Hi Leo,
many thanks for getting back to me!
Regarding cross-references: the format wraps around bookdown so the \@ref()
syntax is supported in the same way as in other BiocStyle format functions
and in BiocWorkflowTools::f1000research.
As for the Mac builder issue, the libraries are:
> openssl version
OpenSSL 0.9.8zf 19 Mar 2015
> pkg-config --version
0.28
and the following call in a fresh R session succeeds.
library('rtracklayer')
x <- import.bw('http://duffel.rail.bio/recount/DRP000366/bw/DRR000897.bw',as
= 'RleList')
So not really sure what's going on. Please let me know in case you have any
other suggestions how to troubleshoot this.
Cheers,
Andrzej
On Tue, Sep 5, 2017 at 4:35 PM, Leonardo Collado Torres <lcoll...@jhu.edu>
wrote:
> Hi Andrzej,
>
> Thank you for replies and looking into this!
>
> Thank you for the detailed explanation about the beta workflow build
> system and the use of rmarkdown::render with a custom template. Does
> it support \@ref() calls?
>
> Now that the Windows build is solved, I believe that the Mac one is
> related to https://support.bioconductor.org/p/93182/. That is, it
> could be due to:
>
> openssl version
> pkg-config --version
>
> Recent versions are required by rtracklayer to support url forwarding.
> We use links like
> http://duffel.rail.bio/recount/SRP045638/bw/mean_SRP045638.bw in
> recount that forward the link to IDIES in case that we need to move
> the data at some point in the future.
>
> As for the size of the BigWig file, don't worry about it. We use a
> small portion of it (chr21) for the workflow so the 2GB RAM limit
> shouldn't be an issue. The recount::expressed_regions() call
> ultimately calls:
>
> rtracklayer::import.bw("http://duffel.rail.bio/recount/
> SRP045638/bw/mean_SRP045638.bw",
> selection = GenomicRanges::GRanges("chr21", IRanges::IRanges(1,
> 46709983)), as = "RleList")[["chr21"]]
>
>
> > x <- rtracklayer::import.bw("http://duffel.rail.bio/recount/
> SRP045638/bw/mean_SRP045638.bw", selection =
> GenomicRanges::GRanges("chr21", IRanges::IRanges(1, 46709983)), as =
> "RleList")[["chr21"]]
> > x
> numeric-Rle of length 46709983 with 8092519 runs
> Lengths: 5010010 66 32
> 2 ... 6 65
> 6 10025
> Values : 0 0.00222299993038177 0.00444599986076355
> 0.00666899979114532 ... 0.00606400007382035 0.00828699953854084
> 0.00606400007382035 0
> > print(object.size(x), units = "Mb")
> 92.6 Mb
> > sessionInfo()
> R version 3.4.1 (2017-06-30)
> Platform: x86_64-apple-darwin15.6.0 (64-bit)
> Running under: macOS Sierra 10.12.6
>
> Matrix products: default
> BLAS: /Library/Frameworks/R.framework/Versions/3.4/
> Resources/lib/libRblas.0.dylib
> LAPACK: /Library/Frameworks/R.framework/Versions/3.4/
> Resources/lib/libRlapack.dylib
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> loaded via a namespace (and not attached):
> [1] lattice_0.20-35 matrixStats_0.52.2
> IRanges_2.10.2 XML_3.98-1.9
> [5] Rsamtools_1.28.0 Biostrings_2.44.2
> GenomicAlignments_1.12.2 bitops_1.0-6
> [9] grid_3.4.1 GenomeInfoDb_1.12.2
> stats4_3.4.1 zlibbioc_1.22.0
> [13] XVector_0.16.0 S4Vectors_0.14.3
> Matrix_1.2-11 BiocParallel_1.10.1
> [17] tools_3.4.1 Biobase_2.36.2
> RCurl_1.95-4.8 DelayedArray_0.2.7
> [21] rtracklayer_1.36.4 parallel_3.4.1
> compiler_3.4.1 BiocGenerics_0.22.0
> [25] GenomicRanges_1.28.4 SummarizedExperiment_1.6.3
> GenomeInfoDbData_0.99.0
>
>
> Best,
> Leo
>
> On Fri, Sep 1, 2017 at 10:54 AM, Andrzej Oleś <andrzej.o...@gmail.com>
> wrote:
> > I've updated pandoc on the win workflow builder to the latest release
> > (1.19.2.1) which resolves the vignette compilation error there.
> >
> > Regarding the Mac builder the workflow fails in the call to
> > derfinder::loadCoverage issued by the line
> >
> > regions <- expressed_regions("SRP045638", "chr21", cutoff = 5L,
> > maxClusterGap = 3000L)
> >
> > 2017-09-01 07:32:44 loadCoverage: loading BigWig file
> > http://duffel.rail.bio/recount/SRP045638/bw/mean_SRP045638.bw
> > Error in .local(con, format, text, ...) : UCSC library operation failed
> > In addition: Warning message:
> > In .local(con, format, text, ...) : End of file reading 4096 bytes (got
> 0)
> >
> > I didn't look into what loadCoverage does internally, but maybe the error
> > has something to do with the fact that the size of mean_SRP045638.bw is
> 7GB,
> > while the builder vagrant box runs only on 2GB(!) of RAM.
> >
> > Best,
> > Andrzej
> >
> >
> > On Thu, Aug 31, 2017 at 11:25 PM, Andrzej Oleś <andrzej.o...@gmail.com>
> > wrote:
> >>
> >> Hi Leo,
> >>
> >> first of all, many thanks for your efforts in troubleshooting workflow
> >> build issues and the detailed description of your findings. Also,
> >> congratulations on the successful publication of your new workflow on
> the
> >> Bioconductor website!
> >>
> >> We are now beta testing a new workflow build engine which enables some
> >> features not possible to achieve in the previous approach, such as
> >> cross-references. The goal is to properly render the output for the BioC
> >> website directly from the Rmd file authored for
> >> BiocWorkflowTools::f1000_article without any special tweaks or hacks.
> This
> >> new engine is enabled by adding the special '.html_output' token file
> in the
> >> vignettes/ dir. Ideally, you should be able to get decent output from
> the
> >> original Rmd file which you used for the F1000 Research submission
> without
> >> any manual Bioc-specific modifications. Note that in principle you could
> >> even leave your primary document output format as
> >> `BiocWorkflowTools::f1000_article`. This is because the workflows for
> the
> >> website are build through a call to `rmarkdown::render` by specifying a
> >> custom render format, so the output format set in the document header is
> >> discarded anyway; it is important only for the vignette included in the
> >> package tarball. But it's also fine to use either of the formats
> provided by
> >> BiocStyle.
> >>
> >> It shouldn't be necessary to use the captioner package anymore, as
> figure
> >> numbering is now handled by bookdown. Gosia used it in cytofWorkflow
> before
> >> I enabled the new html engine for her workflow, which I did only
> yesterday.
> >>
> >> Re the specific builder issues: I've deleted the /tmp/udcCache dir on
> Mac,
> >> but it didn't help. I'm not sure yet what could be the problem there.
> The
> >> citeproc conversion error on Windows might be because of the older
> pandoc
> >> version (1.17.2), will look into this. The convert warnings appear
> because
> >> the new BiocStyle formats set the `knitr::opts_chunk(crop=TRUE)` to
> crop out
> >> excessive white space around plots, will try to sanitize this a little
> bit
> >> too.
> >>
> >> Cheers,
> >> Andrzej
> >>
> >> On Thu, Aug 31, 2017 at 8:15 PM, Leonardo Collado Torres
> >> <lcoll...@jhu.edu> wrote:
> >>>
> >>> Hi,
> >>>
> >>> I recently got a workflow accepted and I've been trying to get the
> >>> workflow builder to successfully complete on Mac and Windows which is
> >>> based on bioc-release. Note that the workflow did build properly on
> >>> those operating systems using the SPB (bioc-devel).
> >>>
> >>>
> >>> ## Linux: working
> >>>
> >>> After looking at
> >>>
> >>> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/
> workflows/cytofWorkflow
> >>> and
> >>> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/
> workflows/rnaseqGene
> >>> I was able to:
> >>>
> >>> (1) get the figure references and captions working using captioner
> >>> (2) actually get the figures to show
> >>> (3) use the new layout (thanks to vignettes/.html_output)
> >>>
> >>> Since the build completes on Linux,
> >>> http://bioconductor.org/help/workflows/recountWorkflow/ is now live.
> >>> Only the links to the Mac and Windows binaries fail.
> >>>
> >>>
> >>> ## Mac: could be a permissions issue
> >>>
> >>> The issue with Mac is (details at
> >>>
> >>> http://docbuilder.bioconductor.org:8080/job/recountWorkflow/label=
> vagrantmac/9/console)
> >>> is that I eventually run into this error:
> >>>
> >>> Quitting from lines 735-747 (recount-workflow.Rmd)
> >>> Error: processing vignette 'recount-workflow.Rmd' failed with
> >>> diagnostics:
> >>> UCSC library operation failed
> >>> Execution halted
> >>>
> >>>
> >>> The referenced lines break because of:
> >>>
> >>> regions <- expressed_regions("SRP045638", "chr21", cutoff = 5L,
> >>> maxClusterGap = 3000L)
> >>>
> >>> This code uses rtracklayer::import.bw() with a URL that gets
> >>> forwarded. I made sure that I am requiring the latest bioc-release
> >>> rtracklayer in the description file, so this leads me to think that
> >>> this issue is a repeat of
> >>> https://stat.ethz.ch/pipermail/bioc-devel/2016-August/009599.html
> >>> where the solution involved changing some permissions. Dan stated in
> >>> that thread (3rd email): "Actually it looks like it was a permissions
> >>> issue with the directory /tmp/udcCache. I removed this directory (as
> >>> superuser) and that error no longer happens."
> >>>
> >>> Does this sound like something that could be happening in the Mac
> >>> builder?
> >>>
> >>>
> >>>
> >>> ## Windows: figure and pandoc-citeproc issues
> >>>
> >>>
> >>> In Windows, I see warnings like this:
> >>>
> >>> Invalid Parameter - -trim
> >>> Warning: running command 'C:\Windows\system32\cmd.exe /c convert
> >>> "exondeanalysis1-1.png" -trim "exondeanalysis1-1.png"' had status 4
> >>> Warning in shell(paste(c(cmd, args), collapse = " ")) :
> >>> 'convert "exondeanalysis1-1.png" -trim "exondeanalysis1-1.png"'
> >>> execution failed with error code 4
> >>>
> >>> Details at
> >>> http://docbuilder.bioconductor.org:8080/job/recountWorkflow/label=
> winbuilder1/9/console.
> >>> I originally thought that it was related to the figure paths, which is
> >>> why I added this knitr code:
> >>>
> >>> knitr::opts_chunk$set(fig.path = "")
> >>>
> >>> But that didn't resolve the issue. I get these warnings only with
> >>> BiocStyle::html_document2 and not with BiocStyle::html_document
> >>>
> >>> (http://docbuilder.bioconductor.org:8080/job/recountWorkflow/label=
> winbuilder1/7/console
> >>> using v0.99.28).
> >>>
> >>> Ultimately, the warnings might not matter. Though I don't see them on
> >>> the build reports for other workflows (cytofWorkflow, rnaseqGene).
> >>>
> >>> The Windows builds fail (with BiocStyle::html_document2 or
> >>> BiocStyle::html_document) with error messages like this:
> >>>
> >>> pandoc.exe: Error running filter pandoc-citeproc Filter returned error
> >>> status 1073807366 Warning: running command
> >>> '"C:/Progra~2/Pandoc/pandoc" +RTS -K512m -RTS recount-workflow.utf8.md
> >>> --to html --from
> >>> markdown+autolink_bare_uris+ascii_identifiers+tex_math_
> single_backslash
> >>> --output recount-workflow.html --smart --email-obfuscation none
> >>> --self-contained --standalone --section-divs --table-of-contents
> >>> --toc-depth 3 --template
> >>> "C:\Windows\TEMP\RtmpchKz3E/BiocStyle/template.html" --no-highlight
> >>> --variable highlightjs=1 --number-sections --css
> >>> "C:\PROGRA~1\R\R-34~1.0\library\BIOCST~1\RESOUR~1\html\BIOCON~2.CSS"
> >>> --variable "theme:bootstrap" --include-in-header
> >>> "C:\Windows\TEMP\RtmpchKz3E\rmarkdown-str3ec7c88cea.html" --mathjax
> >>> --variable
> >>> "mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?
> config=TeX-AMS-MML_HTMLorMML"
> >>> --bibliography recount-workflow.bib --filter pandoc-citeproc' had
> >>> status 83 Error: processing vignette 'recount-workflow.Rmd' failed
> >>> with diagnostics: pandoc document conversion failed with error 83
> >>> Execution halted
> >>>
> >>> (from
> >>> http://docbuilder.bioconductor.org:8080/job/recountWorkflow/label=
> winbuilder1/9/console)
> >>>
> >>>
> >>> Googling the error pointed me towards having weird symbols on the .bib
> >>> file. So I removed some accents and the like, but I still get this
> >>> error. I am using a csl file for the bibliography and like I said,
> >>> this works with the SPB whose last build report was
> >>>
> >>> http://bioconductor.org/spb_reports/recountWorkflow_
> buildreport_20170807114418.html
> >>> (v0.99.18). There's not much different between that version and
> >>> 0.99.30 as you can see at
> >>> https://github.com/LieberInstitute/recountWorkflow/commits/master **.
> >>>
> >>> The Linux machine has pandoc 1.19.2.1 installed
> >>>
> >>> (http://bioconductor.org/help/workflows/recountWorkflow/#
> session-information)
> >>> and I guess that the Windows one has the same version. But maybe that
> >>> could be the issue. BiocStyle 2.5.15 is installed in the Linux machine
> >>> too (Bioconductor/BiocStyle@2a1ba75) which is newer than the latest
> >>> bioc-release (2.4.1), but again, I assume that the Windows machine has
> >>> the same version.
> >>>
> >>>
> >>>
> >>> Anyhow, I haven't been able to fix these issues and was wondering if
> >>> anyone else had ideas that could resolve them. Regardless, I'm happy
> >>> that I got http://bioconductor.org/help/workflows/recountWorkflow/ up
> >>> and looking good ^^. It's just the links to the Mac/Windows
> >>> binaries...
> >>>
> >>>
> >>> Thank you,
> >>> Leo
> >>>
> >>>
> >>>
> >>> ** I've been pushing changes via svn, I know that workflows are not
> >>> part of the git transition. I just keep everything in sync manually
> >>> with the GitHub repo.
> >>>
> >>>
> >>> Leonardo Collado Torres, Ph. D., Data Scientist
> >>> Lieber Institute for Brain Development
> >>> 855 N Wolfe St, Suite 300
> >>> Baltimore, MD 21205
> >>> Website: http://lcolladotor.github.io
> >>>
> >>> _______________________________________________
> >>> Bioc-devel@r-project.org mailing list
> >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>
> >>
> >
>
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