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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_2.58.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/lumi.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘lumi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘lumi’ version ‘2.58.0’
* 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 ... 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 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 54.323  8.633  62.997
getChipInfo      6.971  0.201   7.216
MAplot-methods   6.998  0.062   7.093
nuID2IlluminaID  5.597  0.069   5.666
nuID2probeID     5.502  0.050   5.552
targetID2nuID    5.501  0.048   5.549
probeID2nuID     5.465  0.039   5.507
nuID2targetID    5.361  0.041   5.404
* 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
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/lumi.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL lumi
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/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)