I used AnnotationForge to build an annotation package. And when I use makeDBPackage
function, it does not work as printing "Error: Parameter 0 does not have length 1."
Error: Parameter 0 does not have length 1. 12 stop(structure(list(message = "Parameter 0 does not have length 1.", call = NULL, cppstack = NULL), .Names = c("message", "call", "cppstack"), class = c("Rcpp::exception", "C++Error", "error", "condition"))) 11 rsqlite_bind_params(res@ptr, params) 10 dbBind(rs, params) 9 dbBind(rs, params) 8 .local(conn, statement, ...) 7 dbSendQuery(db, sqlIns, clnVals) 6 dbSendQuery(db, sqlIns, clnVals) at sqlForge_baseMapBuilder.R#134 5 probe2gene(baseMap = baseMap, baseMapType = baseMapType, otherSrc = otherSrcObjs, chipMapSrc = chipMapSrc, chipSrc = chipSrc, pkgName = pkgName, outputDir = outputDir, allowHomologyGene = allowHomologyGene) at sqlForge_baseMapBuilder.R#329 4 getMapForOtherChipPkg(filePath = fileName, pkgName = prefix, chipMapSrc = chipMapSrc, chipSrc = chipSrc, otherSrc = otherSrc, baseMapType = baseMapType, outputDir = outputDir) at sqlForge_schemaGen.R#26 3 popHUMANCHIPDB(affy = affy, prefix = prefix, fileName = fileName, chipMapSrc = chipMapSrc, chipSrc = chipSrc, metaDataSrc = metaDataSrc, otherSrc = otherSrc, baseMapType = baseMapType, outputDir = outputDir, printSchema = FALSE) at sqlForge_makeAnnPkgs.R#28 2 AnnotationForge:::.makeHUMANCHIP_DB(...) at sqlForge_utils.R#44 1 makeDBPackage("HUMANCHIP_DB", affy = FALSE, prefix = "GPL6480", fileName = "./GPL6480_probe_entrez", baseMapType = "eg", outputDir = "./", version = "1.0.0", manufacturer = "Agilent", chipName = "Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Probe Name version)", ...
Code as below:
makeDBPackage("HUMANCHIP_DB",
affy=FALSE,
prefix="GPL6480",
fileName="./GPL6480_probe_entrez",
baseMapType="eg",
outputDir = "./",
version="1.0.0",
manufacturer = "Agilent",
chipName = "Agilent-014850 Whole Human Genome Microarray 4x44K G4112F)",
manufacturerUrl = "http://www.agilent.com/")
where ./GPL6480_probe_entrez has two columns with probe_id and entrez gene id. For example:
A_23_P100001 400451
A_23_P100022 9899
sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux jessie/sid
locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 LC_PAPER=en_GB.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocInstaller_1.20.1 AnnotationForge_1.13.6 org.Hs.eg.db_3.2.3 human.db0_3.2.4 AnnotationDbi_1.32.3
[6] IRanges_2.4.6 S4Vectors_0.8.6 Biobase_2.30.0 BiocGenerics_0.16.1 RSQLite_1.0.9000
loaded via a namespace (and not attached):
[1] roxygen2_5.0.1 Rcpp_0.12.2 seqRFLP_1.0.1 digest_0.6.8 dplyr_0.4.3.9000
[6] assertthat_0.1 R6_2.1.1 DBI_0.3.1.9008 magrittr_1.5 stringi_1.0-1
[11] lazyeval_0.1.10.9000 devtools_1.9.1 tools_3.2.0 stringr_1.0.0 memoise_0.2.1
Thanks for reporting this. I'll look into it.
Valerie