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().
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. 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