On 22 September 2016 15:59, Thomas Lawson wrote:
> Hi Laurent,
>
> Are you testing with valgrind?
>
> The 'Mismatched free() / delete / delete []' only becomes apparent when
> using valgrind.
Oh, I had missed that, thanks. Will apply the path asap, then.
Laurent
> i.e. I have a document called mzR_test.R that contains the following
> code:
>
> #-----------------------------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> library(mzR)
> msmsPths <- list.files(system.file("extdata", "lcms", "mzML",
> package="msPurityData"), full.names = TRUE, pattern = "MSMS")
> mr <- mzR::openMSfile(msmsPths[1])
> #-----------------------------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
>
> And then I run
>
> R -d valgrind -f mzR_test.R
>
>
> Regards,
> Tom
>
>
> On Thu, Sep 22, 2016 at 3:48 PM, Laurent Gatto <lg...@cam.ac.uk> wrote:
>
>>
>> On 22 September 2016 15:22, Kasper Daniel Hansen wrote:
>>
>> > Martin seemed to have fixed the original error, but recovered another
>> one.
>> >
>> > Do we have a reproducible example with the other error (and did Martin's
>> > fix get into mzR) and do we know which platforms it fails on?
>>
>> I haven't updated mzR since this conversation started, so I haven't
>> incorporated any of Martin's patches.
>>
>> I can't see anything in hedgehog's svn log - I have opened an issue on
>> the mzR github repo in the meantime.
>>
>> Also, I can source my local msPurity/doc/msPurity-vignette.R file and it
>> runs fine.
>>
>> Laurent
>>
>> [1] https://github.com/sneumann/mzR/issues/52
>>
>> > Best,
>> > Kasper
>> >
>> > On Thu, Sep 22, 2016 at 10:10 AM, Laurent Gatto <lg...@cam.ac.uk> wrote:
>> >
>> >>
>> >> On 22 September 2016 14:12, Thomas Lawson wrote:
>> >>
>> >> > Hi All,
>> >> >
>> >> > Thanks for the help with this. I have been using valgrind to try and
>> >> > pinpoint in my code the problem and it seems to be from
>> >> mzR::openMSfile().
>> >>
>> >> I can't reproduce this:
>> >>
>> >> > library(mzR)
>> >> Loading required package: Rcpp
>> >> > msmsPths <- list.files(system.file("extdata", "lcms", "mzML",
>> >> package="msPurityData"), full.names = TRUE, pattern = "MSMS")
>> >> > msmsPths
>> >> [1] "/home/lg390/R/x86_64-pc-linux-gnu-library/3.3/
>> >> msPurityData/extdata/lcms/mzML/LCMSMS_1.mzML"
>> >> [2] "/home/lg390/R/x86_64-pc-linux-gnu-library/3.3/
>> >> msPurityData/extdata/lcms/mzML/LCMSMS_2.mzML"
>> >> > tmp <- replicate(1000, mr <- mzR::openMSfile(msmsPths[1]))
>> >> > all(sapply(tmp, validObject))
>> >> [1] TRUE
>> >> > sessionInfo()
>> >> R version 3.3.1 Patched (2016-08-02 r71022)
>> >> Platform: x86_64-pc-linux-gnu (64-bit)
>> >> Running under: Ubuntu 14.04.5 LTS
>> >>
>> >> locale:
>> >> [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
>> >> [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
>> >> [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
>> >> [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C
>> >> [9] LC_ADDRESS=C LC_TELEPHONE=C
>> >> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
>> >>
>> >> attached base packages:
>> >> [1] stats graphics grDevices utils datasets methods base
>> >>
>> >> other attached packages:
>> >> [1] mzR_2.7.4 Rcpp_0.12.7
>> >>
>> >> loaded via a namespace (and not attached):
>> >> [1] ProtGenerics_1.5.1 tools_3.3.1 parallel_3.3.1
>> >> [4] Biobase_2.33.3 codetools_0.2-14 BiocGenerics_0.19.2
>> >>
>> >> What are your mzR and Rcpp versions?
>> >>
>> >> Also, in your code, you will need to explicitly close(mz) after opening
>> >> a connection to the raw data file. Otherwise, you might end up getting
>> >> 'Error: failed opening file: Too many open files'. (This is not the
>> >> reason for your error).
>> >>
>> >> Laurent
>> >>
>> >> > A simplified bit of code just using mzR I think will give the same
>> >> results,
>> >> > see below:
>> >> >
>> >> > #-----------------------------------------------------------
>> >> > ------------------------------------------------------------
>> >> > ------------------------------------------------------------
>> >> > library(mzR)
>> >> > msmsPths <- list.files(system.file("extdata", "lcms", "mzML",
>> >> > package="msPurityData"), full.names = TRUE, pattern = "MSMS")
>> >> > mr <- mzR::openMSfile(msmsPths[1])
>> >> > #-----------------------------------------------------------
>> >> > ------------------------------------------------------------
>> >> > ------------------------------------------------------------
>> >> >
>> >> > This gives the familiar message
>> >> >> mr <- mzR::openMSfile(msmsPths[1])
>> >> > ==38138== Mismatched free() / delete / delete []
>> >> > ==38138== at 0x4C2EDEB: free (in /usr/lib/valgrind/vgpreload_
>> >> > memcheck-amd64-linux.so)
>> >> > ..
>> >> >
>> >> > However, I can prevent the "Mismatched free() / delete / delete []"
>> >> > message by forcing the backend to use the "pwiz" libraries (i think).
>> >> e.g.
>> >> >
>> >> > #-----------------------------------------------------------
>> >> > ------------------------------------------------------------
>> >> > ------------------------------------------------------------
>> >> > mr <- mzR::openMSfile(msmsPths[1], backend="pwiz")
>> >> > #-----------------------------------------------------------
>> >> > ------------------------------------------------------------
>> >> > ------------------------------------------------------------
>> >> >
>> >> > I have updated to code so that a user can choose the backend for mzR
>> >> with a
>> >> > default option of "pwiz" and pushed the changes to svn.
>> >> >
>> >> > Hopefully this will fix the problem on morelia, although I notice that
>> >> the
>> >> > server is down at the moment, when will the next build be?
>> >> >
>> >> > Thanks for your help,
>> >> > Tom
>> >> >
>> >> > PS: Martin: I have removed the msPurity-vignette.R and
>> >> > msPurity-vignette.html files from the vignette folder. Is this
>> correct?
>> >> >
>> >> >
>> >> >
>> >> >
>> >> >
>> >> > On Wed, Sep 21, 2016 at 7:38 PM, Kasper Daniel Hansen <
>> >> > kasperdanielhan...@gmail.com> wrote:
>> >> >
>> >> >> So this seems like a bug in mzR which is the main backend / parser
>> for
>> >> >> proteomics and metabolomics data. Someone should try to fix this.
>> >> >>
>> >> >> Unfortunately, mzR depends on several pieces of software which are
>> >> written
>> >> >> by other people, but bundled with the package. Martin's traceback
>> >> suggests
>> >> >> that some of these files are (partially?) encrypted. This might be
>> >> hard to
>> >> >> address.
>> >> >>
>> >> >> Best,
>> >> >> Kasper
>> >> >>
>> >> >> On Wed, Sep 21, 2016 at 12:43 PM, Dan Tenenbaum <
>> dtene...@fredhutch.org
>> >> >
>> >> >> wrote:
>> >> >>
>> >> >>> One thing I notice is that the crash does not happen every time. I
>> have
>> >> >>> successfully built the package on morelia by hand with "R CMD
>> build".
>> >> >>>
>> >> >>> Similarly I can source the stangled vignette without a crash
>> sometimes.
>> >> >>> But when it does crash, this is what I see:
>> >> >>>
>> >> >>> > source("msPurity-vignette.R", echo=TRUE, max=Inf)
>> >> >>>
>> >> >>> > ## ------------------------------------------------------------
>> >> >>> ------------
>> >> >>> > library(msPurity)
>> >> >>> Loading required package: Rcpp
>> >> >>>
>> >> >>> > msmsPths <- list.files(system.file("extdata", "lcms", "mzML",
>> >> >>> package="msPurityData"), full.names = TRUE, pattern = "MSMS")
>> >> >>>
>> >> >>> > msPths <- list.files(system.file("extdata", "lcms", "mzML",
>> >> >>> package="msPurityData"), full.names = TRUE, pattern = "LCMS_")
>> >> >>>
>> >> >>> > ## ------------------------------------------------------------
>> >> >>> ------------
>> >> >>> > pa <- purityA(msmsPths)
>> >> >>>
>> >> >>> *** caught segfault ***
>> >> >>> address 0x29800000297, cause 'memory not mapped'
>> >> >>>
>> >> >>> Traceback:
>> >> >>> 1: .External(list(name = "CppMethod__invoke_notvoid", address =
>> >> >>> <pointer: 0x7fb56861cb10>, dll = list(name = "Rcpp", path =
>> >> >>> "/Library/Frameworks/R.framework/Versions/3.3/
>> >> Resources/library/Rcpp/libs/Rcpp.so",
>> >> >>> dynamicLookup = TRUE, handle = <pointer: 0x7fb568606180>,
>> >> >>> info = <pointer: 0x1078f8000>), numParameters = -1L), <pointer:
>> >> >>> 0x7fb5686ae9c0>, <pointer: 0x7fb56868cf80>, .pointer, ...)
>> >> >>> 2: object@backend$getPeakList(x)
>> >> >>> 3: FUN(X[[i]], ...)
>> >> >>> 4: lapply(X = X, FUN = FUN, ...)
>> >> >>> 5: sapply(scans, function(x) object@backend$getPeakList(x)$peaks,
>> >> >>> simplify = FALSE)
>> >> >>> 6: sapply(scans, function(x) object@backend$getPeakList(x)$peaks,
>> >> >>> simplify = FALSE)
>> >> >>> 7: .local(object, ...)
>> >> >>> 8: mzR::peaks(mr)
>> >> >>> 9: mzR::peaks(mr)
>> >> >>> 10: getscans(filepth)
>> >> >>> 11: assessPuritySingle(filepth = pa@fileList[[i]], mostIntense =
>> >> >>> mostIntense, nearest = nearest, offsets = offsets, plotP =
>> plotP,
>> >> >>> plotdir = plotdir, interpol = interpol, iwNorm = iwNorm,
>> iwNormFun
>> >> =
>> >> >>> iwNormFun, ilim = ilim)
>> >> >>> 12: eval(expr, envir, enclos)
>> >> >>> 13: eval(xpr, envir = envir)
>> >> >>> 14: doTryCatch(return(expr), name, parentenv, handler)
>> >> >>> 15: tryCatchOne(expr, names, parentenv, handlers[[1L]])
>> >> >>> 16: tryCatchList(expr, classes, parentenv, handlers)
>> >> >>> 17: tryCatch(eval(xpr, envir = envir), error = function(e) e)
>> >> >>> 18: doTryCatch(return(expr), name, parentenv, handler)
>> >> >>> 19: tryCatchOne(expr, names, parentenv, handlers[[1L]])
>> >> >>> 20: tryCatchList(expr, classes, parentenv, handlers)
>> >> >>> 21: tryCatch({ repeat { args <- nextElem(it) if
>> >> >>> (obj$verbose) { cat(sprintf("evaluation # %d:\n", i))
>> >> >>> print(args) } for (a in names(args)) assign(a,
>> >> args[[a]], pos
>> >> >>> = envir, inherits = FALSE) r <-
>> tryCatch(eval(xpr,
>> >> envir
>> >> >>> = envir), error = function(e) e) if (obj$verbose) {
>> >> >>> cat("result of evaluating expression:\n") print(r)
>> }
>> >> >>> tryCatch(accumulator(list(r), i), error = function(e) {
>> >> >>> cat("error calling combine function:\n") print(e)
>> >> >>> NULL }) i <- i + 1 }}, error = function(e) { if
>> >> >>> (!identical(conditionMessage(e), "StopIteration"))
>> >> >>> stop(simpleError(conditionMessage(e), expr))})
>> >> >>> 22: e$fun(obj, substitute(ex), parent.frame(), e$data)
>> >> >>> 23: operator(foreach::foreach(i = 1:length(pa@fileList), .packages
>> =
>> >> >>> "mzR"), assessPuritySingle(filepth = pa@fileList[[i]],
>> >> mostIntense =
>> >> >>> mostIntense, nearest = nearest, offsets = offsets, plotP =
>> >> plotP,
>> >> >>> plotdir = plotdir, interpol = interpol, iwNorm = iwNorm,
>> >> >>> iwNormFun = iwNormFun, ilim = ilim))
>> >> >>> 24: purityA(msmsPths)
>> >> >>> 25: eval(expr, envir, enclos)
>> >> >>> 26: eval(ei, envir)
>> >> >>> 27: withVisible(eval(ei, envir))
>> >> >>> 28: source("msPurity-vignette.R", echo = TRUE, max = Inf)
>> >> >>>
>> >> >>> Possible actions:
>> >> >>> 1: abort (with core dump, if enabled)
>> >> >>> 2: normal R exit
>> >> >>> 3: exit R without saving workspace
>> >> >>> 4: exit R saving workspace
>> >> >>> Selection:
>> >> >>>
>> >> >>> > sessionInfo()
>> >> >>> R version 3.3.1 (2016-06-21)
>> >> >>> Platform: x86_64-apple-darwin13.4.0 (64-bit)
>> >> >>> Running under: OS X 10.9.5 (Mavericks)
>> >> >>>
>> >> >>> locale:
>> >> >>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>> >> >>>
>> >> >>> attached base packages:
>> >> >>> [1] parallel stats graphics grDevices utils datasets
>> methods
>> >> >>> [8] base
>> >> >>>
>> >> >>> other attached packages:
>> >> >>> [1] xcms_1.49.6 Biobase_2.33.3 ProtGenerics_1.5.1
>> >> >>> [4] BiocGenerics_0.19.2 mzR_2.7.4 msPurity_0.99.6
>> >> >>> [7] Rcpp_0.12.7
>> >> >>>
>> >> >>> loaded via a namespace (and not attached):
>> >> >>> [1] sapa_2.0-2 magrittr_1.5 ifultools_2.0-4
>> >> >>> [4] MASS_7.3-45 splines_3.3.1
>> BiocParallel_1.7.8
>> >> >>> [7] lattice_0.20-34 foreach_1.4.3 splus2R_1.2-2
>> >> >>> [10] stringr_1.1.0 fastcluster_1.1.21 plyr_1.8.4
>> >> >>> [13] tools_3.3.1 grid_3.3.1 snow_0.4-1
>> >> >>> [16] iterators_1.0.8 survival_2.39-5 multtest_2.29.0
>> >> >>> [19] doSNOW_1.0.14 Matrix_1.2-7.1
>> RColorBrewer_1.1-2
>> >> >>> [22] reshape2_1.4.1 S4Vectors_0.11.16 codetools_0.2-14
>> >> >>> [25] MassSpecWavelet_1.39.0 stringi_1.1.1 compiler_3.3.1
>> >> >>> [28] stats4_3.3.1 RANN_2.5
>> >> >>>
>> >> >>> ----- Original Message -----
>> >> >>> > From: "Thomas Lawson" <thomas.nigel.law...@gmail.com>
>> >> >>> > To: "Martin Morgan" <martin.mor...@roswellpark.org>
>> >> >>> > Cc: "bioc-devel" <Bioc-devel@r-project.org>
>> >> >>> > Sent: Wednesday, September 21, 2016 8:42:20 AM
>> >> >>> > Subject: Re: [Bioc-devel] msPurity build fail on Mac OS X
>> (morelia)
>> >> >>>
>> >> >>> > Thanks for reply. Some of those errors are a bit cryptic for me
>> also.
>> >> >>> >
>> >> >>> > I have not heard of the valgrind functionality before in R. I will
>> >> test
>> >> >>> a
>> >> >>> > few things out with valgrind and hopefully I can pinpoint the
>> error a
>> >> >>> bit
>> >> >>> > more.
>> >> >>> >
>> >> >>> > Thanks again.
>> >> >>> >
>> >> >>> > Tom
>> >> >>> >
>> >> >>> > On Wed, Sep 21, 2016 at 12:50 PM, Martin Morgan <
>> >> >>> > martin.mor...@roswellpark.org> wrote:
>> >> >>> >
>> >> >>> >> On 09/20/2016 05:18 AM, Thomas Lawson wrote:
>> >> >>> >>
>> >> >>> >>> Hi BioConductor community,
>> >> >>> >>>
>> >> >>> >>> My package (msPurity) is passing the build on the Linux (*zin1*)
>> >> and
>> >> >>> >>> Windows servers (*moscato1*) but failing on the Mac OS X server
>> >> >>> >>> (*morelia*).
>> >> >>> >>> Also I cannot seem to replicate the failure either on a local
>> >> >>> installation
>> >> >>> >>> of Mac OS X (el captain) or with Travis CI.
>> >> >>> >>>
>> >> >>> >>> I should probably note that for Travis CI I did have to install
>> the
>> >> >>> >>> msPurityData dependency directly (without Bioconductor). See
>> line
>> >> 10
>> >> >>> >>> https://raw.githubusercontent.com/Viant-Metabolomics/msPurit
>> >> >>> >>> y/master/.travis.yml
>> >> >>> >>>
>> >> >>> >>> The error I think is coming from a function I have that uses the
>> >> >>> >>> mzR::peaks() function but I am struggling to see why I am
>> getting
>> >> the
>> >> >>> >>> error.
>> >> >>> >>>
>> >> >>> >>> Any help or suggestions would be really appreciated.
>> >> >>> >>>
>> >> >>> >>
>> >> >>> >> Hi Tom --
>> >> >>> >>
>> >> >>> >> This might be fun!
>> >> >>> >>
>> >> >>> >> You can see from
>> >> >>> >>
>> >> >>> >>
>> >> >>> >> http://bioconductor.org/checkResults/3.4/bioc-LATEST/morelia
>> >> >>> >> -R-instpkgs.html
>> >> >>> >>
>> >> >>> >> (linked from http://bioconductor.org/checkR
>> >> >>> esults/3.4/bioc-LATEST/index.
>> >> >>> >> html '1633' installed packages) that in fact msPurityData is
>> >> installed.
>> >> >>> >> Also, segfaults are rarely the result of missing packages.
>> Instead,
>> >> it
>> >> >>> is
>> >> >>> >> likely due to errors in C code of one sort or another. On my
>> linux,
>> >> I
>> >> >>> made
>> >> >>> >> sure I was using the 'devel' version of Bioconductor, and that
>> all
>> >> of
>> >> >>> my
>> >> >>> >> packages were up-to-date via biocLite(). I then checked out
>> msPurity
>> >> >>> from
>> >> >>> >> svn, changed into the msPurity directory and installed it
>> >> >>> >>
>> >> >>> >> R CMD INSTALL .
>> >> >>> >>
>> >> >>> >> then I changed to the vignettes directory, Stangled the source
>> code
>> >> >>> >>
>> >> >>> >> cd vignettes
>> >> >>> >> R CMD Stangle msPurity-vignette.Rmd
>> >> >>> >>
>> >> >>> >> (by the way, the products of build the package / vignette,
>> >> >>> >> msPurity-vignette.R should not be in svn).
>> >> >>> >>
>> >> >>> >> I then ran the vignette under valgrind
>> >> >>> >>
>> >> >>> >> msPurity/vignettes$ R -d valgrind -f msPurity-vignette.R
>> >> >>> >>
>> >> >>> >> leading to
>> >> >>> >>
>> >> >>> >> > pa <- purityA(msmsPths)
>> >> >>> >> ==19611== Mismatched free() / delete / delete []
>> >> >>> >> ==19611== at 0x4C2EDEB: free (in
>> /usr/lib/valgrind/vgpreload_me
>> >> >>> >> mcheck-amd64-linux.so)
>> >> >>> >> ==19611== by 0x11296DA5: cRamp::cRamp(char const*, bool)
>> >> >>> (cramp.cpp:98)
>> >> >>> >> ==19611== by 0x1129FC87: RcppRamp::open(char const*, bool)
>> >> >>> >> (RcppRamp.cpp:23)
>> >> >>> >> ==19611== by 0x112B49C4: Rcpp::CppMethod2<RcppRamp, void, char
>> >> >>> const*,
>> >> >>> >> bool>::operator()(RcppRamp*, SEXPREC**)
>> >> (Module_generated_CppMethod.h:
>> >> >>> 215)
>> >> >>> >> ==19611== by 0x112B0FBF: Rcpp::class_<RcppRamp>::invoke
>> >> >>> _void(SEXPREC*,
>> >> >>> >> SEXPREC*, SEXPREC**, int) (class.h:212)
>> >> >>> >> ==19611== by 0xED73CA0: CppMethod__invoke_void(SEXPREC*)
>> >> >>> >> (Module.cpp:200)
>> >> >>> >> ==19611== by 0x4F0DFD0: do_External (dotcode.c:548)
>> >> >>> >> ==19611== by 0x4F47F9E: Rf_eval (eval.c:713)
>> >> >>> >> ==19611== by 0x4F4A6B7: do_begin (eval.c:1807)
>> >> >>> >> ==19611== by 0x4F47D90: Rf_eval (eval.c:685)
>> >> >>> >> ==19611== by 0x4F4964C: Rf_applyClosure (eval.c:1135)
>> >> >>> >> ==19611== by 0x4F47B6C: Rf_eval (eval.c:732)
>> >> >>> >> ==19611== Address 0x1b8a4220 is 0 bytes inside a block of size
>> 400
>> >> >>> alloc'd
>> >> >>> >> ==19611== at 0x4C2E0EF: operator new(unsigned long) (in
>> >> >>> >> /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
>> >> >>> >> ==19611== by 0x11296949: cRamp::do_ramp(long, eWhatToRead)
>> >> >>> >> (cramp.cpp:215)
>> >> >>> >> ==19611== by 0x11296D9D: cRamp::cRamp(char const*, bool)
>> >> >>> (cramp.cpp:97)
>> >> >>> >> ==19611== by 0x1129FC87: RcppRamp::open(char const*, bool)
>> >> >>> >> (RcppRamp.cpp:23)
>> >> >>> >> ==19611== by 0x112B49C4: Rcpp::CppMethod2<RcppRamp, void, char
>> >> >>> const*,
>> >> >>> >> bool>::operator()(RcppRamp*, SEXPREC**)
>> >> (Module_generated_CppMethod.h:
>> >> >>> 215)
>> >> >>> >> ==19611== by 0x112B0FBF: Rcpp::class_<RcppRamp>::invoke
>> >> >>> _void(SEXPREC*,
>> >> >>> >> SEXPREC*, SEXPREC**, int) (class.h:212)
>> >> >>> >> ==19611== by 0xED73CA0: CppMethod__invoke_void(SEXPREC*)
>> >> >>> >> (Module.cpp:200)
>> >> >>> >> ==19611== by 0x4F0DFD0: do_External (dotcode.c:548)
>> >> >>> >> ==19611== by 0x4F47F9E: Rf_eval (eval.c:713)
>> >> >>> >> ==19611== by 0x4F4A6B7: do_begin (eval.c:1807)
>> >> >>> >> ==19611== by 0x4F47D90: Rf_eval (eval.c:685)
>> >> >>> >> ==19611== by 0x4F4964C: Rf_applyClosure (eval.c:1135)
>> >> >>> >> ==19611==
>> >> >>> >>
>> >> >>> >> which from http://valgrind.org/docs/manual/mc-manual.html#mc-
>> manual
>> >> .
>> >> >>> rudefn
>> >> >>> >> means that memory allocated with new[] is being deallocated with
>> >> free
>> >> >>> >> (rather than delete / delete[]
>> >> >>> >>
>> >> >>> >> Remarkably, this change to mzR removes this particular valgind
>> >> problem
>> >> >>> >>
>> >> >>> >> Index: src/cramp.cpp
>> >> >>> >> ============================================================
>> =======
>> >> >>> >> --- src/cramp.cpp (revision 121179)
>> >> >>> >> +++ src/cramp.cpp (working copy)
>> >> >>> >> @@ -95,7 +95,7 @@
>> >> >>> >> // if (m_runInfo->m_data.scanCount < 0) { //
>> >> undeclared
>> >> >>> scan
>> >> >>> >> count
>> >> >>> >> // this will provoke reading of index, which sets scan
>> >> count
>> >> >>> >> rampScanInfo* tmp = getScanHeaderInfo ( 1 );
>> >> >>> >> - free(tmp);
>> >> >>> >> + delete(tmp);
>> >> >>> >> // }
>> >> >>> >> // END HENRY
>> >> >>> >> }
>> >> >>> >>
>> >> >>> >> but doesn't get us out of the woods -- valgrind now complains
>> >> >>> >>
>> >> >>> >> >
>> >> >>> >> > xset <- xcms::xcmsSet(msmsPths)
>> >> >>> >>
>> >> >>> >> vex: the `impossible' happened:
>> >> >>> >> isZeroU
>> >> >>> >> vex storage: T total 3029292920 bytes allocated
>> >> >>> >> vex storage: P total 640 bytes allocated
>> >> >>> >>
>> >> >>> >> valgrind: the 'impossible' happened:
>> >> >>> >> LibVEX called failure_exit().
>> >> >>> >>
>> >> >>> >> host stacktrace:
>> >> >>> >> ==20822== at 0x38083F48: ??? (in
>> /usr/lib/valgrind/memcheck-amd
>> >> >>> >> 64-linux)
>> >> >>> >> ==20822== by 0x38084064: ??? (in
>> /usr/lib/valgrind/memcheck-amd
>> >> >>> >> 64-linux)
>> >> >>> >> ...
>> >> >>> >> sched status:
>> >> >>> >> running_tid=1
>> >> >>> >>
>> >> >>> >> Thread 1: status = VgTs_Runnable (lwpid 20822)
>> >> >>> >> ==20822== at 0x25A294E0: ??? (in
>> /lib/x86_64-linux-gnu/libcrypt
>> >> >>> >> o.so.1.0.0)
>> >> >>> >> ==20822== by 0x25A086FF: EC_POINT_mul (in
>> >> >>> /lib/x86_64-linux-gnu/libcrypt
>> >> >>> >> o.so.1.0.0)
>> >> >>> >> ==20822== by 0xB67335F: ???
>> >> >>> >> ==20822== by 0xCF7F76F: ???
>> >> >>> >> ==20822== by 0x5EB461A205EFD6FF: ???
>> >> >>> >> ==20822== by 0xC221D2F: ???
>> >> >>> >> ==20822== by 0x25A10E47: EC_KEY_check_key (in
>> >> >>> >> /lib/x86_64-linux-gnu/libcrypto.so.1.0.0)
>> >> >>> >> ==20822== by 0x25A11260: EC_KEY_set_public_key_affine_
>> >> coordinates
>> >> >>> (in
>> >> >>> >> /lib/x86_64-linux-gnu/libcrypto.so.1.0.0)
>> >> >>> >> ==20822== by 0x25ACA882: ??? (in
>> /lib/x86_64-linux-gnu/libcrypt
>> >> >>> >> o.so.1.0.0)
>> >> >>> >> ==20822== by 0x25AC637F: ??? (in
>> /lib/x86_64-linux-gnu/libcrypt
>> >> >>> >> o.so.1.0.0)
>> >> >>> >> ==20822== by 0x25AC5A33: ??? (in
>> /lib/x86_64-linux-gnu/libcrypt
>> >> >>> >> o.so.1.0.0)
>> >> >>> >> ==20822== by 0x2599970C: FIPS_mode_set (in
>> >> >>> >> /lib/x86_64-linux-gnu/libcrypto.so.1.0.0)
>> >> >>> >> ==20822== by 0x25995F89: OPENSSL_init_library (in
>> >> >>> >> /lib/x86_64-linux-gnu/libcrypto.so.1.0.0)
>> >> >>> >> ==20822== by 0x40104E9: call_init.part.0 (dl-init.c:72)
>> >> >>> >> ==20822== by 0x40105FA: call_init (dl-init.c:30)
>> >> >>> >> ==20822== by 0x40105FA: _dl_init (dl-init.c:120)
>> >> >>> >> ==20822== by 0x4015711: dl_open_worker (dl-open.c:575)
>> >> >>> >> ==20822== by 0x4010393: _dl_catch_error (dl-error.c:187)
>> >> >>> >> ==20822== by 0x4014BD8: _dl_open (dl-open.c:660)
>> >> >>> >> ==20822== by 0x6C80F08: dlopen_doit (dlopen.c:66)
>> >> >>> >> ==20822== by 0x4010393: _dl_catch_error (dl-error.c:187)
>> >> >>> >> ==20822== by 0x6C81570: _dlerror_run (dlerror.c:163)
>> >> >>> >> ==20822== by 0x6C80FA0: dlopen@@GLIBC_2.2.5 (dlopen.c:87)
>> >> >>> >> ==20822== by 0x4EA93F0: AddDLL (Rdynload.c:537)
>> >> >>> >> ==20822== by 0x4EA996B: R_moduleCdynload (Rdynload.c:917)
>> >> >>> >> ==20822== by 0x4F68979: internet_Init (internet.c:79)
>> >> >>> >> ==20822== by 0x4F68AF2: R_newsock (internet.c:115)
>> >> >>> >> ==20822== by 0x4EF39C0: do_sockconn (connections.c:3196)
>> >> >>> >> ==20822== by 0x4F3B587: bcEval (eval.c:5658)
>> >> >>> >> ...
>> >> >>> >>
>> >> >>> >> which frankly is too cryptic for me -- it seems perhaps like a
>> call
>> >> >>> >> opening a socket connection is going wrong, but I really don't
>> know
>> >> if
>> >> >>> that
>> >> >>> >> is cause or effect, or even relevant to your problem.
>> >> >>> >>
>> >> >>> >> The bottom line is that this is likely a problem in the C code of
>> >> one
>> >> >>> of
>> >> >>> >> the packages that you are using.
>> >> >>> >>
>> >> >>> >> Do you or a colleague have the expertise to work through this?
>> >> >>> >>
>> >> >>> >> Martin
>> >> >>> >>
>> >> >>> >>
>> >> >>> >>> Kind regards,
>> >> >>> >>> Tom
>> >> >>> >>>
>> >> >>> >>>
>> >> >>> >>> https://github.com/Bioconductor-mirror/msPurity
>> >> >>> >>> http://bioconductor.org/checkResults/devel/bioc-LATEST/
>> >> >>> >>> msPurity/morelia-buildsrc.html
>> >> >>> >>> https://bioconductor.org/packages/devel/bioc/html/msPurity.html
>> >> >>> >>>
>> >> >>> >>> Travis Mac build report:
>> >> >>> >>> https://travis-ci.org/Viant-Metabolomics/msPurity/jobs/
>> 159938167
>> >> >>> >>>
>> >> >>> >>>
>> >> >>> >>> ############################################################
>> >> >>> >>> ##################
>> >> >>> >>> ############################################################
>> >> >>> >>> ##################
>> >> >>> >>> ###
>> >> >>> >>> ### Running command:
>> >> >>> >>> ###
>> >> >>> >>> ### /Library/Frameworks/R.framework/Versions/Current/
>> Resources/
>> >> >>> bin/R
>> >> >>> >>> CMD build --keep-empty-dirs --no-resave-data msPurity
>> >> >>> >>> ###
>> >> >>> >>> ############################################################
>> >> >>> >>> ##################
>> >> >>> >>> ############################################################
>> >> >>> >>> ##################
>> >> >>> >>>
>> >> >>> >>>
>> >> >>> >>> * checking for file ‘msPurity/DESCRIPTION’ ... OK
>> >> >>> >>> * preparing ‘msPurity’:
>> >> >>> >>> * checking DESCRIPTION meta-information ... OK
>> >> >>> >>> * installing the package to build vignettes
>> >> >>> >>> * creating vignettes ...sh: line 1: 62889 Segmentation fault: 11
>> >> >>> >>> '/Library/Frameworks/R.framework/Resources/bin/Rscript'
>> --vanilla
>> >> >>> >>> --default-packages= -e "tools::buildVignettes(dir = '.', tangle
>> =
>> >> >>> >>> TRUE)" > '/tmp/RtmpCXdH7K/xshellf59d5efb2aea' 2>&1
>> >> >>> >>> ERROR
>> >> >>> >>>
>> >> >>> >>> *** caught segfault ***
>> >> >>> >>> address 0x0, cause 'memory not mapped'
>> >> >>> >>>
>> >> >>> >>> Traceback:
>> >> >>> >>> 1: .External(list(name = "CppMethod__invoke_notvoid", address =
>> >> >>> >>> <pointer: 0x7fb83b714be0>, dll = list(name = "Rcpp", path =
>> >> >>> >>> "/Library/Frameworks/R.framework/Versions/3.3/Resources/
>> >> >>> >>> library/Rcpp/libs/Rcpp.so",
>> >> >>> >>> dynamicLookup = TRUE, handle = <pointer:
>> 0x7fb83b70ed10>,
>> >> >>> >>> info = <pointer: 0x1052f30c0>), numParameters = -1L),
>> >> <pointer:
>> >> >>> >>> 0x7fb83b590710>, <pointer: 0x7fb83b5af740>, .pointer, ...)
>> >> >>> >>> 2: object@backend$getPeakList(x)
>> >> >>> >>> 3: FUN(X[[i]], ...)
>> >> >>> >>> 4: lapply(X = X, FUN = FUN, ...)
>> >> >>> >>> 5: sapply(scans, function(x) object@backend$getPeakList(x)$
>> peaks,
>> >> >>> >>> simplify = FALSE)
>> >> >>> >>> 6: sapply(scans, function(x) object@backend$getPeakList(x)$
>> peaks,
>> >> >>> >>> simplify = FALSE)
>> >> >>> >>> 7: .local(object, ...)
>> >> >>> >>> 8: mzR::peaks(mr)
>> >> >>> >>> 9: mzR::peaks(mr)
>> >> >>> >>> 10: .fun(piece, ...)
>> >> >>> >>> 11: (function (i) { piece <- pieces[[i]] if (.inform) {
>> >> >>> >>> res <- try(.fun(piece, ...)) if (inherits(res,
>> >> "try-error")) {
>> >> >>> >>> piece <- paste(utils::capture.output(print(piece)),
>> >> >>> >>> collapse = "\n") stop("with piece ", i, ":
>> \n",
>> >> >>> >>> piece, call. = FALSE) } } else { res <-
>> >> >>> >>> .fun(piece, ...) } progress$step() res})(2L)
>> >> >>> >>> 12: .Call(loop_apply_, as.integer(n), f, env)
>> >> >>> >>> 13: loop_apply(n, do.ply)
>> >> >>> >>> 14: llply(.data = pieces, .fun = .fun, ..., .progress =
>> .progress,
>> >> >>> >>> .inform = .inform, .parallel = .parallel, .paropts = .paropts)
>> >> >>> >>> 15: plyr::alply(files, 1, function(x) { mr <-
>> mzR::openMSfile(x)
>> >> >>> >>> scan_peaks <- mzR::peaks(mr) return(scan_peaks)})
>> >> >>> >>> 16: getscans(filepths)
>> >> >>> >>> 17: purityX(xset, offsets = c(0.5, 0.5), xgroups = c(1, 2))
>> >> >>> >>> 18: eval(expr, envir, enclos)
>> >> >>> >>> 19: eval(expr, envir, enclos)
>> >> >>> >>> 20: withVisible(eval(expr, envir, enclos))
>> >> >>> >>> 21: withCallingHandlers(withVisible(eval(expr, envir, enclos)),
>> >> >>> >>> warning = wHandler, error = eHandler, message = mHandler)
>> >> >>> >>> 22: handle(ev <- withCallingHandlers(withVisible(eval(expr,
>> envir,
>> >> >>> >>> enclos)), warning = wHandler, error = eHandler, message =
>> >> mHandler))
>> >> >>> >>> 23: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos =
>> >> >>> >>> enclos, debug = debug, last = i == length(out), use_try =
>> >> >>> >>> stop_on_error != 2L, keep_warning = keep_warning,
>> >> keep_message
>> >> >>> >>> = keep_message, output_handler = output_handler)
>> >> >>> >>> 24: evaluate(code, envir = env, new_device = FALSE,
>> keep_warning =
>> >> >>> >>> !isFALSE(options$warning), keep_message =
>> >> >>> >>> !isFALSE(options$message), stop_on_error = if (options$error &&
>> >> >>> >>> options$include) 0L else 2L, output_handler =
>> >> >>> >>> knit_handlers(options$render, options))
>> >> >>> >>> 25: in_dir(opts_knit$get("root.dir") %n% input_dir(),
>> >> evaluate(code,
>> >> >>> >>> envir = env, new_device = FALSE, keep_warning =
>> >> >>> >>> !isFALSE(options$warning), keep_message =
>> >> >>> >>> !isFALSE(options$message), stop_on_error = if (options$error &&
>> >> >>> >>> options$include) 0L else 2L, output_handler =
>> >> >>> >>> knit_handlers(options$render, options)))
>> >> >>> >>> 26: block_exec(params)
>> >> >>> >>> 27: call_block(x)
>> >> >>> >>> 28: process_group.block(group)
>> >> >>> >>> 29: process_group(group)
>> >> >>> >>> 30: withCallingHandlers(if (tangle) process_tangle(group) else
>> >> >>> >>> process_group(group), error = function(e) { setwd(wd)
>> >> >>> >>> cat(res, sep = "\n", file = output %n% "")
>> >> message("Quitting
>> >> >>> >>> from lines ", paste(current_lines(i), collapse =
>> "-"),
>> >> "
>> >> >>> >>> (", knit_concord$get("infile"), ") ") })
>> >> >>> >>> 31: process_file(text, output)
>> >> >>> >>> 32: knitr::knit(knit_input, knit_output, envir = envir, quiet =
>> >> quiet,
>> >> >>> >>> encoding = encoding)
>> >> >>> >>> 33: rmarkdown::render(file, encoding = encoding, quiet = quiet,
>> >> envir
>> >> >>> >>> = globalenv())
>> >> >>> >>> 34: vweave_rmarkdown(...)
>> >> >>> >>> 35: engine$weave(file, quiet = quiet, encoding = enc)
>> >> >>> >>> 36: doTryCatch(return(expr), name, parentenv, handler)
>> >> >>> >>> 37: tryCatchOne(expr, names, parentenv, handlers[[1L]])
>> >> >>> >>> 38: tryCatchList(expr, classes, parentenv, handlers)
>> >> >>> >>> 39: tryCatch({ engine$weave(file, quiet = quiet, encoding =
>> enc)
>> >> >>> >>> setwd(startdir) find_vignette_product(name, by = "weave",
>> >> engine =
>> >> >>> >>> engine)}, error = function(e) { stop(gettextf("processing
>> >> vignette
>> >> >>> >>> '%s' failed with diagnostics:\n%s", file,
>> >> >>> >>> conditionMessage(e)), domain = NA, call. = FALSE)})
>> >> >>> >>> 40: tools::buildVignettes(dir = ".", tangle = TRUE)
>> >> >>> >>> An irrecoverable exception occurred. R is aborting now ...
>> >> >>> >>>
>> >> >>> >>> [[alternative HTML version deleted]]
>> >> >>> >>>
>> >> >>> >>> _______________________________________________
>> >> >>> >>> Bioc-devel@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.
>> >> >>> >>
>> >> >>> >
>> >> >>> > [[alternative HTML version deleted]]
>> >> >>> >
>> >> >>> > _______________________________________________
>> >> >>> > Bioc-devel@r-project.org mailing list
>> >> >>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> >> >>>
>> >> >>> _______________________________________________
>> >> >>> Bioc-devel@r-project.org mailing list
>> >> >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> >> >>>
>> >> >>
>> >> >>
>> >> >
>> >> > [[alternative HTML version deleted]]
>> >> >
>> >> > _______________________________________________
>> >> > Bioc-devel@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/
>> >>
>> >> _______________________________________________
>> >> Bioc-devel@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/
>>
--
Laurent Gatto | @lgatt0
http://cpu.sysbiol.cam.ac.uk/
http://lgatto.github.io/
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