[Bioc-devel] msPurity build fail on Mac OS X (morelia)
Thomas Lawson
thomas.nigel.lawson at gmail.com
Thu Sep 22 15:12:39 CEST 2016
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().
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]]
>> >>>
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