Dear all,
I maintain the DEGraph and NCIgraph packages.
They are now fixed, my apologies for the inconvenience.
Best,
Laurent
2017-10-20 17:38 GMT+02:00 Hervé Pagès <hpa...@fredhutch.org>:
> Hi Paolo,
>
> FYI 3 days ago I contacted Gabriele Sale (maintainer of graphite
> and co-author of clipper) about this. See below.
>
> Cheers,
> H.
>
> -------------------------------------------------------------------
>
> Hi Gabriele,
>
> A recent update to the graphite package introduced the following
> change:
>
> library(graphite)
> kegg <- pathways("hsapiens", "kegg")
> graph <- convertIdentifiers(kegg[["Chronic myeloid leukemia"]],
> "entrez")
> graph <- pathwayGraph(graph)
> genes <- nodes(graph)
> head(genes)
> # [1] "ENTREZID:10000" "ENTREZID:1019" "ENTREZID:1021"
> # [4] "ENTREZID:1026" "ENTREZID:1029" "ENTREZID:1147"
>
> This is with version 1.23.4 of the package. With version
> 1.23.3, the same commands gave:
>
> head(genes)
> # [1] "10000" "1019" "1021" "1026" "1029" "1147"
>
> Was this change intended?
>
> Note that this change breaks the clipper package for which you are
> a co-author:
>
> https://bioconductor.org/checkResults/3.6/bioc-LATEST/clipper/
>
> Also please note that the DEGraph package is currently broken
> because it depends on NCIgraph which itself depends on RCytoscape
> which is currently broken and deprecated. Unfortunately this breaks
> the graphite vignette (which seems to use DEGraph):
>
> https://bioconductor.org/checkResults/3.6/bioc-LATEST/graphite/
>
> The DEGraph and NCIgraph authors have been contacted and are aware
> of the situation but have not been able to fix their package yet.
> If they cannot fix it in time for the upcoming BioC 3.6 release,
> their package will be considered as candidate for deprecation in
> Bioc 3.7. So at this point I would strongly suggest that you remove
> graphite's dependency on DEGraph.
>
> Please address these issues at your earliest convenience.
>
> The next Bioconductor release is coming soon (scheduled for end
> of October) and all Bioconductor packages are expected to be
> fixed before Tuesday October 24.
>
> See https://bioconductor.org/developers/release-schedule/ for
> our release schedule.
>
> Don't hesitate to ask on the bioc-devel mailing list if you have
> any questions or concerns about this.
>
> Thanks for your contribution to Bioconductor!
>
> Regards,
> H.
>
>
> On 10/20/2017 02:15 AM, Paolo Martini wrote:
>
>> Thanks a lot.
>> Yesterday I was unable to get the error because the graphite I downloaded
>> was not the latest version (it had a build failure).
>>
>> I'll fix clipper asap.
>>
>> Thanks again.
>>
>> Paolo
>>
>> 2017-10-20 10:12 GMT+02:00 Martin Morgan <martin.mor...@roswellpark.org>:
>>
>> On 10/20/2017 03:43 AM, Paolo Martini wrote:
>>>
>>> Dear all,
>>>>
>>>> I am the clipper package maintainer.
>>>> According to the "Build/check report" for BioC 3.6,
>>>> the clipper package has an error while compiling the vignette.
>>>>
>>>> I try to reproduce the error in my computer using the devel version but
>>>> the
>>>> R CMD check and installation goes smoothly.
>>>>
>>>>
>>> I verified that I'm using devel and my packages are current
>>>
>>> $ R
>>>
>>>> R.version.string # 3.4.2
>>>> BiocInstaller::isDevel() # TRUE
>>>> BiocInstaller::biocValid() # TRUE
>>>>
>>>
>>> I checked out a fresh copy of clipper, into a temporary directory
>>>
>>> $ git clone https://urldefense.proofpoint.com/v2/url?u=https-3A__git.bio
>>> conductor.org_packages_clipper&d=DwICAg&c=eRAMFD45gAfqt84VtB
>>> cfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=fDgotR2
>>> rO-xwDUi1RGfMv9bHkBXP5PMyu5zJNd5SzU8&s=YUUYFTvB1PyiJzzi_eBAU
>>> eOeAjO5VX88g1KVOohJoO0&e=
>>>
>>>
>>> then installed it
>>>
>>> $ R CMD INSTALL clipper
>>>
>>> I then extracted the R source code of the vignette
>>>
>>> $ cd clipper/vignettes
>>> $ R CMD Stangle clipper.Rnw # could have used knitr::purl() for Rmd
>>>
>>> and tried to run the vignette code
>>>
>>> $ R -f clipper.R
>>>
>>> It fails as on the build system
>>>
>>> pathwayAnalysis <- pathQ(exp, classes, graph, nperm=100, alphaV=0.05,
>>>>
>>> b=100)
>>> Error in getExpression(exprs(expr), classes) : Gene names not specified.
>>> Calls: pathQ ... getExpression -> getExpression -> getExpression ->
>>> getExpression
>>> Execution halted
>>>
>>> OK, reproducible without any additional stuff like devtools or RStudio
>>> getting in the way. Time to debug. I started R in my favorite IDE, and
>>> tried to source the vignette
>>>
>>> $ source("clipper.R", echo=TRUE, max=Inf)
>>>
>>> it fails in the same way. I looked for the error, and tried to reproduce
>>> it in a simpler fashion, guessing a bit at what the failing code was
>>> trying
>>> to do ('expr' in the traceback() being the function argument 'exp')
>>>
>>> pathwayAnalysis <- pathQ(exp, classes, graph, nperm=100, alphaV=0.05,
>>>>
>>> b=100)
>>> Error in getExpression(exprs(expr), classes) : Gene names not specified.
>>>
>>>> traceback()
>>>>
>>> 10: stop("Gene names not specified.")
>>> 9: getExpression(exprs(expr), classes)
>>> 8: getExpression(exprs(expr), classes)
>>> 7: getExpression(expr, classes)
>>> 6: getExpression(expr, classes)
>>> 5: pathQ(exp, classes, graph, nperm = 100, alphaV = 0.05, b = 100) at
>>> clipper.R#95
>>> 4: eval(ei, envir)
>>> 3: eval(ei, envir)
>>> 2: withVisible(eval(ei, envir))
>>> 1: source("clipper.R", echo = TRUE, max = Inf)
>>>
>>>> clipper:::getExpression(exprs(exp), classes)
>>>>
>>> Error in clipper:::getExpression(exprs(exp), classes) :
>>> Gene names not specified.
>>>
>>> I found that clipper:::getExpression is and S4 generic, with a likely
>>> method, so set the debugger and tried again
>>>
>>> clipper:::getExpression
>>>>
>>> standardGeneric for "getExpression" defined from package "clipper"
>>>
>>> function (expr, classes)
>>> standardGeneric("getExpression")
>>> <environment: 0x11061920>
>>> Methods may be defined for arguments: expr, classes
>>> Use showMethods("getExpression") for currently available ones.
>>>
>>>> showMethods(clipper:::getExpression)
>>>>
>>> Function: getExpression (package clipper)
>>> expr="ExpressionSet", classes="numeric"
>>> expr="matrix", classes="numeric"
>>>
>>> debug(clipper:::getExpression, signature=c("matrix", "numeric"))
>>>> clipper:::getExpression(exprs(exp), classes)
>>>>
>>> Tracing clipper:::getExpression(exprs(exp), classes) step 2
>>> Called from: eval(expr, p)
>>> Browse[1]> n
>>> debug: if (is.null(rownames(expr))) stop("Gene names not specified.")
>>> Browse[2]> rownames(expr)
>>> NULL
>>> Browse[2]> Q
>>>
>>>>
>>>>
>>> and back at the top level
>>>
>>> rownames(exprs(exp))
>>>>
>>> NULL
>>>
>>> hmm, this looks weird
>>>
>>> dim(exp)
>>>>
>>> Features Samples
>>> 0 79
>>>
>>> In code chunk 3 you'd got the genes from graphite, and
>>>
>>> head(genes)
>>>>
>>> [1] "ENTREZID:10000" "ENTREZID:1019" "ENTREZID:1021"
>>> [4] "ENTREZID:1026" "ENTREZID:1029" "ENTREZID:1147"
>>>
>>> in code chunk 10 you'd calculated the intersection of these genes with
>>> the
>>> row.names of the sample expression set
>>>
>>> intersect(genes, row.names(exprs(all)))
>>>>
>>> character(0)
>>>
>>> and this is because the rownames are in a different format
>>>
>>> head(row.names(exprs(all)))
>>>>
>>> [1] "5595" "7075" "1557" "643" "643" "1843"
>>>
>>> I guess this is because graphite or one of it's dependencies has changed,
>>> accidentally or otherwise, the format of the identifiers returned in
>>> chunk
>>> 3. Likely the reason that you were not able to reproduce this is because
>>> you were using an out-of-date version of graphite (isDevel() and
>>> biocValid() would have diagnosed this). I don't know whether the
>>> resolution
>>> is a bug fix in graphite, or a fix to your own vignette code; it is
>>> always
>>> worth pushing the resolution as close to the source of the problem as
>>> possible, so if it's a change in graphite then engage the
>>> maintainer("graphite") in your investigation.
>>>
>>> Martin
>>>
>>>
>>> Anyone has suggestions on how to debug this?
>>>>
>>>>
>>>>
>>>>
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>>>
>>
>>
>>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpa...@fredhutch.org
> Phone: (206) 667-5791
> Fax: (206) 667-1319
>
>
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>
--
Laurent Jacob
Laboratoire de Biométrie et Biologie Évolutive
CNRS/Université Lyon 1
https://lbbe.univ-lyon1.fr/-Jacob-Laurent-.html
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