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Question: arrayQualityMetrics does not complete successfully
1
gravatar for Jan-Niklas
17 months ago by
Jan-Niklas10
Jan-Niklas10 wrote:

Dear all,

recently I am encountering problems using arrayQualityMetrics. Execution is always stopped at the same point and an error is thrown:

"Error in file.info(x): invalid filename argument"

Figure 1 (Distances between arrays) and Figure 2 (Outlier detection for Distances between arrays) are always created successfully, but nothing more. This happens to me on Ubuntu as well as on OS X.
I tried with different data sets, but nothing worked. I'm calling arrayQualityMetrics() with:

arrayQualityMetrics(raw_data, intgroup = "Group", outdir = quality_report_path, force = T, showWarnings = F)

Error traceback:

14: file.info(x)
13: length.path(paths)
12: length(paths)
11: grobApply(path, function(path) {
        grid.set(path, garnishGrob(grid.get(path), ..., group = group), 
            redraw = redraw)
    }, strict = strict, grep = grep, global = global)
10: grid.garnish(annotationInfo@gridObjId, group = FALSE, grep = TRUE, 
        class = class, onclick = callbacks[, 1], onmouseover = callbacks[, 
            2], onmouseout = callbacks[, 3])
9: annotateSvgGrid(annotationInfo = module@svg, name = name)
8: reportModule(p = p, module = modules[[i]], currentIndex = currentIndex, 
       arrayTable = arrayTableCompact, outdir = outdir)
7: aqm.writereport(modules = m, arrayTable = x$pData, reporttitle = reporttitle, 
       outdir = outdir)
6: arrayQualityMetrics(raw_data, intgroup = "Group", outdir = quality_report_path, 
       force = T, showWarnings = F) at quality_control.r#27
5: eval(expr, envir, enclos)
4: eval(ei, envir)
3: withVisible(eval(ei, envir))
2: source("Src/quality_control.r") at pipeline_structure.r#46
1: run_analysis()

 

Output of sessionInfo():

R version 3.2.2 (2015-08-14)

Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.3 (Yosemite)

locale:
[1] de_DE.UTF-8/de_DE.UTF-8/de_DE.UTF-8/C/de_DE.UTF-8/de_DE.UTF-8

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] hgu133plus2probe_2.18.0    hgu133plus2cdf_2.18.0      plotly_2.0.16              ggplot2_2.0.0              WriteXLS_4.0.0            
 [6] RColorBrewer_1.1-2         gdata_2.17.0               xlsx_0.5.7                 xlsxjars_0.6.1             rJava_0.9-8               
[11] biomaRt_2.26.1             illuminaHumanv4.db_1.26.0  GEOquery_2.36.0            lumi_2.22.1                pd.huex.1.0.st.v2_3.14.1  
[16] oligoData_1.8.0            oligo_1.34.2               Biostrings_2.38.4          XVector_0.10.0             oligoClasses_1.32.0       
[21] hgu133a.db_3.2.2           annaffy_1.42.0             GO.db_3.2.2                affyQCReport_1.48.0        lattice_0.20-33           
[26] affycoretools_1.42.0       affyPLM_1.46.0             preprocessCore_1.32.0      simpleaffy_2.46.0          gcrma_2.42.0              
[31] genefilter_1.52.1          affy_1.48.0                hgu133plus2.db_3.2.2       stringr_1.0.0              pathview_1.10.1           
[36] org.Hs.eg.db_3.2.3         KEGG.db_3.2.2              RSQLite_1.0.0              DBI_0.3.1                  AnnotationDbi_1.32.3      
[41] IRanges_2.4.8              S4Vectors_0.8.11           Biobase_2.30.0             BiocGenerics_0.16.1        limma_3.26.8              
[46] arrayQualityMetrics_3.26.1 BiocInstaller_1.20.1
   

loaded via a namespace (and not attached):
  [1] R.utils_2.2.0              htmlwidgets_0.6            beadarray_2.20.1           grid_3.2.2                 BiocParallel_1.4.3        
  [6] munsell_0.4.3              codetools_0.2-14           nleqslv_3.0                colorspace_1.2-6           BiocInstaller_1.20.1      
 [11] Category_2.36.0            OrganismDbi_1.12.1         knitr_1.12.3               setRNG_2013.9-1            KEGGgraph_1.28.0          
 [16] hwriter_1.3.2              lambda.r_1.1.7             biovizBase_1.18.0          affxparser_1.42.0          R6_2.1.2                  
 [21] GenomeInfoDb_1.6.3         illuminaio_0.12.0          gridSVG_1.5-1              RJSONIO_1.3-0              locfit_1.5-9.1            
 [26] bitops_1.0-6               reshape_0.8.5              RcppArmadillo_0.6.500.4.0  scales_0.4.0               nnet_7.3-12               
 [31] gtable_0.2.0               Cairo_1.5-9                methylumi_2.16.0           ggbio_1.18.5               splines_3.2.2             
 [36] rtracklayer_1.30.2         acepack_1.3-3.3            dichromat_2.0-0            rgl_0.95.1441              reshape2_1.4.1            
 [41] SVGAnnotation_0.93-1       GenomicFeatures_1.22.13    Hmisc_3.17-2               RBGL_1.46.0                tools_3.2.2               
 [46] nor1mix_1.2-1              affyio_1.40.0              gplots_2.17.0              ff_2.2-13                  siggenes_1.44.0           
 [51] Rcpp_0.12.3                plyr_1.8.3                 base64enc_0.1-3            zlibbioc_1.16.0            RCurl_1.95-4.8            
 [56] rpart_4.1-10               viridis_0.3.2              bumphunter_1.10.0          SummarizedExperiment_1.0.2 cluster_2.0.3             
 [61] magrittr_1.5               futile.options_1.0.0       matrixStats_0.50.1         xtable_1.8-2               XML_3.98-1.4              
 [66] mclust_5.1                 gridExtra_2.2.1            ellipse_0.3-8              minfi_1.16.1               KernSmooth_2.23-15        
 [71] htmltools_0.3              ReportingTools_2.10.0      R.oo_1.20.0                GOstats_2.36.0             mgcv_1.8-11               
 [76] corpcor_1.6.8              Formula_1.2-1              geneplotter_1.48.0         MASS_7.3-45                Matrix_1.2-3              
 [81] vsn_3.38.0                 quadprog_1.5-5             R.methodsS3_1.7.1          igraph_1.0.1               GenomicRanges_1.22.4      
 [86] GenomicAlignments_1.6.3    registry_0.3               foreign_0.8-66             foreach_1.4.3              annotate_1.48.0           
 [91] BeadDataPackR_1.22.0       rngtools_1.2.4             pkgmaker_0.22              multtest_2.26.0            beanplot_1.2              
 [96] AnnotationForge_1.12.2     doRNG_1.6                  VariantAnnotation_1.16.4   digest_0.6.9               graph_1.48.0              
[101] base64_1.1                 edgeR_3.12.0               GSEABase_1.32.0            Rsamtools_1.22.0           gtools_3.5.0              
[106] jsonlite_0.9.19            nlme_3.1-125               PFAM.db_3.2.2              mixOmics_5.2.0             futile.logger_1.4.1       
[111] BSgenome_1.38.0            GGally_1.0.1               KEGGREST_1.10.1            httr_1.1.0                 survival_2.38-3           
[116] png_0.1-7                  iterators_1.0.8            bit_1.1-12                 Rgraphviz_2.14.0           stringi_1.0-1             
[121] DESeq2_1.10.1              latticeExtra_0.6-28        caTools_1.17.1  
 

Is anybody experiencing the same problems? Hope someone can help.

Best regards,

Jan-Niklas

ADD COMMENTlink modified 9 months ago by fmunoz10 • written 17 months ago by Jan-Niklas10
1

I'm getting the same error.

ADD REPLYlink written 14 months ago by matheus.cburger20
4
gravatar for ian.roberts
12 months ago by
ian.roberts40
ian.roberts40 wrote:

Hi - I've spent the last 48 hr with this problem and finally tracked it down to a third party package dependency conflict.

For me, this was the length.path function defined in httr package, write-function.R module, ~LN89

Essentially, I had GEOquery and arrayQualityMetrics libraries loaded, and every time I tried to generate a QC report by calling arrayQualityMetrics on my GEO downloaded data it would die with the above error. 

"Error in file.info(x): invalid filename argument", and an incomplete HTML report ... the first 2 plots are generated, but nothing else.

(Short method to recreate error)

> library(arrayQualityMetrics)

> library(httr) 

> load('small_affy_batch.RData')

> z <- arrayQualityMetrics(ab, force=T)

After much back tracking I discovered that gridSVG, an aqm dependency, and httr, a GEOquery dependency both implement length.path, somehow resulting in a conflict (to be sure, I do not understand the exact nature of the error)

I simply added an 's' to the length.path function definition of the httr package (in write-function.R module) and now all is well for my use-case.  Obviously its not a great idea to rename functions at random, however I could not find anywhere that made use of the httr's length.paths ... so for me, no harm done.

Hope this helps.

Ian

 

ADD COMMENTlink written 12 months ago by ian.roberts40

Can you tell me how you did this? I don't get it

Here?

length.path <- function(x) file.info(x)$size
#and here
write_stream <- function(f) {
  stopifnot(is.function(f), length(formals(f)) == 1)
  request(output = write_function("write_stream", f = f))

 

 

}

 

 

ADD REPLYlink modified 9 months ago • written 9 months ago by fmunoz10
1
gravatar for Wolfgang Huber
12 months ago by
EMBL European Molecular Biology Laboratory
Wolfgang Huber13k wrote:

Dear Ian

Thank you for digging into this! This is indeed rather curious, and subtle.

Initially I expected that the code in gridSVG should be shielded from such stray function definitions via R's namespace system, but looking into it, indeed httr has a line S3method(length,path) in its NAMESPACE file, and apparently that method is visible when length(paths) is called within gridSVG (the class of paths is "path") and is unintentionally invoked instead of the default length function, leading to the error.

There is not much I can do at the level of the arrayQualityMetrics package, other than advise not to have the httr package loaded at the same time. And lament on the way how R's handling of the generic function length doesn't work with namespaces.

On another note.... the software technologies used in the arrayQualityMetrics package for the interactive plots are getting dated, and there is limited incentive to maintain them. Someone should implement something like this package, but with Rmarkdown output and ggvis (or plotly?, shiny?). [And a demo for how to look at transformed (DESeq2-VST, edgeR-voom) RNA-Seq count data with the same diagnostics would be a bonus.]

ADD COMMENTlink modified 12 months ago • written 12 months ago by Wolfgang Huber13k
1

Yes, here's a minimal example where loading (but not attaching to the search() path) httr leaks the method in an unavoidable way

> length(structure(1:5, class="path"))
[1] 5
> requireNamespace("httr")
Loading required namespace: httr
> length(structure(1:5, class="path"))
Error in file.info(x) : invalid filename argument
> base::length(structure(1:5, class="path"))
Error in file.info(x) : invalid filename argument
ADD REPLYlink modified 12 months ago • written 12 months ago by Martin Morgan ♦♦ 20k
1
gravatar for fmunoz
9 months ago by
fmunoz10
fmunoz10 wrote:

Here is the issue in the package https://github.com/hadley/httr/issues/395

ADD COMMENTlink written 9 months ago by fmunoz10
0
gravatar for Stane
14 months ago by
Stane20
Stane20 wrote:

Did someone find a fix, I have been trying to debug the exact same problem today, in my case paths is a gpath object :

> attributes(paths)
$names
[1] "path" "name" "n"   

$class
[1] "gPath" "path" 

$vpPath
[1] ""
>paths$name
[1] "plot_01.xyplot.points.panel.1.1"

I am not to familiar with grid package but creating a gPath inside length function result in the exact same error 

> length(gPath("g1"))
Error in file.info(x) : invalid filename argument
ADD COMMENTlink written 14 months ago by Stane20
0
gravatar for sofia.figueiredo
13 months ago by
sofia.figueiredo10 wrote:

Dear Bioconductor community,

I am having exactly the same problem.

> celfiles <- rma (read.celfiles (list) )
> arrayQualityMetrics (expressionset=celfiles, outdir="Report for celfile RMA", force=TRUE)
The report will be written into directory 'Report for celfile RMA'. 
Error in file.info(x) : invalid filename argument

Does anyone know why this happens and how to fix it? Can it be that the normalized cel files are somehow corrupted?

Many thanks in advance,

Sofia

My session info:

sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=German_Germany.1252  LC_CTYPE=German_Germany.1252    LC_MONETARY=German_Germany.1252 LC_NUMERIC=C                   
[5] LC_TIME=German_Germany.1252    

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] pathview_1.12.0            org.Hs.eg.db_3.3.0         AnnotationDbi_1.34.3       arrayQualityMetrics_3.28.2 pd.hugene.2.0.st_3.14.1   
 [6] oligo_1.36.1               RSQLite_1.0.0              DBI_0.4-1                  Biostrings_2.40.2          XVector_0.12.0            
[11] Biobase_2.32.0             oligoClasses_1.34.0        GenomicRanges_1.24.2       GenomeInfoDb_1.8.2         IRanges_2.6.1             
[16] S4Vectors_0.10.1           BiocGenerics_0.18.0        BiocInstaller_1.22.3      

loaded via a namespace (and not attached):
 [1] httr_1.2.1                 vsn_3.40.0                 splines_3.3.1              foreach_1.4.3              setRNG_2013.9-1           
 [6] Formula_1.2-1              affy_1.50.0                latticeExtra_0.6-28        gcrma_2.44.0               lattice_0.20-33           
[11] limma_3.28.14              chron_2.3-47               RColorBrewer_1.1-2         colorspace_1.2-6           preprocessCore_1.34.0     
[16] Matrix_1.2-6               plyr_1.8.4                 XML_3.98-1.4               affxparser_1.44.0          genefilter_1.54.2         
[21] zlibbioc_1.18.0            xtable_1.8-2               scales_0.4.0               affyio_1.42.0              ff_2.2-13                 
[26] openssl_0.9.4              annotate_1.50.0            SVGAnnotation_0.93-1       KEGGREST_1.12.2            ggplot2_2.1.0             
[31] SummarizedExperiment_1.2.3 nnet_7.3-12                survival_2.39-5            RJSONIO_1.3-0              magrittr_1.5              
[36] KEGGgraph_1.30.0           hwriter_1.3.2              foreign_0.8-66             beadarray_2.22.2           Cairo_1.5-9               
[41] graph_1.50.0               tools_3.3.1                data.table_1.9.6           stringr_1.0.0              affyPLM_1.48.0            
[46] munsell_0.4.3              cluster_2.0.4              base64_2.0                 grid_3.3.1                 iterators_1.0.8           
[51] gtable_0.2.0               codetools_0.2-14           R6_2.1.2                   BeadDataPackR_1.24.2       reshape2_1.4.1            
[56] illuminaio_0.14.0          gridExtra_2.2.1            bit_1.1-12                 Hmisc_3.17-4               gridSVG_1.5-0             
[61] Rgraphviz_2.16.0           stringi_1.1.1              Rcpp_0.12.5                png_0.1-7                  rpart_4.1-10              
[66] acepack_1.3-3.3           

 

ADD COMMENTlink written 13 months ago by sofia.figueiredo10

I am getting the same error. Can anyone please fix the problem??

ADD REPLYlink written 11 months ago by leimarembi0
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