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This page was generated on 2024-06-28 17:40 -0400 (Fri, 28 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4760
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4494
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4508
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4466
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4362
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: 2024-06-26 14:00 -0400 (Wed, 26 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
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
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  


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: 2024-06-27 04:00:57 -0400 (Thu, 27 Jun 2024)
EndedAt: 2024-06-27 04:13:56 -0400 (Thu, 27 Jun 2024)
EllapsedTime: 779.5 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
###
##############################################################################
##############################################################################


* 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                  103.048  9.164 112.897
plotAllelicBiasResults           29.539  0.351  28.592
plotAndSummarizeAllelicBiasTest  28.065  0.196  25.962
testForAllelicBiases             26.990  0.244  24.775
plotFDRResults                   25.106  0.191  23.662
annotationBins2                  10.572  0.208  10.780
results                           2.450  8.319  10.770
associateGenotypes                5.070  0.088   5.159
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL SNPhood
###
##############################################################################
##############################################################################


* 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
analyzeSNPhood103.048 9.164112.897
annotation-methods0.2160.0880.304
annotationBins0.1480.0200.168
annotationBins210.572 0.20810.780
annotationDatasets0.1250.0400.164
annotationReadGroups0.1270.0200.146
annotationRegions0.1330.0280.161
associateGenotypes5.0700.0885.159
bins-methods0.1310.0120.143
changeObjectIntegrityChecking0.2130.0000.213
collectFiles0.0290.0000.030
convertToAllelicFractions0.1570.0080.164
counts-method0.2150.0160.231
datasets-methods1.2090.0681.277
deleteDatasets0.1450.0160.161
deleteReadGroups0.1520.0080.160
deleteRegions1.1890.0001.189
enrichment-methods0.1460.0110.157
getDefaultParameterList000
mergeReadGroups0.1730.0000.174
parameters-methods0.1380.0080.146
plotAllelicBiasResults29.539 0.35128.592
plotAllelicBiasResultsOverview0.8550.0520.906
plotAndCalculateCorrelationDatasets0.2170.0150.232
plotAndCalculateWeakAndStrongGenotype1.7670.1361.903
plotAndClusterMatrix0.5700.0160.587
plotAndSummarizeAllelicBiasTest28.065 0.19625.962
plotBinCounts1.1310.0641.195
plotClusterAverage0.4570.0080.465
plotFDRResults25.106 0.19123.662
plotGenotypesPerCluster0.4220.0480.470
plotGenotypesPerSNP0.3080.0120.319
plotRegionCounts1.6120.0321.645
readGroups-methods0.1210.0000.121
regions-methods0.1310.0000.130
renameBins0.1350.0120.148
renameDatasets1.1410.0401.181
renameReadGroups0.1300.0160.145
renameRegions1.9740.0201.994
results 2.450 8.31910.770
testForAllelicBiases26.990 0.24424.775