotAndSummarizeAllelicBiasTest | 11.146 | 0.134 | 11.337 | |
| plotBinCounts | 0.513 | 0.015 | 0.529 | |
| plotClusterAverage | 0.239 | 0.008 | 0.247 | |
| plotFDRResults | 10.607 | 0.129 | 10.754 | |
| plotGenotypesPerCluster | 0.169 | 0.011 | 0.182 | |
| plotGenotypesPerSNP | 0.142 | 0.013 | 0.155 | |
| plotRegionCounts | 1.135 | 0.042 | 1.187 | |
| readGroups-methods | 0.043 | 0.012 | 0.056 | |
| regions-methods | 0.041 | 0.006 | 0.047 | |
| renameBins | 0.054 | 0.012 | 0.067 | |
| renameDatasets | 0.046 | 0.006 | 0.052 | |
| renameReadGroups | 0.052 | 0.010 | 0.061 | |
| renameRegions | 0.631 | 0.018 | 0.650 | |
| results | 0.774 | 2.456 | 3.246 | |
| testForAllelicBiases | 10.388 | 0.173 | 10.570 | |