Hello all, I have been attempting to use virtualArray recently, and have found that code functioning correctly perhaps six months ago no longer works. I have attempted to run the vignette and get an identical error to the one obtained from my own scripts. Specifically, after calling "virtualArrayExpressionSets()" I get the following error: Error: 2 errors; first error: Error in array(x, c(length(x), 1L), if (!is.null(names(x))) list(names(x), : 'data' must be of a vector type, was 'NULL' I have included the complete output of my attempt to run the vignette at the bottom of this email, as it's quite long. The vignette itself is available at http://www.bioconductor.org/packages/devel/bioc/vignet tes/virtualArray/inst/doc/virtualArray.R Here is the output of traceback() 9: stop(paste(msg, collapse = "nn"), call. = FALSE) 8: LastError$store(results = results, is.error = is.error, throw.error = TRUE) 7: bplapply(X = X, FUN = FUN, ..., BPRESUME = BPRESUME, BPPARAM = SerialParam(catch.errors = BPPARAM$catch.errors)) 6: bplapply(X = X, FUN = FUN, ..., BPRESUME = BPRESUME, BPPARAM = SerialParam(catch.errors = BPPARAM$catch.errors)) 5: bplapply(X, FUN, ..., BPRESUME = BPRESUME, BPPARAM = BPPARAM) 4: bplapply(X, FUN, ..., BPRESUME = BPRESUME, BPPARAM = BPPARAM) 3: lapply(all_expression_sets, virtualArrayBuildfData, collapse_fun = collapse_fun, identifier = identifier) 2: lapply(all_expression_sets, virtualArrayBuildfData, collapse_fun = collapse_fun, identifier = identifier) 1: virtualArrayExpressionSets() I would really appreciate any help in getting virtualArray working again. I note that this error has been reported by other users a couple of times in April and May, without any response from the community. It would be great if the package maintainer could take a look. Best wishes, Mick Elliot SFU ------------ Output of my attempt to run the vignette: R version 3.1.0 (2014-04-10) -- "Spring Dance" Copyright (C) 2014 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) 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. Natural language support but running in an English locale 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. > ### R code from vignette source 'vignettes/virtualArray/inst/doc/virtualArray.Rnw' > > ################################################### > ### code chunk number 1: options > ################################################### > options(width=72) > > > ################################################### > ### code chunk number 2: virtualArray.Rnw:68-69 > ################################################### > library(virtualArray) 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 object is masked from ???package:stats???: xtabs The following objects are masked from ???package:base???: anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, do.call, duplicated, eval, evalq, Filter, Find, get, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, table, tapply, union, unique, unlist Loading required package: plyr Loading required package: preprocessCore Creating a generic function for ???hist??? from package ???graphics??? in package ???affyPLM??? Setting options('download.file.method.GEOquery'='auto') To support our work please cite: To cite package 'virtualArray' in publications use: Andreas Heider and R??diger Alt (2013). virtualArray: a R/bioconductor package to merge raw data from different microarray platforms. R package version 1.8.0. A BibTeX entry for LaTeX users is @Article{, title = {virtualArray: a R/bioconductor package to merge raw data from different microarray platforms}, author = {{Andreas Heider} and {R??diger Alt}}, year = {2013}, note = {R package version 1.8.0}, journal = {BMC Bioinformatics}, volume = {14}, pages = {75}, } Thanks. Warning messages: 1: replacing previous import by ???utils::relist??? when loading ???virtualArray??? 2: replacing previous import by ???methods::new??? when loading ???virtualArray??? 3: replacing previous import by ???stats::density??? when loading ???virtualArray??? 4: replacing previous import by ???utils::installed.packages??? when loading ???virtualArray??? 5: replacing previous import by ???utils::read.csv??? when loading ???virtualArray??? 6: replacing previous import by ???utils::read.table??? when loading ???virtualArray??? 7: replacing previous import by ???utils::write.table??? when loading ???virtualArray??? > > > ################################################### > ### code chunk number 3: virtualArray.Rnw:133-136 > ################################################### > library("GEOquery") 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")'. > GSE23402 <- getGEO("GSE23402",GSEMatrix=T,AnnotGPL=FALSE) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE23nnn/GSE23402/matrix/ Found 1 file(s) GSE23402_series_matrix.txt.gz trying URL 'ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE23nnn/GSE23402/ma trix/GSE23402_series_matrix.txt.gz' ftp data connection made, file length 6015534 bytes opened URL downloaded 5.7 Mb File stored at: C:UsersMickAppDataLocalTempRtmp80du0e/GPL570.soft > GSE26428 <- getGEO("GSE26428",GSEMatrix=T,AnnotGPL=FALSE) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE26nnn/GSE26428/matrix/ Found 1 file(s) GSE26428_series_matrix.txt.gz trying URL 'ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE26nnn/GSE26428/ma trix/GSE26428_series_matrix.txt.gz' ftp data connection made, file length 706280 bytes opened URL downloaded 689 Kb File stored at: C:UsersMickAppDataLocalTempRtmp80du0e/GPL6480.soft > > > ################################################### > ### code chunk number 4: virtualArray.Rnw:141-143 > ################################################### > GSE23402 <- GSE23402[[1]][,1:24] > GSE26428 <- GSE26428[[1]] > > > ################################################### > ### code chunk number 5: virtualArray.Rnw:146-150 (eval = FALSE) > ################################################### > ## library(virtualArray) > ## library(affy) > ## GSE23402 <- GSE23402 > ## GSE26428 <- GSE26428 > > > ################################################### > ### code chunk number 6: virtualArray.Rnw:156-158 > ################################################### > summary(exprs(GSE23402)[,1:3]) GSM574058 GSM574059 GSM574060 Min. : 10.06 Min. : 10.06 Min. : 10.06 1st Qu.: 22.92 1st Qu.: 22.92 1st Qu.: 22.92 Median : 59.03 Median : 59.03 Median : 59.03 Mean : 510.00 Mean : 510.00 Mean : 510.00 3rd Qu.: 282.19 3rd Qu.: 282.19 3rd Qu.: 282.19 Max. :28094.15 Max. :28094.15 Max. :28094.15 > summary(exprs(GSE26428)) GSM648497 GSM648498 GSM648499 Min. : 1.054 Min. : 1.054 Min. : 1.054 1st Qu.: 3.080 1st Qu.: 3.080 1st Qu.: 3.080 Median : 7.062 Median : 7.062 Median : 7.062 Mean : 6.983 Mean : 6.983 Mean : 6.983 3rd Qu.:10.233 3rd Qu.:10.233 3rd Qu.:10.233 Max. :18.578 Max. :18.578 Max. :18.578 > > > ################################################### > ### code chunk number 7: virtualArray.Rnw:168-170 > ################################################### > exprs(GSE23402) <- log2(exprs(GSE23402)) > exprs(GSE26428) <- (exprs(GSE26428)/20*16) > > > ################################################### > ### code chunk number 8: virtualArray.Rnw:175-177 > ################################################### > summary(exprs(GSE23402)[,1:4]) GSM574058 GSM574059 GSM574060 GSM574061 Min. : 3.331 Min. : 3.331 Min. : 3.331 Min. : 3.331 1st Qu.: 4.519 1st Qu.: 4.519 1st Qu.: 4.519 1st Qu.: 4.519 Median : 5.883 Median : 5.883 Median : 5.883 Median : 5.883 Mean : 6.491 Mean : 6.491 Mean : 6.491 Mean : 6.491 3rd Qu.: 8.140 3rd Qu.: 8.140 3rd Qu.: 8.140 3rd Qu.: 8.140 Max. :14.778 Max. :14.778 Max. :14.778 Max. :14.778 > summary(exprs(GSE26428)) GSM648497 GSM648498 GSM648499 Min. : 0.8433 Min. : 0.8433 Min. : 0.8433 1st Qu.: 2.4636 1st Qu.: 2.4636 1st Qu.: 2.4636 Median : 5.6495 Median : 5.6495 Median : 5.6495 Mean : 5.5863 Mean : 5.5863 Mean : 5.5863 3rd Qu.: 8.1861 3rd Qu.: 8.1861 3rd Qu.: 8.1861 Max. :14.8623 Max. :14.8623 Max. :14.8623 > > > ################################################### > ### code chunk number 9: virtualArray.Rnw:183-185 > ################################################### > annotation(GSE23402) <- "hgu133plus2" > annotation(GSE26428) <- "hgug4112a" > > > ################################################### > ### code chunk number 10: virtualArray.Rnw:190-191 > ################################################### > my_virtualArrays <- NULL > > > ################################################### > ### code chunk number 11: options > ################################################### > options(width=60) > if(require(BiocParallel)) + register(MulticoreParam(verbose=TRUE)) Loading required package: BiocParallel > > > ################################################### > ### code chunk number 12: virtualArray.Rnw:209-210 > ################################################### > my_virtualArrays$iPSC_hESC_noBatchEffect <- virtualArrayExpressionSets() Now preprocessing raw data of GSE23402: Loading annotations... Usinghgu133plus2as Bioconductor annotation package for datasetGSE23402. Packagehgu133plus2.dbnot available. Atempting to install it. Bioconductor version 2.14 (BiocInstaller 1.14.2), ?biocLite for help Installing package into ???C:/Users/Mick/Documents/R/win- library/3.1??? (as ???lib??? is unspecified) trying URL 'http://bioconductor.org/packages/2.14/data/annotation/bin/ windows/contrib/3.1/hgu133plus2.db_2.14.0.zip' Content type 'application/zip' length 2197467 bytes (2.1 Mb) opened URL downloaded 2.1 Mb The downloaded binary packages are in C:UsersMickAppDataLocalTempRtmp80du0edownloaded_packages Package hgu133plus2.db has been successfully installed! Loading required package: hgu133plus2.db Loading required package: AnnotationDbi Loading required package: GenomeInfoDb Loading required package: org.Hs.eg.db Loading required package: DBI Now preprocessing raw data of GSE23402: Collapsing expression values to their median... Using identifier as id variables Now preprocessing raw data of GSE23402: Annotating expression values with SYMBOL... Now preprocessing raw data of GSE26428: Loading annotations... Usinghgug4112aas Bioconductor annotation package for datasetGSE26428. Packagehgug4112a.dbnot available. Atempting to install it. Bioconductor version 2.14 (BiocInstaller 1.14.2), ?biocLite for help Installing package into ???C:/Users/Mick/Documents/R/win- library/3.1??? (as ???lib??? is unspecified) trying URL 'http://bioconductor.org/packages/2.14/data/annotation/bin/ windows/contrib/3.1/hgug4112a.db_2.14.0.zip' Content type 'application/zip' length 1618802 bytes (1.5 Mb) opened URL downloaded 1.5 Mb The downloaded binary packages are in C:UsersMickAppDataLocalTempRtmp80du0edownloaded_packages Package hgug4112a.db has been successfully installed! Loading required package: hgug4112a.db Now preprocessing raw data of GSE26428: Collapsing expression values to their median... Using identifier as id variables Now preprocessing raw data of GSE26428: Annotating expression values with SYMBOL... Error: 2 errors; first error: Error in array(x, c(length(x), 1L), if (!is.null(names(x))) list(names(x), : 'data' must be of a vector type, was 'NULL' For more information, use bplasterror(). To resume calculation, re-call the function and set the argument 'BPRESUME' to TRUE or wrap the previous call in bpresume(). First traceback: 22: virtualArrayExpressionSets() 21: lapply(all_expression_sets, virtualArrayBuildfData, collapse_fun = collapse_fun, identifier = identifier) 20: lapply(all_expression_sets, virtualArrayBuildfData, collapse_fun = collapse_fun, identifier = identifier) 19: bplapply(X, FUN, ..., BPRESUME = BPRESUME, BPPARAM = BPPARAM) 18: bplapply(X, FUN, ..., BPRESUME = BPRESUME, BPPARAM = BPPARAM) 17: bplapply(X = X, FUN = FUN, ..., BPRESUME = BPRESUME, BPPARAM = SerialParam(catch.errors = BPPARAM$catch.errors)) 16: bplapply(X = X, FUN = FUN, ..., BPRESUME = BPRESUME, BPPARAM = SerialParam(catch.errors = BPPARAM$catch.errors)) -- output of sessionInfo(): R version 3.1.0 (2014-04-10) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United Kingdom.1252 [2] LC_CTYPE=English_United Kingdom.1252 [3] LC_MONETARY=English_United Kingdom.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United Kingdom.1252 attached base packages: [1] parallel stats graphics grDevices utils [6] datasets methods base other attached packages: [1] hgug4112a.db_2.14.0 hgu133plus2.db_2.14.0 [3] org.Hs.eg.db_2.14.0 RSQLite_0.11.4 [5] DBI_0.2-7 AnnotationDbi_1.26.0 [7] GenomeInfoDb_1.0.2 BiocInstaller_1.14.2 [9] BiocParallel_0.6.1 GEOquery_2.30.0 [11] Biobase_2.24.0 virtualArray_1.8.0 [13] preprocessCore_1.26.1 plyr_1.8.1 [15] BiocGenerics_0.10.0 loaded via a namespace (and not attached): [1] affy_1.42.2 affyio_1.32.0 affyPLM_1.40.1 [4] BatchJobs_1.2 BBmisc_1.6 Biostrings_2.32.0 [7] brew_1.0-6 codetools_0.2-8 digest_0.6.4 [10] fail_1.2 foreach_1.4.2 gcrma_2.36.0 [13] grid_3.1.0 IRanges_1.22.9 iterators_1.0.7 [16] lattice_0.20-29 outliers_0.14 quadprog_1.5-5 [19] Rcpp_0.11.2 RCurl_1.95-4.1 reshape2_1.4 [22] sendmailR_1.1-2 splines_3.1.0 stats4_3.1.0 [25] stringr_0.6.2 tools_3.1.0 tseries_0.10-32 [28] XML_3.98-1.1 XVector_0.4.0 zlibbioc_1.10.0 [31] zoo_1.7-11 -- Sent via the guest posting facility at bioconductor.org.