[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: âBiocGenericsâ
The following objects are masked from âpackage:parallelâ:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following object is masked from âpackage:statsâ:
xtabs
The following objects are masked from âpackage:baseâ:
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 âhistâ from package âgraphicsâ in package âaffyPLMâ
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 âutils::relistâ when loading âvirtualArrayâ
2: replacing previous import by âmethods::newâ when loading âvirtualArrayâ
3: replacing previous import by âstats::densityâ when loading âvirtualArrayâ
4: replacing previous import by âutils::installed.packagesâ when loading âvirtualArrayâ
5: replacing previous import by âutils::read.csvâ when loading âvirtualArrayâ
6: replacing previous import by âutils::read.tableâ when loading âvirtualArrayâ
7: replacing previous import by âutils::write.tableâ when loading âvirtualArrayâ
>
>
> ###################################################
> ### 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 âC:/Users/Mick/Documents/R/win-library/3.1â
(as âlibâ 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 âC:/Users/Mick/Documents/R/win-library/3.1â
(as âlibâ 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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