[Bioc-devel] msPurity build fail on Mac OS X (morelia)
Dan Tenenbaum
dtenenba at fredhutch.org
Wed Sep 21 18:43:06 CEST 2016
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/checkResults/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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>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>>
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