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This page was generated on 2024-06-14 14:37 -0400 (Fri, 14 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
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 2015/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SNPhood 1.34.0  (landing page)
Christian Arnold
Snapshot Date: 2024-06-12 14:00 -0400 (Wed, 12 Jun 2024)
git_url: https://git.bioconductor.org/packages/SNPhood
git_branch: RELEASE_3_19
git_last_commit: ac00e2a
git_last_commit_date: 2024-04-30 10:46:24 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for SNPhood on nebbiolo1

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: 1.34.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:SNPhood.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings SNPhood_1.34.0.tar.gz
StartedAt: 2024-06-13 03:47:20 -0400 (Thu, 13 Jun 2024)
EndedAt: 2024-06-13 04:00:36 -0400 (Thu, 13 Jun 2024)
EllapsedTime: 795.5 seconds
RetCode: 0
Status:   OK  
CheckDir: SNPhood.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:SNPhood.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings SNPhood_1.34.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/SNPhood.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘SNPhood/DESCRIPTION’ ... OK
* this is package ‘SNPhood’ version ‘1.34.0’
* 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 ... 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                  102.926  6.509 110.105
plotAllelicBiasResults           30.579  0.489  28.597
plotFDRResults                   28.676  0.264  26.790
plotAndSummarizeAllelicBiasTest  27.451  0.366  26.003
testForAllelicBiases             27.052  0.234  24.639
annotationBins2                  10.427  0.360  10.788
results                           2.477  8.276  10.754
associateGenotypes                4.995  0.172   5.166
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/SNPhood.Rcheck/00check.log’
for details.


Installation output

SNPhood.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL SNPhood
###
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* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/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
analyzeSNPhood102.926 6.509110.105
annotation-methods0.2100.0840.294
annotationBins0.1490.0240.173
annotationBins210.427 0.36010.788
annotationDatasets0.1400.0280.168
annotationReadGroups0.1350.0240.160
annotationRegions0.1400.0160.156
associateGenotypes4.9950.1725.166
bins-methods0.1230.0320.155
changeObjectIntegrityChecking0.2110.0120.223
collectFiles0.0290.0000.029
convertToAllelicFractions0.1640.0000.164
counts-method0.1960.0200.216
datasets-methods1.1400.0881.228
deleteDatasets0.1360.0240.159
deleteReadGroups0.1470.0160.163
deleteRegions1.1520.0601.213
enrichment-methods0.1350.0200.155
getDefaultParameterList000
mergeReadGroups0.1780.0080.186
parameters-methods0.1440.0040.148
plotAllelicBiasResults30.579 0.48928.597
plotAllelicBiasResultsOverview0.8210.0720.893
plotAndCalculateCorrelationDatasets0.2300.0160.245
plotAndCalculateWeakAndStrongGenotype1.8300.1121.941
plotAndClusterMatrix0.5300.0120.541
plotAndSummarizeAllelicBiasTest27.451 0.36626.003
plotBinCounts1.1020.0561.158
plotClusterAverage0.4520.0040.457
plotFDRResults28.676 0.26426.790
plotGenotypesPerCluster0.4240.0400.464
plotGenotypesPerSNP0.3260.0080.334
plotRegionCounts1.7210.0601.781
readGroups-methods0.1300.0040.134
regions-methods0.1310.0040.135
renameBins0.1330.0160.149
renameDatasets1.1300.0281.158
renameReadGroups0.1280.0080.135
renameRegions1.9860.0162.002
results 2.477 8.27610.754
testForAllelicBiases27.052 0.23424.639