[Bioc-devel] Unable to reproduce error!

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>:

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=

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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