############################################################################## ############################################################################## ### ### 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 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, saveRDS, setdiff, 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' 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 /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6zZHcX/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' Content type 'unknown' length 3791 bytes ================================================== 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 ArrayExpress: Reading pheno data from SDRF ArrayExpress: Reading data files Loading required package: pd.hu6800 Attempting to obtain 'pd.hu6800' from BioConductor website. Checking to see if your internet connection works... Package 'pd.hu6800' was not found in the BioConductor repository. The 'pdInfoBuilder' package can often be used in situations like this. Error in oligo::read.celfiles(filenames = file.path(path, unique(files))) : The annotation package, pd.hu6800, could not be loaded. Error in readAEdata(path = path, files = dataFiles, dataCols = dataCols, : Unable to read cel files in /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6zZHcX Error in ae2bioc(mageFiles = expFiles, dataCols = dataCols, drop = drop) : ArrayExpress: Unable to read assay data 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' Content type 'unknown' length 5304968 bytes (5.1 MB) ================================================== 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' Content type 'unknown' length 14207 bytes (13 KB) ================================================== 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 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: 30_v4_v4.gpr /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6zZHcX/30_v4_v4.gpr already exists, skipping. Downloading file: 13_v3_v3.gpr /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6zZHcX/13_v3_v3.gpr already exists, skipping. Downloading file: 31_v4_v4.gpr /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6zZHcX/31_v4_v4.gpr already exists, skipping. Downloading file: 45_4_4.gpr /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6zZHcX/45_4_4.gpr already exists, skipping. Downloading file: 47_3_4.gpr /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6zZHcX/47_3_4.gpr already exists, skipping. Downloading file: 11_v4_v3.gpr /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6zZHcX/11_v4_v3.gpr already exists, skipping. Downloading file: 46_3_3.gpr /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6zZHcX/46_3_3.gpr already exists, skipping. Downloading file: 12_v4_v3.gpr /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6zZHcX/12_v4_v3.gpr already exists, skipping. Downloading file: 29_v4_v4.gpr /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6zZHcX/29_v4_v4.gpr already exists, skipping. Downloading file: E-MEXP-1870.idf.txt /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6zZHcX/E-MEXP-1870.idf.txt already exists, skipping. Downloading file: E-MEXP-1870.sdrf.txt /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6zZHcX/E-MEXP-1870.sdrf.txt already exists, skipping. Downloading file: A-MEXP-1425.adf.txt /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6zZHcX/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/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpL29aJ6/Rbuild11572697e621f/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' Content type 'unknown' length 3791 bytes ================================================== 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 ArrayExpress: Reading pheno data from SDRF ArrayExpress: Reading data files Loading required package: pd.hu6800 Attempting to obtain 'pd.hu6800' from BioConductor website. Checking to see if your internet connection works... Package 'pd.hu6800' was not found in the BioConductor repository. The 'pdInfoBuilder' package can often be used in situations like this. Error in oligo::read.celfiles(filenames = file.path(path, unique(files))) : The annotation package, pd.hu6800, could not be loaded. Error in readAEdata(path = path, files = dataFiles, dataCols = dataCols, : Unable to read cel files in /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpL29aJ6/Rbuild11572697e621f/ArrayExpress/vignettes Error: processing vignette 'ArrayExpress.Rnw' failed with diagnostics: chunk 6 (label = ae2bioc-full) Error in ae2bioc(mageFiles = mexp1422) : ArrayExpress: Unable to read assay data --- failed re-building ‘ArrayExpress.Rnw’ SUMMARY: processing the following file failed: ‘ArrayExpress.Rnw’ Error: Vignette re-building failed. Execution halted