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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:limpa.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings limpa_1.0.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/limpa.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘limpa/DESCRIPTION’ ... OK
* this is package ‘limpa’ version ‘1.0.0’
* 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 ‘limpa’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 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 ... OK
* 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 ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dpcDE.Rd: voomaLmFit
  dpcQuant.Rd: EList-class
  voomaLmFitWithImputation.Rd: vooma, lmFit
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘limpa-Tests.R’
  Comparing ‘limpa-Tests.Rout’ to ‘limpa-Tests.Rout.save’ ... OK
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/limpa.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL limpa
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘limpa’ ...
** this is package ‘limpa’ version ‘1.0.0’
** using staged installation
** R
** inst
** 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 (limpa)

R version 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(limpa)
Loading required package: limma
> options(warnPartialMatchArgs=TRUE,warnPartialMatchAttr=TRUE,warnPartialMatchDollar=TRUE,width=120)
> 
> set.seed(0); u <- runif(100)
> 
> y.peptide <- simProteinDataSet()
> names(y.peptide)
[1] "E"       "genes"   "targets" "other"  
> colSums(is.na(y.peptide$E))
 S1  S2  S3  S4  S5  S6  S7  S8  S9 S10 
 40  53  45  39  44  42  41  48  38  47 
> summary(y.peptide$E[,1])
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max.    NA's 
  2.160   5.695   7.142   6.868   8.587   9.717      40 
> names(y.peptide)
[1] "E"       "genes"   "targets" "other"  
> 
> dpcfit <- dpc(y.peptide)
2 peptides are completely missing in all samples.
> dpcfit$dpc
     beta0      beta1 
-4.2779693  0.7787527 
> 
> y.protein <- dpcQuant(y.peptide,protein.id="Protein",dpcfit)
Estimating hyperparameters ...
Quantifying proteins ...
Proteins: 25 Peptides: 100
> summary(y.protein$E[,1])
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  2.585   4.252   5.929   5.997   7.828   9.117 
> 
> Group <- factor(y.peptide$targets$Group)
> design <- model.matrix(~Group)
> fit <- dpcDE(y.protein, design, plot=FALSE)
> summary(fit$coefficients)
  (Intercept)        Group2        
 Min.   :1.646   Min.   :-1.19082  
 1st Qu.:3.935   1st Qu.:-0.19334  
 Median :5.807   Median :-0.08129  
 Mean   :5.840   Mean   : 0.01623  
 3rd Qu.:7.993   3rd Qu.: 0.16887  
 Max.   :9.398   Max.   : 1.11169  
> summary(fit$sigma)
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
 0.3656  0.8701  0.9755  0.9979  1.1433  1.6496 
> 
> proc.time()
   user  system elapsed 
  0.673   0.104   0.778 

R version 4.5.0 alpha (2025-03-18 r87998 ucrt)
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(limpa)
Loading required package: limma
> options(warnPartialMatchArgs=TRUE,warnPartialMatchAttr=TRUE,warnPartialMatchDollar=TRUE,width=120)
> 
> set.seed(0); u <- runif(100)
> 
> y.peptide <- simProteinDataSet()
> names(y.peptide)
[1] "E"       "genes"   "targets" "other"  
> colSums(is.na(y.peptide$E))
 S1  S2  S3  S4  S5  S6  S7  S8  S9 S10 
 40  53  45  39  44  42  41  48  38  47 
> summary(y.peptide$E[,1])
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max.    NA's 
  2.160   5.695   7.142   6.868   8.587   9.717      40 
> names(y.peptide)
[1] "E"       "genes"   "targets" "other"  
> 
> dpcfit <- dpc(y.peptide)
2 peptides are completely missing in all samples.
> dpcfit$dpc
     beta0      beta1 
-4.2779693  0.7787527 
> 
> y.protein <- dpcQuant(y.peptide,protein.id="Protein",dpcfit)
Estimating hyperparameters ...
Quantifying proteins ...
Proteins: 25 Peptides: 100
> summary(y.protein$E[,1])
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  2.585   4.252   5.929   5.997   7.828   9.117 
> 
> Group <- factor(y.peptide$targets$Group)
> design <- model.matrix(~Group)
> fit <- dpcDE(y.protein, design, plot=FALSE)
> summary(fit$coefficients)
  (Intercept)        Group2        
 Min.   :1.646   Min.   :-1.19082  
 1st Qu.:3.935   1st Qu.:-0.19334  
 Median :5.807   Median :-0.08129  
 Mean   :5.840   Mean   : 0.01623  
 3rd Qu.:7.993   3rd Qu.: 0.16887  
 Max.   :9.398   Max.   : 1.11169  
> summary(fit$sigma)
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
 0.3656  0.8701  0.9755  0.9979  1.1433  1.6496 
> 
> proc.time()
   user  system elapsed 
   0.32    0.15    0.51