[BioC] virtualArray vignette does not work: 'data' must be of a vector type, was 'NULL'

Mick Elliot [guest] guest at bioconductor.org
Sun Jun 15 12:08:57 CEST 2014


Hello all,

I have been attempting to use virtualArray recently, and have found that code functioning correctly perhaps six months ago no longer works. I have attempted to run the vignette and get an identical error to the one obtained from my own scripts. Specifically, after calling "virtualArrayExpressionSets()" I get the following error:

Error: 2 errors; first error:
  Error in array(x, c(length(x), 1L), if (!is.null(names(x))) list(names(x), : 'data' must be of a vector type, was 'NULL'

I have included the complete output of my attempt to run the vignette at the bottom of this email, as it's quite long. The vignette itself is available at http://www.bioconductor.org/packages/devel/bioc/vignettes/virtualArray/inst/doc/virtualArray.R

Here is the output of traceback()

9: stop(paste(msg, collapse = "nn"), call. = FALSE)
8: LastError$store(results = results, is.error = is.error, throw.error = TRUE)
7: bplapply(X = X, FUN = FUN, ..., BPRESUME = BPRESUME, BPPARAM = SerialParam(catch.errors = BPPARAM$catch.errors))
6: bplapply(X = X, FUN = FUN, ..., BPRESUME = BPRESUME, BPPARAM = SerialParam(catch.errors = BPPARAM$catch.errors))
5: bplapply(X, FUN, ..., BPRESUME = BPRESUME, BPPARAM = BPPARAM)
4: bplapply(X, FUN, ..., BPRESUME = BPRESUME, BPPARAM = BPPARAM)
3: lapply(all_expression_sets, virtualArrayBuildfData, collapse_fun = collapse_fun, 
       identifier = identifier)
2: lapply(all_expression_sets, virtualArrayBuildfData, collapse_fun = collapse_fun, 
       identifier = identifier)
1: virtualArrayExpressionSets()


I would really appreciate any help in getting virtualArray working again. I note that this error has been reported by other users a couple of times in April and May, without any response from the community. It would be great if the package maintainer could take a look.

Best wishes,

Mick Elliot
SFU

------------
Output of my attempt to run the vignette:


R version 3.1.0 (2014-04-10) -- "Spring Dance"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> ### R code from vignette source 'vignettes/virtualArray/inst/doc/virtualArray.Rnw'
> 
> ###################################################
> ### code chunk number 1: options
> ###################################################
> options(width=72)
> 
> 
> ###################################################
> ### code chunk number 2: virtualArray.Rnw:68-69
> ###################################################
> library(virtualArray)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from ‘package:stats’:

    xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, as.vector, cbind,
    colnames, do.call, duplicated, eval, evalq, Filter, Find,
    get, intersect, is.unsorted, lapply, Map, mapply, match,
    mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    Position, rank, rbind, Reduce, rep.int, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unlist

Loading required package: plyr
Loading required package: preprocessCore
Creating a generic function for ‘hist’ from package ‘graphics’ in package ‘affyPLM’
Setting options('download.file.method.GEOquery'='auto')
To support our work please cite:

To cite package 'virtualArray' in publications use:

  Andreas Heider and Rüdiger Alt (2013). virtualArray: a
  R/bioconductor package to merge raw data from different
  microarray platforms. R package version 1.8.0.

A BibTeX entry for LaTeX users is

  @Article{,
    title = {virtualArray: a R/bioconductor package to merge raw data from different microarray platforms},
    author = {{Andreas Heider} and {Rüdiger Alt}},
    year = {2013},
    note = {R package version 1.8.0},
    journal = {BMC Bioinformatics},
    volume = {14},
    pages = {75},
  }

Thanks.
Warning messages:
1: replacing previous import by ‘utils::relist’ when loading ‘virtualArray’ 
2: replacing previous import by ‘methods::new’ when loading ‘virtualArray’ 
3: replacing previous import by ‘stats::density’ when loading ‘virtualArray’ 
4: replacing previous import by ‘utils::installed.packages’ when loading ‘virtualArray’ 
5: replacing previous import by ‘utils::read.csv’ when loading ‘virtualArray’ 
6: replacing previous import by ‘utils::read.table’ when loading ‘virtualArray’ 
7: replacing previous import by ‘utils::write.table’ when loading ‘virtualArray’ 
> 
> 
> ###################################################
> ### code chunk number 3: virtualArray.Rnw:133-136
> ###################################################
> library("GEOquery")
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages
    'citation("pkgname")'.

> GSE23402 <- getGEO("GSE23402",GSEMatrix=T,AnnotGPL=FALSE)
ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE23nnn/GSE23402/matrix/
Found 1 file(s)
GSE23402_series_matrix.txt.gz
trying URL 'ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE23nnn/GSE23402/matrix/GSE23402_series_matrix.txt.gz'
ftp data connection made, file length 6015534 bytes
opened URL
downloaded 5.7 Mb

File stored at: 
C:UsersMickAppDataLocalTempRtmp80du0e/GPL570.soft
> GSE26428 <- getGEO("GSE26428",GSEMatrix=T,AnnotGPL=FALSE)
ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE26nnn/GSE26428/matrix/
Found 1 file(s)
GSE26428_series_matrix.txt.gz
trying URL 'ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE26nnn/GSE26428/matrix/GSE26428_series_matrix.txt.gz'
ftp data connection made, file length 706280 bytes
opened URL
downloaded 689 Kb

File stored at: 
C:UsersMickAppDataLocalTempRtmp80du0e/GPL6480.soft
> 
> 
> ###################################################
> ### code chunk number 4: virtualArray.Rnw:141-143
> ###################################################
> GSE23402 <- GSE23402[[1]][,1:24]
> GSE26428 <- GSE26428[[1]]
> 
> 
> ###################################################
> ### code chunk number 5: virtualArray.Rnw:146-150 (eval = FALSE)
> ###################################################
> ## library(virtualArray)
> ## library(affy)
> ## GSE23402 <- GSE23402
> ## GSE26428 <- GSE26428
> 
> 
> ###################################################
> ### code chunk number 6: virtualArray.Rnw:156-158
> ###################################################
> summary(exprs(GSE23402)[,1:3])
   GSM574058          GSM574059          GSM574060       
 Min.   :   10.06   Min.   :   10.06   Min.   :   10.06  
 1st Qu.:   22.92   1st Qu.:   22.92   1st Qu.:   22.92  
 Median :   59.03   Median :   59.03   Median :   59.03  
 Mean   :  510.00   Mean   :  510.00   Mean   :  510.00  
 3rd Qu.:  282.19   3rd Qu.:  282.19   3rd Qu.:  282.19  
 Max.   :28094.15   Max.   :28094.15   Max.   :28094.15  
> summary(exprs(GSE26428))
   GSM648497        GSM648498        GSM648499     
 Min.   : 1.054   Min.   : 1.054   Min.   : 1.054  
 1st Qu.: 3.080   1st Qu.: 3.080   1st Qu.: 3.080  
 Median : 7.062   Median : 7.062   Median : 7.062  
 Mean   : 6.983   Mean   : 6.983   Mean   : 6.983  
 3rd Qu.:10.233   3rd Qu.:10.233   3rd Qu.:10.233  
 Max.   :18.578   Max.   :18.578   Max.   :18.578  
> 
> 
> ###################################################
> ### code chunk number 7: virtualArray.Rnw:168-170
> ###################################################
> exprs(GSE23402) <- log2(exprs(GSE23402))
> exprs(GSE26428) <- (exprs(GSE26428)/20*16)
> 
> 
> ###################################################
> ### code chunk number 8: virtualArray.Rnw:175-177
> ###################################################
> summary(exprs(GSE23402)[,1:4])
   GSM574058        GSM574059        GSM574060        GSM574061     
 Min.   : 3.331   Min.   : 3.331   Min.   : 3.331   Min.   : 3.331  
 1st Qu.: 4.519   1st Qu.: 4.519   1st Qu.: 4.519   1st Qu.: 4.519  
 Median : 5.883   Median : 5.883   Median : 5.883   Median : 5.883  
 Mean   : 6.491   Mean   : 6.491   Mean   : 6.491   Mean   : 6.491  
 3rd Qu.: 8.140   3rd Qu.: 8.140   3rd Qu.: 8.140   3rd Qu.: 8.140  
 Max.   :14.778   Max.   :14.778   Max.   :14.778   Max.   :14.778  
> summary(exprs(GSE26428))
   GSM648497         GSM648498         GSM648499      
 Min.   : 0.8433   Min.   : 0.8433   Min.   : 0.8433  
 1st Qu.: 2.4636   1st Qu.: 2.4636   1st Qu.: 2.4636  
 Median : 5.6495   Median : 5.6495   Median : 5.6495  
 Mean   : 5.5863   Mean   : 5.5863   Mean   : 5.5863  
 3rd Qu.: 8.1861   3rd Qu.: 8.1861   3rd Qu.: 8.1861  
 Max.   :14.8623   Max.   :14.8623   Max.   :14.8623  
> 
> 
> ###################################################
> ### code chunk number 9: virtualArray.Rnw:183-185
> ###################################################
> annotation(GSE23402) <- "hgu133plus2"
> annotation(GSE26428) <- "hgug4112a"
> 
> 
> ###################################################
> ### code chunk number 10: virtualArray.Rnw:190-191
> ###################################################
> my_virtualArrays <- NULL
> 
> 
> ###################################################
> ### code chunk number 11: options
> ###################################################
> options(width=60)
> if(require(BiocParallel))
+     register(MulticoreParam(verbose=TRUE))
Loading required package: BiocParallel
> 
> 
> ###################################################
> ### code chunk number 12: virtualArray.Rnw:209-210
> ###################################################
> my_virtualArrays$iPSC_hESC_noBatchEffect <- virtualArrayExpressionSets()
Now preprocessing raw data of GSE23402: Loading annotations...
Usinghgu133plus2as Bioconductor annotation package for datasetGSE23402.
Packagehgu133plus2.dbnot available. Atempting to install it.
Bioconductor version 2.14 (BiocInstaller 1.14.2),
  ?biocLite for help
Installing package into ‘C:/Users/Mick/Documents/R/win-library/3.1’
(as ‘lib’ is unspecified)
trying URL 'http://bioconductor.org/packages/2.14/data/annotation/bin/windows/contrib/3.1/hgu133plus2.db_2.14.0.zip'
Content type 'application/zip' length 2197467 bytes (2.1 Mb)
opened URL
downloaded 2.1 Mb


The downloaded binary packages are in
        C:UsersMickAppDataLocalTempRtmp80du0edownloaded_packages
Package hgu133plus2.db has been successfully installed!
Loading required package: hgu133plus2.db
Loading required package: AnnotationDbi
Loading required package: GenomeInfoDb
Loading required package: org.Hs.eg.db
Loading required package: DBI


Now preprocessing raw data of GSE23402: Collapsing expression values to their median...
Using identifier as id variables
Now preprocessing raw data of GSE23402: Annotating expression values with SYMBOL...
Now preprocessing raw data of GSE26428: Loading annotations...
Usinghgug4112aas Bioconductor annotation package for datasetGSE26428.
Packagehgug4112a.dbnot available. Atempting to install it.
Bioconductor version 2.14 (BiocInstaller 1.14.2),
  ?biocLite for help
Installing package into ‘C:/Users/Mick/Documents/R/win-library/3.1’
(as ‘lib’ is unspecified)
trying URL 'http://bioconductor.org/packages/2.14/data/annotation/bin/windows/contrib/3.1/hgug4112a.db_2.14.0.zip'
Content type 'application/zip' length 1618802 bytes (1.5 Mb)
opened URL
downloaded 1.5 Mb


The downloaded binary packages are in
        C:UsersMickAppDataLocalTempRtmp80du0edownloaded_packages
Package hgug4112a.db has been successfully installed!
Loading required package: hgug4112a.db

Now preprocessing raw data of GSE26428: Collapsing expression values to their median...
Using identifier as id variables
Now preprocessing raw data of GSE26428: Annotating expression values with SYMBOL...
Error: 2 errors; first error:
  Error in array(x, c(length(x), 1L), if (!is.null(names(x))) list(names(x), : 'data' must be of a vector type, was 'NULL'

For more information, use bplasterror(). To resume
  calculation, re-call the function and set the
  argument 'BPRESUME' to TRUE or wrap the previous
  call in bpresume().

First traceback:
  22: virtualArrayExpressionSets()
  21: lapply(all_expression_sets, virtualArrayBuildfData, collapse_fun = collapse_fun, 
          identifier = identifier)
  20: lapply(all_expression_sets, virtualArrayBuildfData, collapse_fun = collapse_fun, 
          identifier = identifier)
  19: bplapply(X, FUN, ..., BPRESUME = BPRESUME, BPPARAM = BPPARAM)
  18: bplapply(X, FUN, ..., BPRESUME = BPRESUME, BPPARAM = BPPARAM)
  17: bplapply(X = X, FUN = FUN, ..., BPRESUME = BPRESUME, BPPARAM = SerialParam(catch.errors = BPPARAM$catch.errors))
  16: bplapply(X = X, FUN = FUN, ..., BPRESUME = BPRESUME, BPPARAM = SerialParam(catch.errors = BPPARAM$catch.errors))



 -- output of sessionInfo(): 

R version 3.1.0 (2014-04-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United Kingdom.1252 
[2] LC_CTYPE=English_United Kingdom.1252   
[3] LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C                           
[5] LC_TIME=English_United Kingdom.1252    

attached base packages:
[1] parallel  stats     graphics  grDevices utils    
[6] datasets  methods   base     

other attached packages:
 [1] hgug4112a.db_2.14.0   hgu133plus2.db_2.14.0
 [3] org.Hs.eg.db_2.14.0   RSQLite_0.11.4       
 [5] DBI_0.2-7             AnnotationDbi_1.26.0 
 [7] GenomeInfoDb_1.0.2    BiocInstaller_1.14.2 
 [9] BiocParallel_0.6.1    GEOquery_2.30.0      
[11] Biobase_2.24.0        virtualArray_1.8.0   
[13] preprocessCore_1.26.1 plyr_1.8.1           
[15] BiocGenerics_0.10.0  

loaded via a namespace (and not attached):
 [1] affy_1.42.2       affyio_1.32.0     affyPLM_1.40.1   
 [4] BatchJobs_1.2     BBmisc_1.6        Biostrings_2.32.0
 [7] brew_1.0-6        codetools_0.2-8   digest_0.6.4     
[10] fail_1.2          foreach_1.4.2     gcrma_2.36.0     
[13] grid_3.1.0        IRanges_1.22.9    iterators_1.0.7  
[16] lattice_0.20-29   outliers_0.14     quadprog_1.5-5   
[19] Rcpp_0.11.2       RCurl_1.95-4.1    reshape2_1.4     
[22] sendmailR_1.1-2   splines_3.1.0     stats4_3.1.0     
[25] stringr_0.6.2     tools_3.1.0       tseries_0.10-32  
[28] XML_3.98-1.1      XVector_0.4.0     zlibbioc_1.10.0  
[31] zoo_1.7-11       


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