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This page was generated on 2024-12-24 11:47 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4373
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 1983/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SNPhood 1.37.0  (landing page)
Christian Arnold
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/SNPhood
git_branch: devel
git_last_commit: 5ebb343
git_last_commit_date: 2024-10-29 10:04:42 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'DESeq2' which is only available as a source package that needs compilation
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  NO, package depends on 'DESeq2' which is only available as a source package that needs compilation
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  NO, package depends on 'DESeq2' which is only available as a source package that needs compilation
kunpeng2Linux (openEuler 22.03 LTS-SP1) / 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: 1.37.0
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_1.37.0.tar.gz
StartedAt: 2024-12-24 11:25:00 -0000 (Tue, 24 Dec 2024)
EndedAt: 2024-12-24 11:38:03 -0000 (Tue, 24 Dec 2024)
EllapsedTime: 782.9 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_1.37.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/SNPhood.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* 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)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SNPhood/DESCRIPTION’ ... OK
* this is package ‘SNPhood’ version ‘1.37.0’
* 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                  141.836  2.032 146.098
plotAllelicBiasResults           41.313  0.175  41.610
plotFDRResults                   39.849  0.152  40.968
testForAllelicBiases             39.130  0.147  40.195
plotAndSummarizeAllelicBiasTest  38.817  0.127  40.470
annotationBins2                  12.830  0.004  12.850
associateGenotypes                7.951  0.008   7.973
* 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-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘SNPhood’ ...
** 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
analyzeSNPhood141.836 2.032146.098
annotation-methods0.3790.0160.395
annotationBins0.2690.0000.269
annotationBins212.830 0.00412.850
annotationDatasets0.2400.0040.245
annotationReadGroups1.3770.0081.387
annotationRegions0.2610.0080.270
associateGenotypes7.9510.0087.973
bins-methods0.3060.0040.310
changeObjectIntegrityChecking1.3880.0001.389
collectFiles0.0380.0000.039
convertToAllelicFractions0.3190.0000.320
counts-method1.4910.0081.501
datasets-methods0.2540.0040.258
deleteDatasets0.2890.0000.290
deleteReadGroups0.2820.0000.282
deleteRegions1.4150.0001.417
enrichment-methods0.2730.0000.274
getDefaultParameterList000
mergeReadGroups0.3350.0030.339
parameters-methods0.2570.0040.261
plotAllelicBiasResults41.313 0.17541.610
plotAllelicBiasResultsOverview1.3950.0041.405
plotAndCalculateCorrelationDatasets1.6240.0281.656
plotAndCalculateWeakAndStrongGenotype2.1160.0082.132
plotAndClusterMatrix0.8250.0000.827
plotAndSummarizeAllelicBiasTest38.817 0.12740.470
plotBinCounts1.8250.0281.881
plotClusterAverage0.8760.0040.897
plotFDRResults39.849 0.15240.968
plotGenotypesPerCluster0.6590.0200.681
plotGenotypesPerSNP0.5760.0120.591
plotRegionCounts2.7100.0122.799
readGroups-methods0.2460.0000.246
regions-methods0.2530.0000.253
renameBins0.2960.0000.297
renameDatasets1.4540.0561.569
renameReadGroups0.2650.0000.265
renameRegions3.2420.0043.280
results1.7631.1462.945
testForAllelicBiases39.130 0.14740.195