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ABCDEFGHIJK[L]MNOPQRSTUVWXYZ

This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 1124/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
lumi 2.58.0  (landing page)
Lei Huang
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/lumi
git_branch: RELEASE_3_20
git_last_commit: d654263
git_last_commit_date: 2024-10-29 09:27:14 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for lumi on nebbiolo2

To the developers/maintainers of the lumi package:
- 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 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: lumi
Version: 2.58.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:lumi.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings lumi_2.58.0.tar.gz
StartedAt: 2024-12-20 01:56:24 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 02:10:04 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 819.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: lumi.Rcheck
Warnings: 3

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:lumi.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings lumi_2.58.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/lumi.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘lumi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘lumi’ version ‘2.58.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ... NOTE
Problems with news in ‘NEWS’:
  Cannot process chunk/lines:
    release date: 04/23/2011
    1. Adding supports for Infinium 450K methylation microarrays, which includes updating the color bias correction and other related functions.
  Cannot process chunk/lines:
    release date: 01/31/2011
    1. Bug fix related with Methylation File GEO submission
  Cannot process chunk/lines:
    release date: 01/22/2011
    1. Moved the MethyLumiM class and related methods from lumi to methylumi package
    2. Add some methylation status estimation functions and updated vignette
  Cannot process chunk/lines:
    release date: 01/12/2011
    1. Add methylated.N and unmethylated.N matrix to the assayData slot of the MethyLumiM class
  Cannot process chunk/lines:
    Thanks Tim Tiche, Jr. adding this!
  Cannot process chunk/lines:
    release date: 01/03/2011
    1. Add controlData slot to the MethyLumiM class
    2. Update functions handling controlData, which include: addControlData2methyLumiM, estimateMethylationBG, getControlType, plotControlData and lumiMethyR
  Cannot process chunk/lines:
    release date: 12/29/2010
    1. Add functions of estimating methylation status
  Cannot process chunk/lines:
    release date: 12/21/2010
  Cannot process chunk/lines:
    Multiple minor updates, which includes 
    1. vignettes of methylation analysis
    2. annotation field of example.lumi dataset
    3. detectionCall for methylation data
    4. Auto check of parameter validation of lumiExpresso 
  Cannot process chunk/lines:
    release date: 11/08/2010
    1. Multiple updates related with methylation analysis
    2. Update of GEO submission file, make it be able to create GEO submission file based on a data matrix
    3. Update of getChipInfo to make it be able to check based on address IDs
  Cannot process chunk/lines:
    release data: 10/11/2010
    1. Add a treatment and control example dataset
    2. many updates of vignette 
    3. Add lumiMethyR function to wrap the methylumiR function from methylumi package
    4. add the addColorChannelInfo function in case of no color channel information was included in the data.
  Cannot process chunk/lines:
    release data: 09/22/2010
    1. Enable lumiMethyB, lumiMethyC and lumiMethyN to run user defined functions
    2. update of vignette 
  Cannot process chunk/lines:
    release data: 09/17/2010
    1. Major update of the package by adding many functions related with Illumina Methylation microarray analysis.
    2. Add the vignette of analyzing Illumina Infinium methylation microarray data 
  Cannot process chunk/lines:
    release data: 08/28/2010
    1. Import several classes and functions from methylumi package for methylation analysis
    2. Organize all generic functions together in a new file: AllGnereics.R
  Cannot process chunk/lines:
    release data: 08/25/2010
    1. Add na.rm setting to lumiB, lumiT and lumiN
    (Thanks Wieliang Qiu from Harvard reporting this!)
  Cannot process chunk/lines:
    release data: 08/16/2010
    1. Add Illumina Methylation data analysis components
    2. Change the package dependence as NameSpaces
  Cannot process chunk/lines:
    Sorry, many many updates and fixes not reported here ...
  Cannot process chunk/lines:
    release data: 02/08/2008
    1. The default normalization method is changed as 'quantile' instead of 'rsn'.
    2. update lumiR for the changes of BeadStudio output.
  Cannot process chunk/lines:
    release data: 02/03/2008
    1. lumiR can also input the annotation information outputted by BeadStuio
    2. Add plot functions dealing with the control probe data outputted by BeadStudio.
  Cannot process chunk/lines:
    release data: 12/05/2007
    1. Add functions dealing with the control probe data outputted by BeadStudio.
    2. Extended VST algorithm for processing the Affymetrix data.
    3. Add SSN (simple scaling normalization) algorithm for conservative normalization.
    4. other updates of help and vignette
  Cannot process chunk/lines:
    release data: 09/30/2007
    1. update the code to make vst accept negative values.
    2. fixed bug of combine and subset functions dealing with controlData slot
    3. add bg.Adjust background adjustment function to deal with the control probe information
    4. add lumiR.batch function to input multiple files in batch
    5. remove stdCorrection parameter from lumiR to lumiT, which converts the standard error of the mean to standard deviation in variance stabilization.
    6. other small updates of help and vignette
  Cannot process chunk/lines:
    Thanks Wei Shi and Gordon Smith for reporting problems and suggestions for improvements.
  Cannot process chunk/lines:
    release data: 08/25/2007
    1. Updated the vst function in version 1.3.25. (estimate the c3 based on the background probes).
    2. Updated the inverseVST and other related functions to allow the recover to the raw scale of the preprocessed data.
    3. Added the evaluation of VST vignette
    3. Updated the lumi vignette
  Cannot process chunk/lines:
    release data: 07/11/2007
    1. Add the correction of the STDEV column values of the BeadStudio output file (transfer the standard error of the mean as the standard deviation).
    2. Updated the vignette.
  Cannot process chunk/lines:
    Thanks Gordon Smith provided the information of STDEV column of BeadStudio output file.
  Cannot process chunk/lines:
    release data: 06/29/2007
    1. Updated the vignette with added performance evaluation section.
    2. Added "dec" option in lumiR function
    3. Add density funciton
    4. Allow user to select and customize the input columns of BeadStudio output files
  Cannot process chunk/lines:
    Thanks Renee McElhaney for checking the vignette, Martin Morgan, Ingrid H. G. Østense and Michal Blazejczyk for the suggestion or reporting problems.
  Cannot process chunk/lines:
    release data: 06/16/2007
  Cannot process chunk/lines:
    Add the annotation library information when run addNuId2lumi function.
  Cannot process chunk/lines:
    Thanks Vincent Carey (Harvard) for the suggestion.
  Cannot process chunk/lines:
    release date: 04/22/2007-06/15/2007
  Cannot process chunk/lines:
    Major updates:
    1. All the major functions compatible with ExpressionSet class
    2. presentCount was removed from the featureData. use detectionCall function to estimate presentCount
    3. lumiR function now allows user to select the input data columns
    4. Add lumiB function for background correction
    5. lumiExpresso function to encapsulate all preprocessing functions
    6. Vignette tutorial has major updates.
  Cannot process chunk/lines:
    Thanks Ryan Gordon, DeokHoon Kim, Danilo Licastro, Matthias Kohl, Ezhou Lori Long (NIH), Sean Davis (NIH) and others for the suggestions and reporting problems.
  Cannot process chunk/lines:
    release date: 04/22/2007
    1. Major updates of the vignette.
    2. A simpleOutput option was added for the lumiT function.
    3. Added nuID and targetID/probeID mapping functions.
  Cannot process chunk/lines:
    release date: 04/17/2007
    1. Updated lumiR function for better robustness.
    2. Added subset parameter to all plot functions.
    3. Add 'forcePositive' method to the lumiB function to avoid negative values.
    4. Other related updates.
  Cannot process chunk/lines:
    release date: 04/12/2007
    1. Fixed the bug of combine function.
  Cannot process chunk/lines:
    Thanks Jiexin Zhang (M.D. Anderson Cancer Center) finding the bug.
  Cannot process chunk/lines:
    release date: 04/11/2007
    1. Updated lumiR to compatible with BeadStudio output file without header
  Cannot process chunk/lines:
    release date: 03/24/2007
    1. Updated lumiR to compatible with BeadStudio 3.0 output format
    2. Removed LumiQC class and added QC slot in the LumiBatch class
    3. Updated the functions related with updates 1 and 2
  Cannot process chunk/lines:
    Thanks Sean Davis (NIH) and Michael Stevens (Washington University) for providing BeadStudio 3.0 files and testing.
  Cannot process chunk/lines:
    release date: 03/20/2007
    1. Updated lumiN.rsn to allow the targetArray to be vector or LumiBatch object with one sample
    2. Update the help documents
  Cannot process chunk/lines:
    Thanks Jiexin Zhang (M.D. Anderson Cancer Center) providing the suggestion of targetArray.
  Cannot process chunk/lines:
    release date: 03/18/2007
    1. Updated lumiN to make it accept ExpressionSet inherited object or data matrix
    2. Update the some help files
  Cannot process chunk/lines:
    release date: 02/20/2007
    1. Updated the vignette and lumiN.rsn function
  Cannot process chunk/lines:
    release date: 02/15/2007
    1. Updated the combine method of LumiBatch class, addNuId2lumi, lumiR for better adaptiveness.
  Cannot process chunk/lines:
    release date: 02/14/2007
    1. Updated lumiR function to allow directly adding nuID when reading the data;
    2. Updated addNuId2lumi to add the tracking history:
  Cannot process chunk/lines:
    release date: 02/08/2007
    1. Updated lumiR function to make it compatible with R 2.5;
    2. Updated addNuId2lumi and lumiN function to fix some typos.
  Cannot process chunk/lines:
    Thanks Jean-Eudes DAZARD (Case Western Reserve University) reporting this problem.
  Cannot process chunk/lines:
    release date: 01/21/2007
    1. Updated lumiR and addNuId2lumi functions to allow them mapping TargetId or ProbeId to nuID;
  Cannot process chunk/lines:
    release date: 01/01/2007
    1. Changed the S3 function "plot.lumiQC" as the S4 function "plot" with signature "LumiQC, missing";
    2. Added S4 function "hist" with signature "ExpressionSet";
    3. Added rownames duplication checking code in the "addNuId2lumi" and "lumiR" functions;
    4. Added varMetadata information in the LumiBatch object produced in "lumiR" function;
    5. Updated the help and tutorial files.
  Cannot process chunk/lines:
    Thanks Kevin Coombes (M.D. Anderson Cancer Center) for the testing and suggestions of the lumi package.
  Cannot process chunk/lines:
    release date: 12/11/2006
    1. Updated the summary (show) functions of LumiBatch and LumiQC objects;
    2. Added subsetting code for the LumiQC and LumiBatch objects;
    3. Updated the help and tutorial files.
  Cannot process chunk/lines:
    Thanks Peter Bram (Leiden University Medical Center) for the testing and suggestions of the lumi package.
  Cannot process chunk/lines:
    First release date: 12/05/2006
* 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 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) plot-methods.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot-methods.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot-methods.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot-methods.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot-methods.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot-methods.Rd:33-34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot-methods.Rd:35: Lost braces in \itemize; meant \describe ?
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 Rd file '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 36.917  0.201  37.119
* checking package vignettes ... NOTE
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/lumi.Rcheck/00check.log’
for details.


Installation output

lumi.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL lumi
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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)

Tests output


Example timings

lumi.Rcheck/lumi-Ex.timings

nameusersystemelapsed
LumiBatch-class0.8650.0670.932
MAplot-methods3.8530.0623.916
addAnnotationInfo0.0470.0000.046
addControlData2lumi000
addNuID2lumi000
adjColorBias.quantile1.4470.0981.546
adjColorBias.ssn0.3280.0000.329
bgAdjust0.0670.0030.071
bgAdjustMethylation0.1250.0010.126
boxplot-MethyLumiM-methods0.3430.0080.352
boxplot-methods0.0840.0020.086
boxplotColorBias0.1020.0030.105
density-methods0.0750.0000.076
detectOutlier0.0730.0020.075
detectionCall0.1270.0040.130
estimateBeta0.1460.0000.146
estimateIntensity0.1490.0010.150
estimateLumiCV0.0830.0010.084
estimateM0.3210.0000.321
estimateMethylationBG0.1020.0000.101
example.lumi0.0670.0000.066
example.lumiMethy0.0450.0000.045
example.methyTitration0.1640.0010.165
gammaFitEM2.0960.0182.115
getChipInfo3.0490.1123.166
getControlData0.0010.0000.001
getControlProbe0.0000.0000.001
getControlType0.0010.0000.001
getNuIDMappingInfo1.5810.1031.684
hist-methods0.1000.0020.102
id2seq0.0000.0010.000
inverseVST0.2980.0140.313
is.nuID0.0010.0000.000
lumiB0.0730.0060.080
lumiExpresso0.1740.0190.195
lumiMethyB0.0460.0020.050
lumiMethyC0.7140.0140.728
lumiMethyN0.0710.0030.074
lumiMethyStatus36.917 0.20137.119
lumiN0.3510.0020.355
lumiQ0.2290.0050.234
lumiR000
lumiR.batch000
lumiT0.2790.0020.280
methylationCall2.0760.0162.092
normalizeMethylation.quantile0.1400.0010.141
normalizeMethylation.ssn0.1120.0020.114
nuID2EntrezID0.6110.0050.617
nuID2IlluminaID2.6690.0112.681
nuID2RefSeqID0.6040.0020.607
nuID2probeID2.5550.0142.568
nuID2targetID2.6660.0012.667
pairs-methods0.6110.0080.618
plot-methods1.5270.0131.540
plotCDF0.1280.0010.129
plotColorBias1D0.1650.0020.168
plotColorBias2D0.1310.0000.132
plotControlData0.0010.0000.001
plotDensity0.0980.0020.101
plotGammaFit2.4720.0032.475
plotHousekeepingGene0.0000.0000.001
plotSampleRelation0.3540.0040.358
plotStringencyGene0.0000.0000.001
plotVST0.2680.0040.272
probeID2nuID2.5360.0042.540
produceGEOPlatformFile000
produceGEOSubmissionFile000
produceMethylationGEOSubmissionFile0.0010.0000.000
seq2id000
targetID2nuID2.5250.0012.527
vst0.1970.0020.200