Movatterモバイル変換

################################################################################################################################################################## Running command:######   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:limpa.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings limpa_1.2.1.tar.gz###############################################################################################################################################################* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/limpa.Rcheck’* using R version 4.5.2 (2025-10-31)* using platform: x86_64-pc-linux-gnu* R was compiled by    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0* running under: Ubuntu 24.04.3 LTS* using session charset: UTF-8* checking for file ‘limpa/DESCRIPTION’ ... OK* this is package ‘limpa’ version ‘1.2.1’* 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 loading without being on the library search path ... 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 ... NOTEFound the following Rd file(s) with Rd \link{} targets missing packageanchors:  readSpectronaut.Rd: EList-classPlease provide package anchors for all Rd \link{} targets not in thepackage 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 re-building of vignette outputs ... OK* checking PDF version of manual ... OK* DONEStatus: 1 NOTESee  ‘/home/biocbuild/bbs-3.22-bioc/meat/limpa.Rcheck/00check.log’for details.

################################################################################################################################################################## Running command:######   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL limpa###############################################################################################################################################################* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’* installing *source* package ‘limpa’ ...** this is package ‘limpa’ version ‘1.2.1’** 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 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"Copyright (C) 2025 The R Foundation for Statistical ComputingPlatform: x86_64-pc-linux-gnuR 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$E)) S1  S2  S3  S4  S5  S6  S7  S8  S9 S10  35  48  43  36  44  44  38  41  35  47 > summary(y.peptide$E[,1])   Min. 1st Qu.  Median    Mean 3rd Qu.    Max.    NA's   2.160   5.548   7.025   6.711   8.586   9.717      35 > names(y.peptide)[1] "E"       "genes"   "targets" "other"  > > dpcfit <- dpc(y.peptide)1 peptides are completely missing in all samples.> dpcfit$dpc     beta0      beta1 -4.2061461  0.8003111 > > y.protein <- dpcQuant(y.peptide,protein.id="Protein",dpcfit)Estimating hyperparameters ...Quantifying proteins ...Proteins: 25 Peptides: 100> summary(y.protein$E[,1])   Min. 1st Qu.  Median    Mean 3rd Qu.    Max.   2.601   4.097   5.933   5.980   7.824   9.118 > > Group <- factor(y.peptide$targets$Group)> design <- model.matrix(~Group)> fit <- dpcDE(y.protein, design, plot=FALSE)> summary(fit$coefficients)  (Intercept)        Group2         Min.   :1.933   Min.   :-1.08953   1st Qu.:3.701   1st Qu.:-0.16402   Median :5.845   Median :-0.07588   Mean   :5.843   Mean   : 0.04373   3rd Qu.:7.990   3rd Qu.: 0.24114   Max.   :9.427   Max.   : 1.11731  > summary(fit$sigma)   Min. 1st Qu.  Median    Mean 3rd Qu.    Max.  0.3688  0.8261  0.9631  0.9871  1.1006  1.8352 > > proc.time()   user  system elapsed   0.563   0.047   0.600

R version 4.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six"Copyright (C) 2025 The R Foundation for Statistical ComputingPlatform: x86_64-w64-mingw32/x64R 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$E)) S1  S2  S3  S4  S5  S6  S7  S8  S9 S10  35  48  43  36  44  44  38  41  35  47 > summary(y.peptide$E[,1])   Min. 1st Qu.  Median    Mean 3rd Qu.    Max.    NA's   2.160   5.548   7.025   6.711   8.586   9.717      35 > names(y.peptide)[1] "E"       "genes"   "targets" "other"  > > dpcfit <- dpc(y.peptide)1 peptides are completely missing in all samples.> dpcfit$dpc     beta0      beta1 -4.2061461  0.8003111 > > y.protein <- dpcQuant(y.peptide,protein.id="Protein",dpcfit)Estimating hyperparameters ...Quantifying proteins ...Proteins: 25 Peptides: 100> summary(y.protein$E[,1])   Min. 1st Qu.  Median    Mean 3rd Qu.    Max.   2.601   4.097   5.933   5.980   7.824   9.118 > > Group <- factor(y.peptide$targets$Group)> design <- model.matrix(~Group)> fit <- dpcDE(y.protein, design, plot=FALSE)> summary(fit$coefficients)  (Intercept)        Group2         Min.   :1.933   Min.   :-1.08953   1st Qu.:3.701   1st Qu.:-0.16402   Median :5.845   Median :-0.07588   Mean   :5.843   Mean   : 0.04373   3rd Qu.:7.990   3rd Qu.: 0.24114   Max.   :9.427   Max.   : 1.11731  > summary(fit$sigma)   Min. 1st Qu.  Median    Mean 3rd Qu.    Max.  0.3688  0.8261  0.9631  0.9871  1.1006  1.8352 > > proc.time()   user  system elapsed    0.34    0.10    0.54