Package check result: ERROR Check: CRAN incoming feasibility, Result: NOTE Maintainer: ‘Ha Nguyen ’ New submission Package was archived on CRAN Possibly misspelled words in DESCRIPTION: Efron (10:453) Gu (10:519) Korotkevich (10:403) Ritchie (10:243) al (10:179, 10:254, 10:299, 10:355, 10:418, 10:462) et (10:176, 10:251, 10:296, 10:352, 10:415, 10:459) CRAN repository db overrides: X-CRAN-Comment: Archived on 2024-10-10 for policy violation. On Internet access. Check: examples, Result: ERROR Running examples in ‘RCPA-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: runDEAnalysis > ### Title: Differential expression analysis > ### Aliases: runDEAnalysis > > ### ** Examples > > ## No test: > library(RCPA) > library(SummarizedExperiment) Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: ‘matrixStats’ The following object is masked from ‘package:dplyr’: count Attaching package: ‘MatrixGenerics’ The following objects are masked from ‘package:matrixStats’: colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Attaching package: ‘BiocGenerics’ The following object is masked from ‘package:RCPA’: plotMA The following objects are masked from ‘package:dplyr’: combine, intersect, setdiff, union 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, aperm, 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, saveRDS, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: ‘S4Vectors’ The following objects are masked from ‘package:dplyr’: first, rename The following object is masked from ‘package:tidyr’: expand The following object is masked from ‘package:utils’: findMatches The following objects are masked from ‘package:base’: I, expand.grid, unname Loading required package: IRanges Attaching package: ‘IRanges’ The following objects are masked from ‘package:dplyr’: collapse, desc, slice Loading required package: GenomeInfoDb 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")'. Attaching package: ‘Biobase’ The following object is masked from ‘package:MatrixGenerics’: rowMedians The following objects are masked from ‘package:matrixStats’: anyMissing, rowMedians > > # GSE5281 > affyDataset <- loadData("affyDataset") > affyDesign <- model.matrix(~0 + condition + region + condition:region, + data = colData(affyDataset)) > colnames(affyDesign) <- make.names(colnames(affyDesign)) > affyContrast <- limma::makeContrasts(conditionalzheimer-conditionnormal, + levels=affyDesign) > > if (require("hgu133plus2.db", quietly = TRUE)){ + affyDEExperiment <- RCPA::runDEAnalysis(affyDataset, method = "limma", + design = affyDesign, + contrast = affyContrast, + annotation = "GPL570") + + # check the DE analysis results + + print(head(rowData(affyDEExperiment))) + } Attaching package: ‘AnnotationDbi’ The following object is masked from ‘package:dplyr’: select DataFrame with 6 rows and 9 columns PROBEID ID p.value statistic logFC avgExpr 55101 45828_at 55101 1.53872e-23 -11.8893 -0.465108 2.89383 92840 226597_at 92840 3.56750e-23 -11.7546 -0.661995 2.32582 727957 227778_at 727957 3.55470e-22 -11.3858 -0.525213 2.63851 339229 50374_at 339229 4.15816e-22 -11.3607 -0.574966 2.79106 79050 218860_at 79050 5.79814e-22 -11.3073 -0.509452 2.44794 7016 204106_at 7016 7.81072e-22 -11.2594 -0.409152 2.83118 logFCSE sampleSize pFDR 55101 0.0394296 161 3.28640e-19 92840 0.0567640 161 3.80973e-19 727957 0.0464940 161 2.22025e-18 339229 0.0510112 161 2.22025e-18 79050 0.0454122 161 2.47673e-18 7016 0.0366266 161 2.78036e-18 > > > > # GSE61196 > agilDataset <- loadData("agilDataset") > agilDesign <- model.matrix(~0 + condition, + data = colData(agilDataset)) > agilContrast <- limma::makeContrasts(conditionalzheimer-conditionnormal, + levels=agilDesign) > > # Create Probe mapping > GPL4133Anno <- GEOquery::dataTable(GEOquery::getGEO("GPL4133"))@table Error in h(simpleError(msg, call)) : error in evaluating the argument 'object' in selecting a method for function 'dataTable': invalid 'type' (list) of argument Calls: ... getGEOfile -> downloadFile -> .handleSimpleError -> h Execution halted Check: for detritus in the temp directory, Result: NOTE Found the following files/directories: ‘calibre_7.19.0_tmp_jwg7xmcq’ ‘calibre_7.19.0_tmp_lf1ckjcn’