[Bioc-devel] Unable to reproduce error!
Hervé Pagès
hpages at fredhutch.org
Sat Oct 21 21:52:19 CEST 2017
Great! Thanks Paolo. H.
On 10/21/2017 09:33 AM, Paolo Martini wrote:
> I see,
> thanks a lot!
>
> I changed clipper package. The next release should work!
>
> Thanks again.
>
>
>
> 2017-10-20 17:38 GMT+02:00 Hervé Pagès <hpages at fredhutch.org
> <mailto:hpages at 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/
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_checkResults_3.6_bioc-2DLATEST_clipper_&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=9G9q_TvInbHlLdtcxyW7QVmYuSOLceAdambgjncU7_8&s=KxHFqKG35j7Iav7rt5HEx0OhaACt0wG3rGnfFxb6fSE&e=>
>
> 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/
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_checkResults_3.6_bioc-2DLATEST_graphite_&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=9G9q_TvInbHlLdtcxyW7QVmYuSOLceAdambgjncU7_8&s=vgNDkZkS_yo7Dms8yEhAS7qJRpLsHtyDJMQNKo6or8g&e=>
>
> 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/
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_developers_release-2Dschedule_&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=9G9q_TvInbHlLdtcxyW7QVmYuSOLceAdambgjncU7_8&s=Mk5j3POHIWhZ50I20mkbISWT3HbCqzP1X2jtEEJ7Xg4&e=>
> 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.morgan at roswellpark.org
> <mailto:martin.morgan at 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.bioconductor.org_packages_clipper&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=fDgotR2rO-xwDUi1RGfMv9bHkBXP5PMyu5zJNd5SzU8&s=YUUYFTvB1PyiJzzi_eBAUeOeAjO5VX88g1KVOohJoO0&e=
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__git.bioconductor.org_packages_clipper&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=fDgotR2rO-xwDUi1RGfMv9bHkBXP5PMyu5zJNd5SzU8&s=YUUYFTvB1PyiJzzi_eBAUeOeAjO5VX88g1KVOohJoO0&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: hpages at fredhutch.org <mailto:hpages at fredhutch.org>
> Phone: (206) 667-5791 <tel:%28206%29%20667-5791>
> Fax: (206) 667-1319 <tel:%28206%29%20667-1319>
>
>
>
>
> --
> *******************************
> Paolo Martini
> c/o Lab Romualdi
> via U. Bassi 58/b
> 35121 Padova, Italy
> Tel: 049 8276319
> Fax: 049 8276159
> e-mail: paolo.martini at unipd.it <mailto:paolo.martini at unipd.it>
> http://romualdi.bio.unipd.it/
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__romualdi.bio.unipd.it_&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=9G9q_TvInbHlLdtcxyW7QVmYuSOLceAdambgjncU7_8&s=5VEllY9RTKhE62TDpNt0fQkQo5LejDkaSNgIKE-QM8k&e=>
> *******************************
--
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: hpages at fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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