On 22 September 2016 14:12, Thomas Lawson wrote: > 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().
I can't reproduce this: > library(mzR) Loading required package: Rcpp > msmsPths <- list.files(system.file("extdata", "lcms", "mzML", > package="msPurityData"), full.names = TRUE, pattern = "MSMS") > msmsPths [1] "/home/lg390/R/x86_64-pc-linux-gnu-library/3.3/msPurityData/extdata/lcms/mzML/LCMSMS_1.mzML" [2] "/home/lg390/R/x86_64-pc-linux-gnu-library/3.3/msPurityData/extdata/lcms/mzML/LCMSMS_2.mzML" > tmp <- replicate(1000, mr <- mzR::openMSfile(msmsPths[1])) > all(sapply(tmp, validObject)) [1] TRUE > sessionInfo() R version 3.3.1 Patched (2016-08-02 r71022) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 14.04.5 LTS locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] mzR_2.7.4 Rcpp_0.12.7 loaded via a namespace (and not attached): [1] ProtGenerics_1.5.1 tools_3.3.1 parallel_3.3.1 [4] Biobase_2.33.3 codetools_0.2-14 BiocGenerics_0.19.2 What are your mzR and Rcpp versions? Also, in your code, you will need to explicitly close(mz) after opening a connection to the raw data file. Otherwise, you might end up getting 'Error: failed opening file: Too many open files'. (This is not the reason for your error). Laurent > 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 < > kasperdanielhan...@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 <dtene...@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@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)$peaks, >>> simplify = FALSE) >>> 7: .local(object, ...) >>> 8: mzR::peaks(mr) >>> 9: mzR::peaks(mr) >>> 10: getscans(filepth) >>> 11: assessPuritySingle(filepth = pa@fileList[[i]], mostIntense = >>> mostIntense, nearest = nearest, offsets = offsets, plotP = plotP, >>> plotdir = plotdir, interpol = interpol, iwNorm = iwNorm, iwNormFun = >>> iwNormFun, ilim = ilim) >>> 12: eval(expr, envir, enclos) >>> 13: eval(xpr, envir = envir) >>> 14: doTryCatch(return(expr), name, parentenv, handler) >>> 15: tryCatchOne(expr, names, parentenv, handlers[[1L]]) >>> 16: tryCatchList(expr, classes, parentenv, handlers) >>> 17: tryCatch(eval(xpr, envir = envir), error = function(e) e) >>> 18: doTryCatch(return(expr), name, parentenv, handler) >>> 19: tryCatchOne(expr, names, parentenv, handlers[[1L]]) >>> 20: tryCatchList(expr, classes, parentenv, handlers) >>> 21: tryCatch({ repeat { args <- nextElem(it) if >>> (obj$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@fileList), .packages = >>> "mzR"), assessPuritySingle(filepth = pa@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.law...@gmail.com> >>> > To: "Martin Morgan" <martin.mor...@roswellpark.org> >>> > Cc: "bioc-devel" <Bioc-devel@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.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/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@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 >>> >>> _______________________________________________ >>> Bioc-devel@r-project.org mailing list >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>> >> >> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Laurent Gatto | @lgatt0 http://cpu.sysbiol.cam.ac.uk/ http://lgatto.github.io/ _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel