Re: [Bioc-devel] Unable to reproduce chimeraviz 3.10 build failure

[Pages, Herve]

Hi Stian,

The 3.10 builds use BioC 3.10 which is the current **devel** version of 
BioC so make sure you also use this if you want to reproduce a 3.10 
build failure.

Here is how to quickly reproduce the error:

   library(chimeraviz)

   defuse833ke <- system.file(
 "extdata",
 "defuse_833ke_results.filtered.tsv",
 package="chimeraviz")
   fusions <- import_defuse(defuse833ke, "hg19", 1)
   fusion <- get_fusion_by_id(fusions, 5267)

   edbSqliteFile <- system.file(
 "extdata",
 "Homo_sapiens.GRCh37.74.sqlite",
 package="chimeraviz")
   edb <- ensembldb::EnsDb(edbSqliteFile)

   fusion5267and11759reads <- system.file(
 "extdata",
 "fusion5267and11759reads.bam",
 package="chimeraviz")

   plot_fusion_transcript(
 fusion,
 edb,
 fusion5267and11759reads)

   # Error in normarg_mcols(value, class(x), length(x)) :
   #   trying to set zero length metadata columns on a non-zero length 
object

See my sessionInfo() below.

Anyway, this error is actually caused by a regression I introduced 
recently to the S4Vectors package. Should be fixed now (in S4Vectors 
0.23.25). Some details here:

 
https://github.com/Bioconductor/S4Vectors/commit/e53a50d4003b0d45aee69779998fcfb76a685690

If everything goes as expected, the build error in chimeraviz should go 
away on tomorrow's report.

Sorry for the inconvenience,

H.

 > sessionInfo()
R version 3.6.0 Patched (2019-05-02 r76454)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.5 LTS

Matrix products: default
BLAS:   /home/hpages/R/R-3.6.r76454/lib/libRblas.so
LAPACK: /home/hpages/R/R-3.6.r76454/lib/libRlapack.so

locale:
  [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
  [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
  [7] LC_PAPER=en_US.UTF-8   LC_NAME=C
  [9] LC_ADDRESS=C   LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
  [1] grid  stats4parallel  stats graphics  grDevices utils
  [8] datasets  methods   base

other attached packages:
  [1] chimeraviz_1.11.0  data.table_1.12.2  ensembldb_2.9.6
  [4] AnnotationFilter_1.9.0 GenomicFeatures_1.37.4 AnnotationDbi_1.47.1
  [7] Biobase_2.45.1 Gviz_1.29.3GenomicRanges_1.37.16
[10] GenomeInfoDb_1.21.2Biostrings_2.53.2  XVector_0.25.0
[13] IRanges_2.19.16S4Vectors_0.23.24  BiocGenerics_0.31.6

loaded via a namespace (and not attached):
  [1] ProtGenerics_1.17.4 bitops_1.0-6
  [3] matrixStats_0.55.0  bit64_0.9-7
  [5] RColorBrewer_1.1-2  progress_1.2.2
  [7] httr_1.4.1  tools_3.6.0
  [9] backports_1.1.4 DT_0.9
[11] R6_2.4.0rpart_4.1-15
[13] Hmisc_4.2-0 DBI_1.0.0
[15] lazyeval_0.2.2  colorspace_1.4-1
[17] nnet_7.3-12 tidyselect_0.2.5
[19] gridExtra_2.3   prettyunits_1.0.2
[21] bit_1.1-14  curl_4.2
[23] compiler_3.6.0  htmlTable_1.13.2
[25] DelayedArray_0.11.6 rtracklayer_1.45.6
[27] scales_1.0.0checkmate_1.9.4
[29] askpass_1.1 RCircos_1.2.1
[31] rappdirs_0.3.1  stringr_1.4.0
[33] digest_0.6.21   Rsamtools_2.1.6
[35] foreign_0.8-72  rmarkdown_1.16
[37] base64enc_0.1-3 dichromat_2.0-0
[39] pkgconfig_2.0.3 htmltools_0.3.6
[41] dbplyr_1.4.2BSgenome_1.53.2
[43] htmlwidgets_1.3 rlang_0.4.0
[45] rstudioapi_0.10 RSQLite_2.1.2
[47] BiocParallel_1.19.3 acepack_1.4.1
[49] dplyr_0.8.3 VariantAnnotation_1.31.4
[51] RCurl_1.95-4.12 magrittr_1.5
[53] GenomeInfoDbData_1.2.1  Formula_1.2-3
[55] Matrix_1.2-17   Rcpp_1.0.2
[57] munsell_0.5.0   yaml_2.2.0
[59] stringi_1.4.3   SummarizedExperiment_1.15.9
[61] zlibbioc_1.31.0 plyr_1.8.4
[63] org.Hs.eg.db_3.8.2  BiocFileCache_1.9.1
[65] blob_1.2.0  crayon_1.3.4
[67] lattice_0.20-38 splines_3.6.0
[69] hms_0.5.1   zeallot_0.1.0
[71] knitr_1.25  pillar_1.4.2
[73] biomaRt_2.41.8  XML_3.98-1.20
[75] glue_1.3.1  evaluate_0.14
[77] biovizBase_1.33.1   latticeExtra_0.6-28
[79] BiocManager_1.30.4  vctrs_0.2.0
[81] org.Mm.eg.db_3.8.2  gtable_0.3.0
[83] openssl_1.4.1   purrr_0.3.2
[85] assertthat_0.2.1ggplot2_3.2.1
[87] xfun_0.10   ArgumentCheck_0.10.2
[89] survival_2.44-1.1   tibble_2.1.3
[91] GenomicAlignments_1.21.7memoise_1.1.0
[93] cluster_2.1.0   BiocStyle_2.13.2

On 10/2/19 11:27, Stian Lågstad wrote:
> Hi,
> 
> The most recent build of chimeraviz fails when rebuilding the vignette:
> 

[Bioc-devel] Unable to reproduce chimeraviz 3.10 build failure

[Stian Lågstad]

Hi,

The most recent build of chimeraviz fails when rebuilding the vignette:
https://bioconductor.org/checkResults/3.10/bioc-LATEST/chimeraviz/malbec1-buildsrc.html,
and I'm unable to reproduce this locally. Does anyone have ideas as to how
I can dig deeper into this?

Thank you.

Here's an excerpt from build log in case it disappears when the new build
is done:
```
Quitting from lines 564-591 (chimeraviz-vignette.Rmd)
Error: processing vignette 'chimeraviz-vignette.Rmd' failed with
diagnostics:
trying to set zero length metadata columns on a non-zero length
  object
--- failed re-building ‘chimeraviz-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘chimeraviz-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
```

-- 
Stian Lågstad
+47 41 80 80 25

[[alternative HTML version deleted]]

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Re: [Bioc-devel] Reference manual as HTML

[Ludwig Geistlinger]

Thanks a lot for the insights.
I think I am then indeed resorting to pkgdown and the rdrr site.

Ludwig

From: Bioc-devel  on behalf of Pages, Herve 

Sent: Friday, September 27, 2019 2:02 AM
To: Laurent Gatto; Martin Maechler; Martin Morgan
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Reference manual as HTML

Hopefully they'll remedy these problems. They've clearly put a enormous
effort on this.

It sounds like a non-trivial effort to generate the tens of thousands of
Bioconductor man pages in HTML and keep them in sync with whatever comes
out of the nightly builds every day. Plus, if we want the links in the
man pages to work, we would need to also generate and host the HTML man
pages of all CRAN dependencies. I'm not sure we (the core team) have the
resource for that. Maybe an easier/cheaper path is to rely on some
already existing resource like rdrr.io (and maybe help them by reporting
problems etc...)

Best,
H.


On 9/26/19 22:35, Laurent Gatto wrote:
> But it has been  badly out-of-data in the past, not sure devel is available 
> and buggy (examples don't run, despite the Run button and outdated 
> installation instructions still using 
> `source("https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_biocLite.R=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=V2DMbdkOnMOEDmM-NTXRK2Upst5xq5TTNfoiTX4FlbQ=g7u2I_OwcuL2CSwFfDGK-FX8zsC54IyHxCxV78Zy4kk=
>  ")`)
>
> Laurent
>
> 
> From: Bioc-devel  on behalf of Pages, Herve 
> 
> Sent: 27 September 2019 00:14
> To: Martin Maechler; Martin Morgan
> Cc: bioc-devel@r-project.org
> Subject: Re: [Bioc-devel] Reference manual as HTML
>
> and let's not forget the rdrr site that provides HTML versions of all R
> package man pages in the known world:
>
> 
> https://urldefense.proofpoint.com/v2/url?u=https-3A__eur03.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Frdrr.io-252Fbioc-252FDESeq2-252Fman-252FDESeq.html-26amp-3Bdata-3D02-257C01-257Claurent.gatto-2540uclouvain.be-257Ceab709733a714ae52f1d08d742cf05d4-257C7ab090d4fa2e4ecfbc7c4127b4d582ec-257C0-257C0-257C637051329265489883-26amp-3Bsdata-3D82CPHhbrpMfjL1iZy8OMBO6T-252FBt0Kgms3VauzT-252FxlqQ-253D-26amp-3Breserved-3D0=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=V2DMbdkOnMOEDmM-NTXRK2Upst5xq5TTNfoiTX4FlbQ=E9M_UM64RYYAPZvTbx0XaGVwWY-g9je6xgvHj9Xs6qU=
>
> Unfortunately the links across man pages are not clickable :-/
>
> H.
>
>
> On 9/26/19 06:19, Martin Maechler wrote:
>>> Martin Morgan
>>>   on Wed, 25 Sep 2019 21:10:24 + writes:
>>
>>   > Our recollection is that there is no 'flag' in R CMD build to create 
>> HTML rather than PDF vignettes; without that it would be non-trivial to 
>> create html output, e.g., links across pages. (I *think* the installed 
>> package html help pages are generated on the fly...)
>>
>> Yes, by default.
>> But you may (or not) remember that for R itself, I (and my
>> university, ETH Zurich) have provided static HTML help pages and
>> manuals since "forever" -> 
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__eur03.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Furldefense.proofpoint.com-252Fv2-252Furl-253Fu-253Dhttps-2D3A-5F-5Fstat.ethz.ch-5FR-2D2Dmanual-5F-2526d-253DDwIDaQ-2526c-253DeRAMFD45gAfqt84VtBcfhQ-2526r-253DBK7q3XeAvimeWdGbWY-5FwJYbW0WYiZvSXAJJKaaPhzWA-2526m-253Dc4VdSQh-5FZ9zl5XbA2uoUx-2DcLMNMKpPP7NOvfAEo82ms-2526s-253DC4NHQqM1TjSqBsj4QBM8g6rtiU4U-5FxgOigegtYPO8pc-2526e-26amp-3Bdata-3D02-257C01-257Claurent.gatto-2540uclouvain.be-257Ceab709733a714ae52f1d08d742cf05d4-257C7ab090d4fa2e4ecfbc7c4127b4d582ec-257C0-257C0-257C637051329265489883-26amp-3Bsdata-3DDujWDlOjIMeiA-252FDSh9IyBdfDwqvisOHu8vY9qTrbkHc-253D-26amp-3Breserved-3D0-3D=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=V2DMbdkOnMOEDmM-NTXRK2Upst5xq5TTNfoiTX4FlbQ=NhxQUIrorkTLVJqvSA_BXQ033CzLPBmbKEeeljVfkX0=
>> and my cron job that creates (and daily updates) them "starts
>> with"
>>
>> ../R/configure --with-prebuilt-html
>>
>> As it does provide static html help pages for all "base R" +
>> Recommended packages,
>>
>>see, e.g., 
>>