############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/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 (it is needed to build vignettes) * creating vignettes ... ERROR --- re-building ‘ArrayExpress.Rnw’ using Sweave Loading required package: Biobase Loading required package: BiocGenerics Loading required package: generics Attaching package: ‘generics’ The following objects are masked from ‘package:base’: as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union 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, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, 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' Content type 'unknown' length 7317392 bytes (7.0 MB) ================================================== 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 'Failure when receiving data from the peer' 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' Content type 'unknown' length 7340006 bytes (7.0 MB) ================================================== Downloading file: 1202aa.cel trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1202aa.cel' Content type 'unknown' length 7329097 bytes (7.0 MB) ================================================== Downloading file: 1204aa.cel trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1204aa.cel' Content type 'unknown' length 7343156 bytes (7.0 MB) ================================================== 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' Content type 'unknown' length 1683750 bytes (1.6 MB) ================================================== 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' Content type 'unknown' length 7299 bytes ================================================== 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 'Failure when receiving data from the peer' 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; charset=UTF-8' length 790789 bytes (772 KB) ================================================== downloaded 772 KB Unpacking data files Warning in file(file, "rt") : 'raw = FALSE' but '/tmp/RtmpfTgAlB/' is not a regular file Warning in file(file, "rt") : cannot open file '/tmp/RtmpfTgAlB/': it is a directory Error in file(file, "rt") : cannot open the connection Downloading file: 30_v4_v4.gpr trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/870/E-MEXP-1870/Files/30_v4_v4.gpr' Content type 'unknown' length 5350610 bytes (5.1 MB) ================================================== Downloading file: 13_v3_v3.gpr trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/870/E-MEXP-1870/Files/13_v3_v3.gpr' Content type 'unknown' length 5277770 bytes (5.0 MB) ================================================== Downloading file: 31_v4_v4.gpr trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/870/E-MEXP-1870/Files/31_v4_v4.gpr' Content type 'unknown' length 5264983 bytes (5.0 MB) ================================================== Downloading file: 45_4_4.gpr trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/870/E-MEXP-1870/Files/45_4_4.gpr' Content type 'unknown' length 5493312 bytes (5.2 MB) ================================================== Downloading file: 47_3_4.gpr trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/870/E-MEXP-1870/Files/47_3_4.gpr' Content type 'unknown' length 5335570 bytes (5.1 MB) ================================================== Downloading file: 11_v4_v3.gpr trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/870/E-MEXP-1870/Files/11_v4_v3.gpr' Content type 'unknown' length 5385618 bytes (5.1 MB) ================================================== Downloading file: 46_3_3.gpr trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/870/E-MEXP-1870/Files/46_3_3.gpr' Warning in download.file(url, filedest) : URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/870/E-MEXP-1870/Files/46_3_3.gpr': status was 'Failure when receiving data from the peer' Error in download.file(url, filedest) : cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/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/fire/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/fire/E-MEXP-/870/E-MEXP-1870/Files/12_v4_v3.gpr' Content type 'unknown' length 5358829 bytes (5.1 MB) ================================================== Downloading file: 29_v4_v4.gpr trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/870/E-MEXP-1870/Files/29_v4_v4.gpr' Content type 'unknown' length 5344579 bytes (5.1 MB) ================================================== Downloading file: E-MEXP-1870.idf.txt trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/870/E-MEXP-1870/Files/E-MEXP-1870.idf.txt' Content type 'unknown' length 17908 bytes (17 KB) ================================================== Downloading file: E-MEXP-1870.sdrf.txt trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/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/fire/E-MEXP-/870/E-MEXP-1870/Files/E-MEXP-1870.sdrf.txt': status was 'Failure when receiving data from the peer' Error in download.file(url, filedest) : cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/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/fire/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; charset=UTF-8' length 768845 bytes (750 KB) ================================================== downloaded 750 KB Unpacking data files Warning in file(file, "rt") : 'raw = FALSE' but '/tmp/RtmpfTgAlB/' is not a regular file Warning in file(file, "rt") : cannot open file '/tmp/RtmpfTgAlB/': it is a directory Error in file(file, "rt") : cannot open the connection Downloading file: 30_v4_v4.gpr /tmp/RtmpfTgAlB/30_v4_v4.gpr already exists, skipping. Downloading file: 13_v3_v3.gpr /tmp/RtmpfTgAlB/13_v3_v3.gpr already exists, skipping. Downloading file: 31_v4_v4.gpr /tmp/RtmpfTgAlB/31_v4_v4.gpr already exists, skipping. Downloading file: 45_4_4.gpr /tmp/RtmpfTgAlB/45_4_4.gpr already exists, skipping. Downloading file: 47_3_4.gpr /tmp/RtmpfTgAlB/47_3_4.gpr already exists, skipping. Downloading file: 11_v4_v3.gpr /tmp/RtmpfTgAlB/11_v4_v3.gpr already exists, skipping. Downloading file: 46_3_3.gpr trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/870/E-MEXP-1870/Files/46_3_3.gpr' Content type 'unknown' length 5304968 bytes (5.1 MB) ================================================== Downloading file: 12_v4_v3.gpr /tmp/RtmpfTgAlB/12_v4_v3.gpr already exists, skipping. Downloading file: 29_v4_v4.gpr /tmp/RtmpfTgAlB/29_v4_v4.gpr already exists, skipping. Downloading file: E-MEXP-1870.idf.txt /tmp/RtmpfTgAlB/E-MEXP-1870.idf.txt already exists, skipping. Downloading file: E-MEXP-1870.sdrf.txt trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/870/E-MEXP-1870/Files/E-MEXP-1870.sdrf.txt' Content type 'unknown' length 14207 bytes (13 KB) ================================================== Downloading file: A-MEXP-1425.adf.txt /tmp/RtmpfTgAlB/A-MEXP-1425.adf.txt already exists, skipping. Unpacking data files Duplicates found in SDRF file Removed duplicates in SDRF file ArrayExpress: Reading pheno data from SDRF Warning: non-unique values when setting 'row.names': ‘11_v4_v3.gpr’, ‘12_v4_v3.gpr’, ‘13_v3_v3.gpr’, ‘29_v4_v4.gpr’, ‘30_v4_v4.gpr’, ‘31_v4_v4.gpr’, ‘45_4_4.gpr’, ‘46_3_3.gpr’, ‘47_3_4.gpr’ Error in `.rowNamesDF<-`(x, value = value) : duplicate 'row.names' are not allowed Downloading file: 1203aa.cel trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1203aa.cel' Content type 'unknown' length 7317392 bytes (7.0 MB) ================================================== 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' Content type 'unknown' length 1683750 bytes (1.6 MB) ================================================== Downloading file: 1205aa.cel trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1205aa.cel' Content type 'unknown' length 7340006 bytes (7.0 MB) ================================================== Downloading file: 1202aa.cel trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1202aa.cel' Content type 'unknown' length 7329097 bytes (7.0 MB) ================================================== Downloading file: 1204aa.cel trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1204aa.cel' Content type 'unknown' length 7343156 bytes (7.0 MB) ================================================== Downloading file: E-MEXP-21-processed-data-2487199618.txt /private/tmp/Rtmph3Ggq8/Rbuild872f2f00c70/ArrayExpress/vignettes/E-MEXP-21-processed-data-2487199618.txt already exists, skipping. 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' Content type 'unknown' length 7299 bytes ================================================== 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 'Failure when receiving data from the peer' 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; charset=UTF-8' length 790789 bytes (772 KB) ================================================== downloaded 772 KB Unpacking data files Warning in file(file, "rt") : 'raw = FALSE' but '/private/tmp/Rtmph3Ggq8/Rbuild872f2f00c70/ArrayExpress/vignettes/' is not a regular file Warning in file(file, "rt") : cannot open file '/private/tmp/Rtmph3Ggq8/Rbuild872f2f00c70/ArrayExpress/vignettes/': it is a directory Error: processing vignette 'ArrayExpress.Rnw' failed with diagnostics: chunk 6 (label = ae2bioc-full) Error in file(file, "rt") : cannot open the connection --- failed re-building ‘ArrayExpress.Rnw’ SUMMARY: processing the following file failed: ‘ArrayExpress.Rnw’ Error: Vignette re-building failed. Execution halted