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.mor...@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@backend$getPeakList(x) >> 3: FUN(X[[i]], ...) >> 4: lapply(X = X, FUN = FUN, ...) >> 5: sapply(scans, function(x) object@backend$getPeakList(x)$peaks, >> simplify = FALSE) >> 6: sapply(scans, function(x) object@backend$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@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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
