Trying examples in vignette

[BenoitFiset]

Hi,

trying out the examples in: http://www.bioconductor.org/packages/release/bioc/vignettes/chimeraviz/inst/doc/chimeraviz-vignette.html

And when I get to the example at 4.2 The fusion report, the output.html file never generates...

if(!exists("soapfuse833ke"))
  soapfuse833ke <- system.file(
    "extdata",
    "soapfuse_833ke_final.Fusion.specific.for.genes",
    package = "chimeraviz")
fusions <- import_soapfuse(soapfuse833ke, "hg38", 10)
# Create report!
create_fusion_report(fusions, "output.html")

No file in the getwd() directory....

Also tried the example in https://www.bioconductor.org/packages/devel/bioc/manuals/chimeraviz/man/chimeraviz.pdf

defuse833ke <- system.file("extdata","defuse_833ke_results.filtered.tsv",package="chimeraviz")
fusions <- import_defuse(defuse833ke, "hg19", 3)
# Temporary file to store the report
output_filename <- tempfile(pattern = "fusionReport",fileext = ".html",tmpdir = tempdir())
# Create report
create_fusion_report(fusions, output_filename)

Nothing in the "output_filename" temp directory.

The rest of the examples work.

Any tips to start to debug this ?

Thanks

B.

=====

> sessionInfo()
R version 3.5.3 (2019-03-11)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.3

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

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

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

other attached packages:
 [1] chimeraviz_1.8.5       data.table_1.12.0      ensembldb_2.6.7        AnnotationFilter_1.6.0 GenomicFeatures_1.34.7
 [6] AnnotationDbi_1.44.0   Biobase_2.42.0         Gviz_1.26.5            GenomicRanges_1.34.0   GenomeInfoDb_1.18.2   
[11] Biostrings_2.50.2      XVector_0.22.0         IRanges_2.16.0         S4Vectors_0.20.1       BiocGenerics_0.28.0   

loaded via a namespace (and not attached):
 [1] ProtGenerics_1.14.0         bitops_1.0-6                matrixStats_0.54.0          bit64_0.9-7                
 [5] RColorBrewer_1.1-2          progress_1.2.0              httr_1.4.0                  Rgraphviz_2.26.0           
 [9] tools_3.5.3                 backports_1.1.3             DT_0.5                      R6_2.4.0                   
[13] rpart_4.1-13                Hmisc_4.2-0                 DBI_1.0.0                   lazyeval_0.2.2             
[17] colorspace_1.4-1            nnet_7.3-12                 tidyselect_0.2.5            gridExtra_2.3              
[21] prettyunits_1.0.2           bit_1.1-14                  curl_3.3                    compiler_3.5.3             
[25] graph_1.60.0                htmlTable_1.13.1            DelayedArray_0.8.0          rtracklayer_1.42.2         
[29] scales_1.0.0                checkmate_1.9.1             RCircos_1.2.1               stringr_1.4.0              
[33] digest_0.6.18               Rsamtools_1.34.1            foreign_0.8-71              rmarkdown_1.12             
[37] base64enc_0.1-3             dichromat_2.0-0             pkgconfig_2.0.2             htmltools_0.3.6            
[41] BSgenome_1.50.0             htmlwidgets_1.3             rlang_0.3.2                 rstudioapi_0.10            
[45] RSQLite_2.1.1               shiny_1.2.0                 jsonlite_1.6                crosstalk_1.0.0            
[49] gtools_3.8.1                BiocParallel_1.16.6         acepack_1.4.1               dplyr_0.8.0.1              
[53] VariantAnnotation_1.28.13   RCurl_1.95-4.12             magrittr_1.5                GenomeInfoDbData_1.2.0     
[57] Formula_1.2-3               Matrix_1.2-15               Rcpp_1.0.1                  munsell_0.5.0              
[61] stringi_1.4.3               yaml_2.2.0                  SummarizedExperiment_1.12.0 zlibbioc_1.28.0            
[65] org.Hs.eg.db_3.7.0          plyr_1.8.4                  blob_1.1.1                  promises_1.0.1             
[69] crayon_1.3.4                lattice_0.20-38             splines_3.5.3               hms_0.4.2                  
[73] knitr_1.22                  pillar_1.3.1                biomaRt_2.38.0              XML_3.98-1.19              
[77] glue_1.3.1                  evaluate_0.13               biovizBase_1.30.1           latticeExtra_0.6-28        
[81] BiocManager_1.30.4          httpuv_1.5.0                org.Mm.eg.db_3.7.0          gtable_0.3.0               
[85] purrr_0.3.2                 assertthat_0.2.1            ggplot2_3.1.0               xfun_0.5                   
[89] mime_0.6                    xtable_1.8-3                later_0.8.0                 ArgumentCheck_0.10.2       
[93] survival_2.43-3             tibble_2.1.1                GenomicAlignments_1.18.1    memoise_1.1.0              
[97] cluster_2.0.7-1             BiocStyle_2.10.0           
> 

[stianlagstad]

Hi @BenoitFiset !

I just tried it on my own computer, and here it worked as expected. Could you try to specify the full file path for the output file? Like this: create_fusion_report(fusions, "/home/stian/output.html").

[BenoitFiset]

Hi Stian,

Yep that did the trick. Full path created the file. My setwd() is the same as the full path ...

Even this doesn't generate the file

create_fusion_report(fusions, "./Output-02.html")

Putting the full path, as suggested, was the only way to get it to work and get the report.

Thanks for the help,

B.

[stianlagstad]

Glad you got it working. I'll keep the issue open to remind me to make a change so that getwd() is used instead :)

[xizhihui]

Hi, it only works when the output is "/path/to/output.html", even file.path(getwd(), "output.html") does not work ( may be it takes a long time to generate report ? ) in R3.6 chimeraviz 1.10.0 @stianlagstad Have you forgotten to fix it ?

[stianlagstad]

This issue is still open, so the status is the same @xizhihui. If you wish to submit a pull requests for fixing this I'd be happy to review it :)

[stianlagstad]

The default behaviour will be changed from version 1.13.5 onward. The report will then be created in the current working directory.