[Bioc-devel] msPurity build fail on Mac OS X (morelia)
Thomas Lawson
thomas.nigel.lawson at gmail.com
Wed Sep 21 17:42:20 CEST 2016
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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>>
>>
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