############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data ArrayExpress ### ############################################################################## ############################################################################## * checking for file ‘ArrayExpress/DESCRIPTION’ ... OK * preparing ‘ArrayExpress’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘ArrayExpress.Rnw’ using Sweave Loading required package: Biobase Loading required package: BiocGenerics Attaching package: ‘BiocGenerics’ 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, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Downloading file: 1203aa.cel trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1203aa.cel' Warning in download.file(url, filedest) : URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1203aa.cel': status was 'Couldn't connect to server' Error in download.file(url, filedest) : cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1203aa.cel' Warning in getAE(accession, path = path, type = "full") : ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1203aa.cel does not exist or is empty. Downloading file: E-MEXP-21-processed-data-2487199618.txt trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21-processed-data-2487199618.txt' Warning in download.file(url, filedest) : URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21-processed-data-2487199618.txt': status was 'Couldn't connect to server' Error in download.file(url, filedest) : cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21-processed-data-2487199618.txt' Warning in getAE(accession, path = path, type = "full") : ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21-processed-data-2487199618.txt does not exist or is empty. Downloading file: 1205aa.cel trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1205aa.cel' Warning in download.file(url, filedest) : URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1205aa.cel': status was 'Couldn't connect to server' Error in download.file(url, filedest) : cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1205aa.cel' Warning in getAE(accession, path = path, type = "full") : ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1205aa.cel does not exist or is empty. Downloading file: 1202aa.cel trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1202aa.cel' Warning in download.file(url, filedest) : URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1202aa.cel': status was 'Couldn't connect to server' Error in download.file(url, filedest) : cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1202aa.cel' Warning in getAE(accession, path = path, type = "full") : ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1202aa.cel does not exist or is empty. Downloading file: 1204aa.cel trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1204aa.cel' Warning in download.file(url, filedest) : URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1204aa.cel': status was 'Couldn't connect to server' Error in download.file(url, filedest) : cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1204aa.cel' Warning in getAE(accession, path = path, type = "full") : ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1204aa.cel does not exist or is empty. Downloading file: E-MEXP-21-processed-data-2487199618.txt trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21-processed-data-2487199618.txt' Warning in download.file(url, filedest) : URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21-processed-data-2487199618.txt': status was 'Couldn't connect to server' Error in download.file(url, filedest) : cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21-processed-data-2487199618.txt' Warning in getAE(accession, path = path, type = "full") : ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21-processed-data-2487199618.txt does not exist or is empty. Downloading file: E-MEXP-21.idf.txt trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21.idf.txt' Warning in download.file(url, filedest) : URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21.idf.txt': status was 'Couldn't connect to server' Error in download.file(url, filedest) : cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21.idf.txt' Warning in getAE(accession, path = path, type = "full") : ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21.idf.txt does not exist or is empty. Downloading file: E-MEXP-21.sdrf.txt trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21.sdrf.txt' Warning in download.file(url, filedest) : URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21.sdrf.txt': status was 'Couldn't connect to server' Error in download.file(url, filedest) : cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21.sdrf.txt' Warning in getAE(accession, path = path, type = "full") : ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21.sdrf.txt does not exist or is empty. Downloading file: A-AFFY-32.adf.txt trying URL 'https://www.ebi.ac.uk/biostudies/files/A-AFFY-32/A-AFFY-32.adf.txt' Content type 'text/plain' length 790789 bytes (772 KB) ================================================== downloaded 772 KB Unpacking data files Error in ae2bioc(mageFiles = expFiles, dataCols = dataCols, drop = drop) : No SDRF file found. Downloading file: 30_v4_v4.gpr trying URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/30_v4_v4.gpr' Warning in download.file(url, filedest) : URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/30_v4_v4.gpr': status was 'Couldn't connect to server' Error in download.file(url, filedest) : cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/30_v4_v4.gpr' Warning in getAE(accession, path = path, type = "full") : ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/30_v4_v4.gpr does not exist or is empty. Downloading file: 13_v3_v3.gpr trying URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/13_v3_v3.gpr' Warning in download.file(url, filedest) : URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/13_v3_v3.gpr': status was 'Couldn't connect to server' Error in download.file(url, filedest) : cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/13_v3_v3.gpr' Warning in getAE(accession, path = path, type = "full") : ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/13_v3_v3.gpr does not exist or is empty. Downloading file: 31_v4_v4.gpr trying URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/31_v4_v4.gpr' Warning in download.file(url, filedest) : URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/31_v4_v4.gpr': status was 'Couldn't connect to server' Error in download.file(url, filedest) : cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/31_v4_v4.gpr' Warning in getAE(accession, path = path, type = "full") : ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/31_v4_v4.gpr does not exist or is empty. Downloading file: 45_4_4.gpr trying URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/45_4_4.gpr' Warning in download.file(url, filedest) : URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/45_4_4.gpr': status was 'Couldn't connect to server' Error in download.file(url, filedest) : cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/45_4_4.gpr' Warning in getAE(accession, path = path, type = "full") : ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/45_4_4.gpr does not exist or is empty. Downloading file: 47_3_4.gpr trying URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/47_3_4.gpr' Warning in download.file(url, filedest) : URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/47_3_4.gpr': status was 'Couldn't connect to server' Error in download.file(url, filedest) : cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/47_3_4.gpr' Warning in getAE(accession, path = path, type = "full") : ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/47_3_4.gpr does not exist or is empty. Downloading file: 11_v4_v3.gpr trying URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/11_v4_v3.gpr' Warning in download.file(url, filedest) : URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/11_v4_v3.gpr': status was 'Couldn't connect to server' Error in download.file(url, filedest) : cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/11_v4_v3.gpr' Warning in getAE(accession, path = path, type = "full") : ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/11_v4_v3.gpr does not exist or is empty. Downloading file: 46_3_3.gpr trying URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/46_3_3.gpr' Warning in download.file(url, filedest) : URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/46_3_3.gpr': status was 'Couldn't connect to server' Error in download.file(url, filedest) : cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/46_3_3.gpr' Warning in getAE(accession, path = path, type = "full") : ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/46_3_3.gpr does not exist or is empty. Downloading file: 12_v4_v3.gpr trying URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/12_v4_v3.gpr' Warning in download.file(url, filedest) : URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/12_v4_v3.gpr': status was 'Couldn't connect to server' Error in download.file(url, filedest) : cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/12_v4_v3.gpr' Warning in getAE(accession, path = path, type = "full") : ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/12_v4_v3.gpr does not exist or is empty. Downloading file: 29_v4_v4.gpr trying URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/29_v4_v4.gpr' Warning in download.file(url, filedest) : URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/29_v4_v4.gpr': status was 'Couldn't connect to server' Error in download.file(url, filedest) : cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/29_v4_v4.gpr' Warning in getAE(accession, path = path, type = "full") : ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/29_v4_v4.gpr does not exist or is empty. Downloading file: E-MEXP-1870.idf.txt trying URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/E-MEXP-1870.idf.txt' Warning in download.file(url, filedest) : URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/E-MEXP-1870.idf.txt': status was 'Couldn't connect to server' Error in download.file(url, filedest) : cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/E-MEXP-1870.idf.txt' Warning in getAE(accession, path = path, type = "full") : ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/E-MEXP-1870.idf.txt does not exist or is empty. Downloading file: E-MEXP-1870.sdrf.txt trying URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/E-MEXP-1870.sdrf.txt' Warning in download.file(url, filedest) : URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/E-MEXP-1870.sdrf.txt': status was 'Couldn't connect to server' Error in download.file(url, filedest) : cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/E-MEXP-1870.sdrf.txt' Warning in getAE(accession, path = path, type = "full") : ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/E-MEXP-1870.sdrf.txt does not exist or is empty. Downloading file: A-MEXP-1425.adf.txt trying URL 'https://www.ebi.ac.uk/biostudies/files/A-MEXP-1425/A-MEXP-1425.adf.txt' Content type 'text/plain' length 768845 bytes (750 KB) ================================================== downloaded 750 KB Unpacking data files Error in ae2bioc(mageFiles = expFiles, dataCols = dataCols, drop = drop) : No SDRF file found. Downloading file: 30_v4_v4.gpr trying URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/30_v4_v4.gpr' Warning in download.file(url, filedest) : URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/30_v4_v4.gpr': status was 'Couldn't connect to server' Error in download.file(url, filedest) : cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/30_v4_v4.gpr' Warning in getAE(accession, path = path, type = "full") : ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/30_v4_v4.gpr does not exist or is empty. Downloading file: 13_v3_v3.gpr trying URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/13_v3_v3.gpr' Warning in download.file(url, filedest) : URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/13_v3_v3.gpr': status was 'Couldn't connect to server' Error in download.file(url, filedest) : cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/13_v3_v3.gpr' Warning in getAE(accession, path = path, type = "full") : ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/13_v3_v3.gpr does not exist or is empty. Downloading file: 31_v4_v4.gpr trying URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/31_v4_v4.gpr' Warning in download.file(url, filedest) : URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/31_v4_v4.gpr': status was 'Couldn't connect to server' Error in download.file(url, filedest) : cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/31_v4_v4.gpr' Warning in getAE(accession, path = path, type = "full") : ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/31_v4_v4.gpr does not exist or is empty. Downloading file: 45_4_4.gpr trying URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/45_4_4.gpr' Warning in download.file(url, filedest) : URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/45_4_4.gpr': status was 'Couldn't connect to server' Error in download.file(url, filedest) : cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/45_4_4.gpr' Warning in getAE(accession, path = path, type = "full") : ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/45_4_4.gpr does not exist or is empty. Downloading file: 47_3_4.gpr trying URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/47_3_4.gpr' Warning in download.file(url, filedest) : URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/47_3_4.gpr': status was 'Couldn't connect to server' Error in download.file(url, filedest) : cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/47_3_4.gpr' Warning in getAE(accession, path = path, type = "full") : ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/47_3_4.gpr does not exist or is empty. Downloading file: 11_v4_v3.gpr trying URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/11_v4_v3.gpr' Warning in download.file(url, filedest) : URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/11_v4_v3.gpr': status was 'Couldn't connect to server' Error in download.file(url, filedest) : cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/11_v4_v3.gpr' Warning in getAE(accession, path = path, type = "full") : ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/11_v4_v3.gpr does not exist or is empty. Downloading file: 46_3_3.gpr trying URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/46_3_3.gpr' Warning in download.file(url, filedest) : URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/46_3_3.gpr': status was 'Couldn't connect to server' Error in download.file(url, filedest) : cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/46_3_3.gpr' Warning in getAE(accession, path = path, type = "full") : ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/46_3_3.gpr does not exist or is empty. Downloading file: 12_v4_v3.gpr trying URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/12_v4_v3.gpr' Warning in download.file(url, filedest) : URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/12_v4_v3.gpr': status was 'Couldn't connect to server' Error in download.file(url, filedest) : cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/12_v4_v3.gpr' Warning in getAE(accession, path = path, type = "full") : ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/12_v4_v3.gpr does not exist or is empty. Downloading file: 29_v4_v4.gpr trying URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/29_v4_v4.gpr' Warning in download.file(url, filedest) : URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/29_v4_v4.gpr': status was 'Couldn't connect to server' Error in download.file(url, filedest) : cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/29_v4_v4.gpr' Warning in getAE(accession, path = path, type = "full") : ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/29_v4_v4.gpr does not exist or is empty. Downloading file: E-MEXP-1870.idf.txt trying URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/E-MEXP-1870.idf.txt' Warning in download.file(url, filedest) : URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/E-MEXP-1870.idf.txt': status was 'Couldn't connect to server' Error in download.file(url, filedest) : cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/E-MEXP-1870.idf.txt' Warning in getAE(accession, path = path, type = "full") : ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/E-MEXP-1870.idf.txt does not exist or is empty. Downloading file: E-MEXP-1870.sdrf.txt trying URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/E-MEXP-1870.sdrf.txt' Warning in download.file(url, filedest) : URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/E-MEXP-1870.sdrf.txt': status was 'Couldn't connect to server' Error in download.file(url, filedest) : cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/E-MEXP-1870.sdrf.txt' Warning in getAE(accession, path = path, type = "full") : ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/E-MEXP-1870.sdrf.txt does not exist or is empty. Downloading file: A-MEXP-1425.adf.txt /tmp/Rtmp3Bn6g7/A-MEXP-1425.adf.txt already exists, skipping. Unpacking data files Error in ae2bioc(mageFiles = expFiles, dataCols = dataCols, drop = drop) : No SDRF file found. Downloading file: 1203aa.cel trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1203aa.cel' Warning in download.file(url, filedest) : URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1203aa.cel': status was 'Couldn't connect to server' Error in download.file(url, filedest) : cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1203aa.cel' Warning in getAE("E-MEXP-21", type = "full") : ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1203aa.cel does not exist or is empty. Downloading file: E-MEXP-21-processed-data-2487199618.txt trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21-processed-data-2487199618.txt' Warning in download.file(url, filedest) : URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21-processed-data-2487199618.txt': status was 'Couldn't connect to server' Error in download.file(url, filedest) : cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21-processed-data-2487199618.txt' Warning in getAE("E-MEXP-21", type = "full") : ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21-processed-data-2487199618.txt does not exist or is empty. Downloading file: 1205aa.cel trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1205aa.cel' Warning in download.file(url, filedest) : URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1205aa.cel': status was 'Couldn't connect to server' Error in download.file(url, filedest) : cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1205aa.cel' Warning in getAE("E-MEXP-21", type = "full") : ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1205aa.cel does not exist or is empty. Downloading file: 1202aa.cel trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1202aa.cel' Warning in download.file(url, filedest) : URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1202aa.cel': status was 'Couldn't connect to server' Error in download.file(url, filedest) : cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1202aa.cel' Warning in getAE("E-MEXP-21", type = "full") : ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1202aa.cel does not exist or is empty. Downloading file: 1204aa.cel trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1204aa.cel' Warning in download.file(url, filedest) : URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1204aa.cel': status was 'Couldn't connect to server' Error in download.file(url, filedest) : cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1204aa.cel' Warning in getAE("E-MEXP-21", type = "full") : ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1204aa.cel does not exist or is empty. Downloading file: E-MEXP-21-processed-data-2487199618.txt trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21-processed-data-2487199618.txt' Warning in download.file(url, filedest) : URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21-processed-data-2487199618.txt': status was 'Couldn't connect to server' Error in download.file(url, filedest) : cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21-processed-data-2487199618.txt' Warning in getAE("E-MEXP-21", type = "full") : ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21-processed-data-2487199618.txt does not exist or is empty. Downloading file: E-MEXP-21.idf.txt trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21.idf.txt' Warning in download.file(url, filedest) : URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21.idf.txt': status was 'Couldn't connect to server' Error in download.file(url, filedest) : cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21.idf.txt' Warning in getAE("E-MEXP-21", type = "full") : ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21.idf.txt does not exist or is empty. Downloading file: E-MEXP-21.sdrf.txt trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21.sdrf.txt' Warning in download.file(url, filedest) : URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21.sdrf.txt': status was 'Couldn't connect to server' Error in download.file(url, filedest) : cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21.sdrf.txt' Warning in getAE("E-MEXP-21", type = "full") : ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21.sdrf.txt does not exist or is empty. Downloading file: A-AFFY-32.adf.txt trying URL 'https://www.ebi.ac.uk/biostudies/files/A-AFFY-32/A-AFFY-32.adf.txt' Content type 'text/plain' length 790789 bytes (772 KB) ================================================== downloaded 772 KB Unpacking data files Error: processing vignette 'ArrayExpress.Rnw' failed with diagnostics: chunk 6 (label = ae2bioc-full) Error in ae2bioc(mageFiles = mexp1422) : No SDRF file found. --- failed re-building ‘ArrayExpress.Rnw’ SUMMARY: processing the following file failed: ‘ArrayExpress.Rnw’ Error: Vignette re-building failed. Execution halted