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.morgan at roswellpark.org>:
On 10/20/2017 03:43 AM, Paolo Martini wrote:
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.
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?
This email message may contain legally privileged and/or confidential
information. If you are not the intended recipient(s), or the employee
or
agent responsible for the delivery of this message to the intended
recipient(s), you are hereby notified that any disclosure, copying,
distribution, or use of this email message is prohibited. If you have
received this message in error, please notify the sender immediately by
e-mail and delete this email message from your computer. Thank you.
--
Herv? Pag?s
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