AnnotationForge failed due to "Parameter 0 does not have length 1"
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zhilongjia • 0
@zhilongjia-7339
Last seen 3 months ago
United Kingdom

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

AnnotationForge • 1.8k views
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Thanks for reporting this. I'll look into it.

Valerie

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@valerie-obenchain-4275
Last seen 4 months ago
United States

I can't reproduce this error. I tested with a  much reduced GPL6480_probe_entrez file - just a couple of rows. There may be a problem with the original. Can you send me your GPL6380_probe_entrez off line? (valerie.obenchain@roswellpark.org)?

Valerie

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Sent. Thank you.

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Thanks for the file and reproducible example. The problem was an NA value in the probe identifier column of GPL6480_probe_entrez:

> tbl <- read.table("GPL6480_probe_entrez")
> head(tbl)
            V1     V2
1 A_23_P100001 400451
2 A_23_P100011     NA
3 A_23_P100022   9899
4 A_23_P100056 348093
5 A_23_P100074  57099
6 A_23_P100092 146050
> which(is.na(tbl[,1]))
[1] 41034

After removing this line the package is created as expected.

I've added a check for this condition and error message reporting which row(s) are the problem. Changes are in AnnotationForge devel (1.13.7) and release (1.12.2). Both should be available via biocLite() Sunday 1/16 after noon PST.

Valerie

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