[Bioc-devel] msPurity build fail on Mac OS X (morelia)
Thomas Lawson
thomas.nigel.lawson at gmail.com
Thu Sep 22 16:59:42 CEST 2016
Hi Laurent,
Are you testing with valgrind?
The 'Mismatched free() / delete / delete []' only becomes apparent when
using valgrind. 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 <lg390 at 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 <lg390 at 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 <
> >> > kasperdanielhansen at 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 <
> dtenenba at 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 at backend$getPeakList(x)
> >> >>> 3: FUN(X[[i]], ...)
> >> >>> 4: lapply(X = X, FUN = FUN, ...)
> >> >>> 5: sapply(scans, function(x) object at backend$getPeakList(x)$peaks,
> >> >>> simplify = FALSE)
> >> >>> 6: sapply(scans, function(x) object at backend$getPeakList(x)$peaks,
> >> >>> simplify = FALSE)
> >> >>> 7: .local(object, ...)
> >> >>> 8: mzR::peaks(mr)
> >> >>> 9: mzR::peaks(mr)
> >> >>> 10: getscans(filepth)
> >> >>> 11: assessPuritySingle(filepth = pa at fileList[[i]], mostIntense =
> >> >>> mostIntense, nearest = nearest, offsets = offsets, plotP =
> plotP,
> >> >>> plotdir = plotdir, interpol = interpol, iwNorm = iwNorm,
> iwNormFun
> >> =
> >> >>> iwNormFun, ilim = ilim)
> >> >>> 12: eval(expr, envir, enclos)
> >> >>> 13: eval(xpr, envir = envir)
> >> >>> 14: doTryCatch(return(expr), name, parentenv, handler)
> >> >>> 15: tryCatchOne(expr, names, parentenv, handlers[[1L]])
> >> >>> 16: tryCatchList(expr, classes, parentenv, handlers)
> >> >>> 17: tryCatch(eval(xpr, envir = envir), error = function(e) e)
> >> >>> 18: doTryCatch(return(expr), name, parentenv, handler)
> >> >>> 19: tryCatchOne(expr, names, parentenv, handlers[[1L]])
> >> >>> 20: tryCatchList(expr, classes, parentenv, handlers)
> >> >>> 21: tryCatch({ repeat { args <- nextElem(it) if
> >> >>> (obj$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 at fileList), .packages
> =
> >> >>> "mzR"), assessPuritySingle(filepth = pa at 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.lawson at gmail.com>
> >> >>> > To: "Martin Morgan" <martin.morgan at roswellpark.org>
> >> >>> > Cc: "bioc-devel" <Bioc-devel at 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.morgan at 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 at backend$getPeakList(x)
> >> >>> >>> 3: FUN(X[[i]], ...)
> >> >>> >>> 4: lapply(X = X, FUN = FUN, ...)
> >> >>> >>> 5: sapply(scans, function(x) object at backend$getPeakList(x)$
> peaks,
> >> >>> >>> simplify = FALSE)
> >> >>> >>> 6: sapply(scans, function(x) object at 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 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.
> >> >>> >>
> >> >>> >
> >> >>> > [[alternative HTML version deleted]]
> >> >>> >
> >> >>> > _______________________________________________
> >> >>> > Bioc-devel at r-project.org mailing list
> >> >>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >> >>>
> >> >>> _______________________________________________
> >> >>> Bioc-devel at r-project.org mailing list
> >> >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >> >>>
> >> >>
> >> >>
> >> >
> >> > [[alternative HTML version deleted]]
> >> >
> >> > _______________________________________________
> >> > 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/
> >>
> >> _______________________________________________
> >> 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/
>
[[alternative HTML version deleted]]
More information about the Bioc-devel
mailing list