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This page was generated on 2024-02-18 02:28:44 -0500 (Sun, 18 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4657
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4397
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4424
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4400
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 1106/2244HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
lumi 2.55.0  (landing page)
Lei Huang
Snapshot Date: 2024-02-16 14:10:20 -0500 (Fri, 16 Feb 2024)
git_url: https://git.bioconductor.org/packages/lumi
git_branch: devel
git_last_commit: 6331e8a
git_last_commit_date: 2023-10-24 09:37:44 -0500 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  

CHECK results for lumi on merida1


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: 2.55.0
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_2.55.0.tar.gz
StartedAt: 2024-02-17 05:58:26 -0500 (Sat, 17 Feb 2024)
EndedAt: 2024-02-17 06:14:40 -0500 (Sat, 17 Feb 2024)
EllapsedTime: 973.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: lumi.Rcheck
Warnings: 3

Command output

##############################################################################
##############################################################################
###
### 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_2.55.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/lumi.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-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 Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘lumi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘lumi’ version ‘2.55.0’
* 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 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 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 74.309  8.160  94.345
getChipInfo      7.394  0.540  10.168
MAplot-methods   6.389  0.125   7.684
plotGammaFit     5.388  0.384   6.956
nuID2IlluminaID  5.337  0.075   6.491
probeID2nuID     4.886  0.056   5.833
nuID2probeID     4.879  0.059   5.810
targetID2nuID    4.863  0.058   5.892
nuID2targetID    4.845  0.057   5.831
gammaFitEM       4.402  0.311   5.609
methylationCall  4.146  0.386   5.451
* 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-3.19-bioc/meat/lumi.Rcheck/00check.log’
for details.



Installation output

lumi.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL lumi
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/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)

Tests output


Example timings

lumi.Rcheck/lumi-Ex.timings

nameusersystemelapsed
LumiBatch-class2.2870.1812.859
MAplot-methods6.3890.1257.684
addAnnotationInfo0.0770.0050.101
addControlData2lumi0.0010.0000.001
addNuID2lumi0.0000.0000.001
adjColorBias.quantile1.1210.0801.422
adjColorBias.ssn0.6120.0300.759
bgAdjust0.1230.0050.158
bgAdjustMethylation0.2380.0120.294
boxplot-MethyLumiM-methods0.8370.0181.022
boxplot-methods0.1370.0080.179
boxplotColorBias0.1950.0170.247
density-methods0.1350.0070.168
detectOutlier0.1380.0050.171
detectionCall0.2380.0110.294
estimateBeta0.2970.0150.360
estimateIntensity0.3290.0090.398
estimateLumiCV0.1550.0070.195
estimateM0.7720.0170.978
estimateMethylationBG0.1870.0060.234
example.lumi0.1210.0060.153
example.lumiMethy0.0760.0050.101
example.methyTitration0.2870.0120.344
gammaFitEM4.4020.3115.609
getChipInfo 7.394 0.54010.168
getControlData0.0020.0010.005
getControlProbe0.0010.0020.003
getControlType0.0010.0010.004
getNuIDMappingInfo1.8660.1542.402
hist-methods0.1740.0080.229
id2seq0.0010.0000.002
inverseVST0.7030.0210.887
is.nuID0.0010.0010.001
lumiB0.1350.0060.164
lumiExpresso0.3480.0150.446
lumiMethyB0.0840.0050.102
lumiMethyC1.4540.0941.827
lumiMethyN0.1150.0050.139
lumiMethyStatus74.309 8.16094.345
lumiN0.7300.0670.979
lumiQ0.4300.0230.535
lumiR0.0000.0000.001
lumiR.batch0.0000.0010.001
lumiT0.4790.0300.609
methylationCall4.1460.3865.451
normalizeMethylation.quantile0.2330.0230.298
normalizeMethylation.ssn0.2110.0070.268
nuID2EntrezID1.6450.0451.994
nuID2IlluminaID5.3370.0756.491
nuID2RefSeqID1.8780.0652.311
nuID2probeID4.8790.0595.810
nuID2targetID4.8450.0575.831
pairs-methods1.1580.0851.506
plot-methods2.5330.0773.099
plotCDF0.1950.0130.260
plotColorBias1D0.3620.0230.451
plotColorBias2D0.2570.0100.313
plotControlData0.0020.0010.003
plotDensity0.1720.0070.224
plotGammaFit5.3880.3846.956
plotHousekeepingGene0.0020.0010.003
plotSampleRelation1.1140.0141.334
plotStringencyGene0.0020.0010.002
plotVST0.5390.0510.743
probeID2nuID4.8860.0565.833
produceGEOPlatformFile0.0000.0000.001
produceGEOSubmissionFile0.0000.0010.001
produceMethylationGEOSubmissionFile0.0000.0010.001
seq2id0.0010.0010.003
targetID2nuID4.8630.0585.892
vst0.2850.0130.415