Hi Laurent, Are you testing with valgrind?
The 'Mismatched free() / delete / delete []' only becomes apparent when using valgrind. i.e. I have a document called mzR_test.R that contains the following code: #----------------------------------------------------------- ------------------------------------------------------------ ------------------------------------------------------------ library(mzR) msmsPths <- list.files(system.file("extdata", "lcms", "mzML", package="msPurityData"), full.names = TRUE, pattern = "MSMS") mr <- mzR::openMSfile(msmsPths[1]) #----------------------------------------------------------- ------------------------------------------------------------ ------------------------------------------------------------ And then I run R -d valgrind -f mzR_test.R Regards, Tom On Thu, Sep 22, 2016 at 3:48 PM, Laurent Gatto <lg...@cam.ac.uk> wrote: > > On 22 September 2016 15:22, Kasper Daniel Hansen wrote: > > > Martin seemed to have fixed the original error, but recovered another > one. > > > > Do we have a reproducible example with the other error (and did Martin's > > fix get into mzR) and do we know which platforms it fails on? > > I haven't updated mzR since this conversation started, so I haven't > incorporated any of Martin's patches. > > I can't see anything in hedgehog's svn log - I have opened an issue on > the mzR github repo in the meantime. > > Also, I can source my local msPurity/doc/msPurity-vignette.R file and it > runs fine. > > Laurent > > [1] https://github.com/sneumann/mzR/issues/52 > > > Best, > > Kasper > > > > On Thu, Sep 22, 2016 at 10:10 AM, Laurent Gatto <lg...@cam.ac.uk> wrote: > > > >> > >> 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 > >> > > > -- > Laurent Gatto | @lgatt0 > http://cpu.sysbiol.cam.ac.uk/ > http://lgatto.github.io/ > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel