Lei Huang
| Snapshot Date: 2023-02-01 14:00:21 -0500 (Wed, 01 Feb 2023) |
| git_url: https://git.bioconductor.org/packages/lumi |
| git_branch: master |
| git_last_commit: 95a906f |
| git_last_commit_date: 2022-11-01 10:42:41 -0500 (Tue, 01 Nov 2022) |
| Back to Multiple platform build/check report for BioC 3.17 |
|
This page was generated on 2023-02-02 11:10:19 -0500 (Thu, 02 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" | 4483 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2023-01-10 r83596 ucrt) -- "Unsuffered Consequences" | 4249 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" | 4272 |
| 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 | ||||
|
To the developers/maintainers of the lumi package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/lumi.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1052/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| lumi 2.51.0 (landing page) Lei Huang
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: lumi |
| Version: 2.51.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:lumi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings lumi_2.51.0.tar.gz |
| StartedAt: 2023-02-02 02:58:56 -0500 (Thu, 02 Feb 2023) |
| EndedAt: 2023-02-02 03:16:02 -0500 (Thu, 02 Feb 2023) |
| EllapsedTime: 1026.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: lumi.Rcheck |
| Warnings: 3 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:lumi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings lumi_2.51.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/lumi.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* R was compiled by
Apple clang version 12.0.0 (clang-1200.0.32.29)
GNU Fortran (GCC) 8.2.0
* running under: macOS Mojave 10.14.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘lumi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘lumi’ version ‘2.51.0’
* 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 ‘lumi’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R 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 dependencies in R code ... WARNING
'::' or ':::' imports not declared from:
‘IRanges’ ‘bigmemoryExtras’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) addNuID2lumi.Rd:21: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) getChipInfo.Rd:22: Escaped LaTeX specials: \_ \_ \_ \_
checkRd: (-1) getNuIDMappingInfo.Rd:17: Escaped LaTeX specials: \_
checkRd: (-1) lumiR.Rd:22: Escaped LaTeX specials: \_
checkRd: (-1) lumiR.Rd:34: Escaped LaTeX specials: \_
checkRd: (-1) lumiR.Rd:36: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_
checkRd: (-1) lumiR.Rd:40: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_ \_ \_ \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) lumiR.batch.Rd:24: Escaped LaTeX specials: \_ \_ \_ \_ \_
checkRd: (-1) nuID2EntrezID.Rd:19: Escaped LaTeX specials: \_
checkRd: (-1) nuID2IlluminaID.Rd:21: Escaped LaTeX specials: \_ \_
checkRd: (-1) nuID2RefSeqID.Rd:19: Escaped LaTeX specials: \_
checkRd: (-1) produceGEOSampleInfoTemplate.Rd:18: Escaped LaTeX specials: \_ \_
checkRd: (-1) produceGEOSampleInfoTemplate.Rd:18: Escaped LaTeX specials: \#
checkRd: (-1) produceGEOSubmissionFile.Rd:23: Escaped LaTeX specials: \_ \_ \_ \_
checkRd: (-1) produceMethylationGEOSubmissionFile.Rd:23: Escaped LaTeX specials: \_ \_ \_ \_
checkRd: (-1) seq2id.Rd:18: Escaped LaTeX specials: \_
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Unknown package ‘bigmemoryExtras’ in Rd xrefs
Missing link or links in documentation object 'lumiN.Rd':
‘[vsn]{vsn}’
See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
‘IlluminaAnnotation.R’ ‘IlluminaAnnotation.pdf’ ‘lumi.R’ ‘lumi.pdf’
‘lumi_VST_evaluation.R’ ‘lumi_VST_evaluation.pdf’
‘methylationAnalysis.R’ ‘methylationAnalysis.pdf’
Package has no Sweave vignette sources and no VignetteBuilder field.
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
lumiMethyStatus 75.938 5.448 119.190
getChipInfo 7.232 0.331 10.575
plotGammaFit 5.573 0.295 8.405
nuID2IlluminaID 5.355 0.036 7.799
MAplot-methods 5.299 0.079 7.417
targetID2nuID 5.168 0.030 7.722
probeID2nuID 5.164 0.031 7.543
nuID2probeID 5.086 0.036 7.504
nuID2targetID 5.054 0.031 7.632
gammaFitEM 4.297 0.301 6.291
methylationCall 4.154 0.292 6.391
* checking PDF version of manual ... OK
* DONE
Status: 3 WARNINGs, 1 NOTE
See
‘/Users/biocbuild/bbs-3.17-bioc/meat/lumi.Rcheck/00check.log’
for details.
lumi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL lumi ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3/Resources/library’ * installing *source* package ‘lumi’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’ ** testing if installed package can be loaded from final location No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’ ** testing if installed package keeps a record of temporary installation path * DONE (lumi)
lumi.Rcheck/lumi-Ex.timings
| name | user | system | elapsed | |
| LumiBatch-class | 3.406 | 0.093 | 4.672 | |
| MAplot-methods | 5.299 | 0.079 | 7.417 | |
| addAnnotationInfo | 0.092 | 0.004 | 0.127 | |
| addControlData2lumi | 0.001 | 0.000 | 0.000 | |
| addNuID2lumi | 0.001 | 0.001 | 0.000 | |
| adjColorBias.quantile | 2.216 | 0.064 | 3.153 | |
| adjColorBias.ssn | 0.614 | 0.031 | 0.861 | |
| bgAdjust | 0.122 | 0.003 | 0.175 | |
| bgAdjustMethylation | 0.256 | 0.011 | 0.355 | |
| boxplot-MethyLumiM-methods | 0.815 | 0.017 | 1.131 | |
| boxplot-methods | 0.139 | 0.005 | 0.188 | |
| boxplotColorBias | 0.210 | 0.017 | 0.303 | |
| density-methods | 0.135 | 0.005 | 0.198 | |
| detectOutlier | 0.136 | 0.006 | 0.197 | |
| detectionCall | 0.232 | 0.008 | 0.327 | |
| estimateBeta | 0.308 | 0.010 | 0.453 | |
| estimateIntensity | 0.331 | 0.006 | 0.461 | |
| estimateLumiCV | 0.151 | 0.004 | 0.211 | |
| estimateM | 0.778 | 0.012 | 1.051 | |
| estimateMethylationBG | 0.219 | 0.006 | 0.291 | |
| example.lumi | 0.114 | 0.003 | 0.159 | |
| example.lumiMethy | 0.091 | 0.003 | 0.132 | |
| example.methyTitration | 0.273 | 0.007 | 0.371 | |
| gammaFitEM | 4.297 | 0.301 | 6.291 | |
| getChipInfo | 7.232 | 0.331 | 10.575 | |
| getControlData | 0.002 | 0.001 | 0.002 | |
| getControlProbe | 0.001 | 0.000 | 0.001 | |
| getControlType | 0.001 | 0.000 | 0.004 | |
| getNuIDMappingInfo | 1.776 | 0.092 | 2.619 | |
| hist-methods | 0.172 | 0.008 | 0.244 | |
| id2seq | 0.001 | 0.000 | 0.002 | |
| inverseVST | 0.818 | 0.024 | 1.165 | |
| is.nuID | 0.001 | 0.000 | 0.001 | |
| lumiB | 0.135 | 0.003 | 0.190 | |
| lumiExpresso | 0.354 | 0.009 | 0.516 | |
| lumiMethyB | 0.098 | 0.003 | 0.140 | |
| lumiMethyC | 1.716 | 0.056 | 2.587 | |
| lumiMethyN | 0.130 | 0.004 | 0.183 | |
| lumiMethyStatus | 75.938 | 5.448 | 119.190 | |
| lumiN | 0.724 | 0.046 | 1.044 | |
| lumiQ | 0.421 | 0.012 | 0.612 | |
| lumiR | 0 | 0 | 0 | |
| lumiR.batch | 0 | 0 | 0 | |
| lumiT | 0.467 | 0.015 | 0.665 | |
| methylationCall | 4.154 | 0.292 | 6.391 | |
| normalizeMethylation.quantile | 0.256 | 0.018 | 0.394 | |
| normalizeMethylation.ssn | 0.222 | 0.004 | 0.312 | |
| nuID2EntrezID | 1.637 | 0.032 | 2.350 | |
| nuID2IlluminaID | 5.355 | 0.036 | 7.799 | |
| nuID2RefSeqID | 1.560 | 0.021 | 2.333 | |
| nuID2probeID | 5.086 | 0.036 | 7.504 | |
| nuID2targetID | 5.054 | 0.031 | 7.632 | |
| pairs-methods | 1.249 | 0.044 | 2.019 | |
| plot-methods | 2.563 | 0.045 | 4.045 | |
| plotCDF | 0.204 | 0.008 | 0.323 | |
| plotColorBias1D | 0.278 | 0.007 | 0.452 | |
| plotColorBias2D | 0.264 | 0.006 | 0.397 | |
| plotControlData | 0.001 | 0.001 | 0.001 | |
| plotDensity | 0.170 | 0.005 | 0.262 | |
| plotGammaFit | 5.573 | 0.295 | 8.405 | |
| plotHousekeepingGene | 0.001 | 0.001 | 0.001 | |
| plotSampleRelation | 1.157 | 0.008 | 1.687 | |
| plotStringencyGene | 0.001 | 0.001 | 0.002 | |
| plotVST | 0.449 | 0.015 | 0.660 | |
| probeID2nuID | 5.164 | 0.031 | 7.543 | |
| produceGEOPlatformFile | 0 | 0 | 0 | |
| produceGEOSubmissionFile | 0.001 | 0.000 | 0.000 | |
| produceMethylationGEOSubmissionFile | 0.001 | 0.000 | 0.001 | |
| seq2id | 0.000 | 0.000 | 0.001 | |
| targetID2nuID | 5.168 | 0.030 | 7.722 | |
| vst | 0.388 | 0.009 | 0.596 | |