[Bioc-devel] msPurity build fail on Mac OS X (morelia)

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/msPurity/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_memcheck-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-amd64-linux)
==20822==    by 0x38084064: ??? (in /usr/lib/valgrind/memcheck-amd64-linux)
...
sched status:
   running_tid=1

Thread 1: status = VgTs_Runnable (lwpid 20822)
==20822==    at 0x25A294E0: ??? (in 
/lib/x86_64-linux-gnu/libcrypto.so.1.0.0)
==20822==    by 0x25A086FF: EC_POINT_mul (in 
/lib/x86_64-linux-gnu/libcrypto.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/libcrypto.so.1.0.0)
==20822==    by 0x25AC637F: ??? (in 
/lib/x86_64-linux-gnu/libcrypto.so.1.0.0)
==20822==    by 0x25AC5A33: ??? (in 
/lib/x86_64-linux-gnu/libcrypto.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...{{dropped:2}}