Hi BioC team, In all the mzR troubles, it slipped through that RMassBank had a build error of it's own presumably caused by an update to MSnbase - for some reason we never received the email with the build error reports?! We have discovered the error now, very late, and are onto finding out the cause to fix it but it is not straightforward. Now that it is the day of the deadline to pass build without error, are we able to have a little leeway if needed? It's taken us the whole day to get the right binaries to actually have a chance to start fixing... Can someone also check or explain why we no longer receive the emails reporting errors to us? Thanks, Emma (on behalf of the others)
[Bioc-devel] RMassBank build error
4 messages · Schymanski, Emma, Obenchain, Valerie, Laurent Gatto +1 more
Hi Emma, Yes, there is leeway for working on the package. Thank you for actively trying to fix it! Unfortunately the notification emails stopped (broke) at some point this dev cycle - we plan to reinstate them after the release on the new build machines. Thanks for your patience. Valerie
On 10/07/2016 09:03 AM, Schymanski, Emma wrote:
Hi BioC team, In all the mzR troubles, it slipped through that RMassBank had a build error of it's own presumably caused by an update to MSnbase - for some reason we never received the email with the build error reports?! We have discovered the error now, very late, and are onto finding out the cause to fix it but it is not straightforward. Now that it is the day of the deadline to pass build without error, are we able to have a little leeway if needed? It's taken us the whole day to get the right binaries to actually have a chance to start fixing... Can someone also check or explain why we no longer receive the emails reporting errors to us? Thanks, Emma (on behalf of the others)
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
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.
Dear Emma, The error is very strange indeed, and I hope Martin can help us out here. With the latest RMassBank and MSnbase, I get
new("RmbSpectrum2")
Error in initialize(value, ...) :
'initialize' method returned an object of class ?Spectrum2? instead of
the required class ?RmbSpectrum2?
which reproduces the error.
The RmbSpectrum2 class is defined in a standard way
.RmbSpectrum2 <- setClass("RmbSpectrum2",
representation = representation(
satellite="logical",
low="logical",
rawOK ="logical",
good = "logical",
mzCalc = "numeric",
formula = "character",
dbe = "numeric",
formulaCount = "integer",
dppm = "numeric",
dppmBest = "numeric",
ok = "logical",
info = "list"
),
contains=c("Spectrum2"),
prototype = prototype(
satellite = logical(),
low = logical(),
rawOK = logical(),
good = logical(),
mzCalc = numeric(),
formula = character(),
dbe = numeric(),
formulaCount = integer(),
dppm = numeric(),
dppmBest = numeric(),
ok = logical(),
info = list(),
new("Versioned", versions=c(classVersion("Spectrum2"),
RmbSpectrum2 = "0.1.0"))
))
and
new("Spectrum2")
Object of class "Spectrum2"
Precursor: NA
Retention time: :
Charge: NA
MSn level: 2
Peaks count: 0
Total ion count: 0
works.
The MSnbase maintainers have had a bit of a struggle with spurious and
stange failures in the recent past (see [1]). This ans a whole new
backend in the package have led to the following initialize method, that
constructs the class directly in C
setMethod("initialize",
"Spectrum2",
function(.Object, msLevel = 2L, peaksCount = length(mz),
rt = numeric(), acquisitionNum = NA_integer_,
scanIndex = integer(), tic = 0L, mz = numeric(),
intensity = numeric(), fromFile = numeric(),
centroided = NA, smoothed = NA,
polarity = NA_integer_, merged = 1,
precScanNum = NA_integer_, precursorMz = NA,
precursorIntensity = NA, precursorCharge = NA_integer_,
collisionEnergy = NA) {
.Object <- Spectrum2_mz_sorted(msLevel, peaksCount, rt,
acquisitionNum, scanIndex,
tic, mz, intensity, fromFile,
centroided, smoothed, polarity,
merged, precScanNum, precursorMz,
precursorIntensity, precursorCharge,
collisionEnergy)
if (validObject(.Object))
.Object
})
Why is calling new("RmbSpectrum2") direclty returning an Spectrum2
object? Is this due to us not calling callNextMethod?
Laurent
[1] https://github.com/lgatto/MSnbase/issues/138
On 7 October 2016 17:02, Schymanski, Emma wrote:
Hi BioC team, In all the mzR troubles, it slipped through that RMassBank had a build error of it's own presumably caused by an update to MSnbase - for some reason we never received the email with the build error reports?! We have discovered the error now, very late, and are onto finding out the cause to fix it but it is not straightforward. Now that it is the day of the deadline to pass build without error, are we able to have a little leeway if needed? It's taken us the whole day to get the right binaries to actually have a chance to start fixing... Can someone also check or explain why we no longer receive the emails reporting errors to us? Thanks, Emma (on behalf of the others)
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Laurent Gatto | @lgatt0 http://cpu.sysbiol.cam.ac.uk/ http://lgatto.github.io/
On 10/07/2016 01:52 PM, Laurent Gatto wrote:
Dear Emma, The error is very strange indeed, and I hope Martin can help us out here.
I did look at this a little but not completely, and it seems like you've
come up with another solution? So I'll stop.
also for the intermittent error you mention, I skimmed the issue and saw
the problem with the reference class finalizer. Roughly my understanding
of what happens is
env = new.env()
env$f = function(...) message("done")
reg.finalizer(env, env$f)
rm(env); gc()
The garbage collector runs, marking env and other objects as available
for re-use. Once the garbage collector is finished (not just collecting
env, but all objects), any finalizers that are now eligible for
evaluation are run. So there is a chance that the environment itself has
been re-used by the time the finalizer runs, leading to intermittent errors.
This makes finalizers on reference classes unreliable.
Martin
With the latest RMassBank and MSnbase, I get
new("RmbSpectrum2")
Error in initialize(value, ...) :
'initialize' method returned an object of class ?Spectrum2? instead of
the required class ?RmbSpectrum2?
which reproduces the error.
The RmbSpectrum2 class is defined in a standard way
.RmbSpectrum2 <- setClass("RmbSpectrum2",
representation = representation(
satellite="logical",
low="logical",
rawOK ="logical",
good = "logical",
mzCalc = "numeric",
formula = "character",
dbe = "numeric",
formulaCount = "integer",
dppm = "numeric",
dppmBest = "numeric",
ok = "logical",
info = "list"
),
contains=c("Spectrum2"),
prototype = prototype(
satellite = logical(),
low = logical(),
rawOK = logical(),
good = logical(),
mzCalc = numeric(),
formula = character(),
dbe = numeric(),
formulaCount = integer(),
dppm = numeric(),
dppmBest = numeric(),
ok = logical(),
info = list(),
new("Versioned", versions=c(classVersion("Spectrum2"),
RmbSpectrum2 = "0.1.0"))
))
and
new("Spectrum2")
Object of class "Spectrum2"
Precursor: NA
Retention time: :
Charge: NA
MSn level: 2
Peaks count: 0
Total ion count: 0
works.
The MSnbase maintainers have had a bit of a struggle with spurious and
stange failures in the recent past (see [1]). This ans a whole new
backend in the package have led to the following initialize method, that
constructs the class directly in C
setMethod("initialize",
"Spectrum2",
function(.Object, msLevel = 2L, peaksCount = length(mz),
rt = numeric(), acquisitionNum = NA_integer_,
scanIndex = integer(), tic = 0L, mz = numeric(),
intensity = numeric(), fromFile = numeric(),
centroided = NA, smoothed = NA,
polarity = NA_integer_, merged = 1,
precScanNum = NA_integer_, precursorMz = NA,
precursorIntensity = NA, precursorCharge = NA_integer_,
collisionEnergy = NA) {
.Object <- Spectrum2_mz_sorted(msLevel, peaksCount, rt,
acquisitionNum, scanIndex,
tic, mz, intensity, fromFile,
centroided, smoothed, polarity,
merged, precScanNum, precursorMz,
precursorIntensity, precursorCharge,
collisionEnergy)
if (validObject(.Object))
.Object
})
Why is calling new("RmbSpectrum2") direclty returning an Spectrum2
object? Is this due to us not calling callNextMethod?
Laurent
[1] https://github.com/lgatto/MSnbase/issues/138
On 7 October 2016 17:02, Schymanski, Emma wrote:
Hi BioC team, In all the mzR troubles, it slipped through that RMassBank had a build error of it's own presumably caused by an update to MSnbase - for some reason we never received the email with the build error reports?! We have discovered the error now, very late, and are onto finding out the cause to fix it but it is not straightforward. Now that it is the day of the deadline to pass build without error, are we able to have a little leeway if needed? It's taken us the whole day to get the right binaries to actually have a chance to start fixing... Can someone also check or explain why we no longer receive the emails reporting errors to us? Thanks, Emma (on behalf of the others)
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
This email message may contain legally privileged and/or...{{dropped:2}}