* using log directory 'C:/msys64/home/tomas/utf/ucrt64/inst_all/affyPLM.Rcheck' * using R Under development (unstable) (2020-06-23 r78739) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * checking for file 'affyPLM/DESCRIPTION' ... OK * this is package 'affyPLM' version '1.60.0' * checking package namespace information ... OK * checking package dependencies ... NOTE Package suggested but not available for checking: 'affydata' * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'affyPLM' can be installed ... WARNING Found the following significant warnings: rlm_PLM.c:868:25: warning: '%d' directive output may be truncated writing between 1 and 10 bytes into a region of size 9 [-Wformat-truncation=] See 'C:/msys64/home/tomas/utf/ucrt64/inst_all/affyPLM.Rcheck/00install.out' for details. * 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 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 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 ... OK * 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 line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'C_code_tests.R' Running 'PLM_tests.R' Running 'preprocess_tests.R' ERROR Running the tests in 'tests/preprocess_tests.R' failed. Last 13 lines of output: tapply, union, unique, unsplit, which, which.max, which.min Loading required package: affy Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: gcrma Loading required package: preprocessCore > library(affydata) Error in library(affydata) : there is no package called 'affydata' Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking running R code from vignettes ... 'AffyExtensions.Rnw'... failed 'MAplots.Rnw'... failed 'QualityAssess.Rnw'... failed 'ThreeStep.Rnw'... OK WARNING Errors in running code in vignettes: when running code in 'AffyExtensions.Rnw' ... there is no package called 'affydata' > data(Dilution) Warning in data(Dilution) : data set 'Dilution' not found > Dilution = updateObject(Dilution) When sourcing 'AffyExtensions.R': Error: error in evaluating the argument 'object' in selecting a method for function 'updateObject': object 'Dilution' not found Execution halted when running code in 'MAplots.Rnw' ... there is no package called 'affydata' > data(Dilution) Warning in data(Dilution) : data set 'Dilution' not found > eset.Dilution <- rma(Dilution) When sourcing 'MAplots.R': Error: error in evaluating the argument 'object' in selecting a method for function 'probeNames': object 'Dilution' not found Execution halted when running code in 'QualityAssess.Rnw' ... there is no package called 'affydata' > data(Dilution) Warning in data(Dilution) : data set 'Dilution' not found > Dilution = updateObject(Dilution) When sourcing 'QualityAssess.R': Error: error in evaluating the argument 'object' in selecting a method for function 'updateObject': object 'Dilution' not found Execution halted * checking re-building of vignette outputs ... NOTE Error(s) in re-building vignettes: --- re-building 'AffyExtensions.Rnw' using Sweave Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Loading required package: affy Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: gcrma Loading required package: preprocessCore Loading required package: affydata Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called 'affydata' Warning in data(Dilution) : data set 'Dilution' not found Error: processing vignette 'AffyExtensions.Rnw' failed with diagnostics: chunk 1 (label = loadData) Error in h(simpleError(msg, call)) : error in evaluating the argument 'object' in selecting a method for function 'updateObject': object 'Dilution' not found --- failed re-building 'AffyExtensions.Rnw' --- re-building 'MAplots.Rnw' using Sweave Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Loading required package: affy Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: gcrma Loading required package: preprocessCore Loading required package: affydata Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called 'affydata' Warning in data(Dilution) : data set 'Dilution' not found Error: processing vignette 'MAplots.Rnw' failed with diagnostics: chunk 2 (label = makeExpressionSet) Error in h(simpleError(msg, call)) : error in evaluating the argument 'object' in selecting a method for function 'probeNames': object 'Dilution' not found --- failed re-building 'MAplots.Rnw' --- re-building 'QualityAssess.Rnw' using Sweave Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Loading required package: affy Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: gcrma Loading required package: preprocessCore Loading required package: affydata Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called 'affydata' Warning in data(Dilution) : data set 'Dilution' not found Error: processing vignette 'QualityAssess.Rnw' failed with diagnostics: chunk 2 (label = loadData) Error in h(simpleError(msg, call)) : error in evaluating the argument 'object' in selecting a method for function 'updateObject': object 'Dilution' not found --- failed re-building 'QualityAssess.Rnw' --- re-building 'ThreeStep.Rnw' using Sweave Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Loading required package: affy Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: gcrma Loading required package: preprocessCore --- finished re-building 'ThreeStep.Rnw' SUMMARY: processing the following files failed: 'AffyExtensions.Rnw' 'MAplots.Rnw' 'QualityAssess.Rnw' Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 2 WARNINGs, 2 NOTEs See 'C:/msys64/home/tomas/utf/ucrt64/inst_all/affyPLM.Rcheck/00check.log' for details.