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This page was generated on 2024-06-11 15:41 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
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 1959/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SNPhood 1.35.0  (landing page)
Christian Arnold
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/SNPhood
git_branch: devel
git_last_commit: 147ba41
git_last_commit_date: 2024-04-30 10:46:24 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for SNPhood on palomino4

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: 1.35.0
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SNPhood.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings SNPhood_1.35.0.tar.gz
StartedAt: 2024-06-10 10:05:48 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 10:21:32 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 944.7 seconds
RetCode: 0
Status:   OK  
CheckDir: SNPhood.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SNPhood.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings SNPhood_1.35.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/SNPhood.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'SNPhood/DESCRIPTION' ... OK
* this is package 'SNPhood' version '1.35.0'
* 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 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 ... OK
* 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                  68.45   5.45   75.67
plotAndSummarizeAllelicBiasTest 19.58   0.26   19.78
plotAllelicBiasResults          19.13   0.28   19.40
testForAllelicBiases            19.02   0.14   19.11
plotFDRResults                  18.69   0.20   18.84
results                          4.91   4.51    9.44
* 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: 2 NOTEs
See
  'F:/biocbuild/bbs-3.20-bioc/meat/SNPhood.Rcheck/00check.log'
for details.


Installation output

SNPhood.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL SNPhood
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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
analyzeSNPhood68.45 5.4575.67
annotation-methods0.310.060.37
annotationBins0.210.050.26
annotationBins21.350.131.47
annotationDatasets0.110.090.20
annotationReadGroups0.970.111.08
annotationRegions0.140.030.17
associateGenotypes4.780.194.97
bins-methods0.200.010.22
changeObjectIntegrityChecking1.080.021.10
collectFiles0.050.000.04
convertToAllelicFractions0.180.000.19
counts-method1.100.021.11
datasets-methods0.120.030.16
deleteDatasets0.110.040.15
deleteReadGroups1.020.081.10
deleteRegions0.160.020.17
enrichment-methods1.030.001.03
getDefaultParameterList000
mergeReadGroups0.190.040.24
parameters-methods0.150.020.18
plotAllelicBiasResults19.13 0.2819.40
plotAllelicBiasResultsOverview0.870.201.08
plotAndCalculateCorrelationDatasets0.380.110.53
plotAndCalculateWeakAndStrongGenotype1.780.091.88
plotAndClusterMatrix0.780.070.86
plotAndSummarizeAllelicBiasTest19.58 0.2619.78
plotBinCounts1.090.051.14
plotClusterAverage0.470.090.56
plotFDRResults18.69 0.2018.84
plotGenotypesPerCluster0.410.050.46
plotGenotypesPerSNP0.320.050.37
plotRegionCounts3.080.253.35
readGroups-methods0.100.050.15
regions-methods0.110.040.16
renameBins0.150.050.20
renameDatasets0.130.060.19
renameReadGroups0.200.030.23
renameRegions3.230.073.30
results4.914.519.44
testForAllelicBiases19.02 0.1419.11