[Bioc-devel] vignette problems
campos
campos at mpipz.mpg.de
Wed Apr 11 16:47:44 CEST 2018
Hi Martin,
when I run git status I get this:
On branch master
Your branch is up-to-date with 'origin/master'.
nothing to commit, working directory clean
shouldn't I see that my version in my machine is some commits behind?
$git remote -v
origin git at git.bioconductor.org:packages/STAN (fetch)
origin git at git.bioconductor.org:packages/STAN (push)
Thanks a lot,
Rafa
On 11.04.2018 16:43, Martin Morgan wrote:
>
>
> On 04/11/2018 09:58 AM, campos wrote:
>> Hi Martin,
>>
>> thank you very much for your time and effort!
>>
>> I pulled the branch to my computer updated the DESCRIPTION file and
>> pushed the changes. That should be enough right?
>
> actually I seemed to have messed up the git commit, but I fixed it
> from my end; you should git pull and not worry about pushing any
> further commits for the moment.
>
>>
>> Best,
>>
>> Rafa
>>
>> PS: If you ever stop by Cologne please let me know. I owe you a beer
>> or two!
>
> tasty!
>
> Martin
>
>>
>>
>> On 10.04.2018 23:44, Martin Morgan wrote:
>>> Hi --
>>>
>>> I'm not sure what you mean; the 'devel' builld report does not
>>> include mac (the build system experienced problems with disk space
>>> last night, so the build did not complete)
>>>
>>> https://bioconductor.org/checkResults/devel/bioc-LATEST/STAN/
>>>
>>> and STAN failed in Release
>>>
>>> https://bioconductor.org/checkResults/release/bioc-LATEST/STAN/
>>>
>>>
>>> HOWEVER, I spent some time with your package. First, I compiled it
>>> with compiler flages -Wall -pedantic, which makes the compiler quite
>>> sensitive. I did this by creating, on my Linux, a file
>>>
>>> $ cat ~/.R/Makevars
>>> CFLAGS = -g -O0 -Wall -pedantic
>>> CXXFLAGS = -g -O0 -Wall -pedantic
>>>
>>> and then installing the package from the source directory
>>>
>>> STAN master$ rm -f src/*o && R CMD INSTALL .
>>>
>>> There were a number of minor issues (unused variables, incorrect
>>> printf formatting [and use of printf() rather than Rprintf()]) as
>>> well as somewhat more substantial problems (virtual destructors for
>>> polymorphic base classes); a few problems remain, of the form
>>>
>>> RWrapper.cpp:950:5: warning: control reaches end of non-void
>>> function [-Wreturn-type]
>>> }
>>>
>>> where the problem is obvious -- no return value if parallel != 0 --
>>> but also innocuous, since it seems from inspection that in fact this
>>> function is always invoked with parallel == 0
>>>
>>> HMM* createHMM(int parallel, int K, InitialProbability*
>>> initProb, TransitionMatrix* transMat, EmissionFunction** myEmissions)
>>> {
>>> if(parallel == 0)
>>> {
>>> return new HMM(K, initProb, transMat, myEmissions);
>>> }
>>> }
>>>
>>> You should fix these problems, e.g., by removing the parallel
>>> argument from the function and body. After cleaning up as best I
>>> could, I install the package again and ran the vignette through
>>> valgrind
>>>
>>> STAN master$ R CMD INSTALL .
>>> ...
>>> STAN master$ cd vignettes
>>> STAN/vignettes master$ R CMD Stangle STAN-knitr.Rnw
>>> STAN/vignettes master$ R CMD Stangle STAN-knitr.Rnw
>>> STAN/vignettes master$ R -d valgrind -f STAN-knitr.R
>>>
>>> leading to an about mismatched new[] / delete[] -- memory allocated
>>> by 'new x[]' must be deleted with 'delete[]', but the package code
>>> had simply 'delete'.
>>>
>>> With these changes, the vignette builds without segfaulting or
>>> valgrind errors on my machine, and on the Mac builder; I did not
>>> check the full build and check of the package.
>>>
>>> The changes are summarized in the following commits:
>>>
>>> STAN master$ git log --oneline
>>> a719f42 version bump
>>> b8e2123 make destructors for polymorhpic base classes virtual
>>> 18ac6ba mismatch new[] / delete[]
>>> 985768b restore EmissionFactory::createEmissionFunctionMixed
>>> 8b749db provide return value for non-void functions
>>> 26ca36e update poor printf statements
>>> 0bb83ab clear 'unused variable' -Wall -pedantic warnings
>>> a3b7666 remove vignette product STAN-knitr.R
>>>
>>> You should pull these down to your local git repository, e.g., for
>>> me I have
>>>
>>> STAN master$ git remote -v
>>> origin git at git.bioconductor.org:packages/STAN (fetch)
>>> origin git at git.bioconductor.org:packages/STAN (push)
>>>
>>> So I would
>>>
>>> STAN master$ git pull origin master
>>>
>>> to incorporate the changes.
>>>
>>> It would be good to port these changes to the RELEASE_3_6 branch;
>>> remember to bump the version of the RELEASE_3_6 branch to 2.6.1.
>>>
>>> Unfortunately, I pushed the changes after tonight's builds started,
>>> so the effect of the changes will not be reported until Thursday
>>> mid-morning, Eastern time, if the build system does not have problems.
>>>
>>> Martin
>>>
>>> On 04/10/2018 02:14 PM, campos wrote:
>>>> Hi Martin,
>>>>
>>>> it seems like mac is ok now. What has changed??
>>>>
>>>> Thank you very much,
>>>>
>>>> Rafael
>>>>
>>>>
>>>> On 10.04.2018 11:33, Martin Morgan wrote:
>>>>>
>>>>>
>>>>> On 04/10/2018 05:27 AM, campos wrote:
>>>>>> Hi Martin,
>>>>>>
>>>>>> Thank you very much, I am a bit concerned about the option of:
>>>>>>
>>>>>>
>>>>>> Last Changed Date: 2018-04-05 09:37:37 -0400 (Thu, 05 Apr 2018)
>>>>>>
>>>>>> I did a change yesterday and push it, why isn't it visible?
>>>>>
>>>>> Notice that at the top of the build report it says
>>>>>
>>>>> This page was generated on 2018-04-09 09:50:05 -0400 (Mon, 09
>>>>> Apr 2018).
>>>>>
>>>>> Snapshot Date: 2018-04-08 16:45:28 -0400 (Sun, 08 Apr 2018)
>>>>>
>>>>> If you pushed after the snapshot date then your changes are not
>>>>> yet visible.
>>>>>
>>>>> Martin
>>>>>
>>>>>>
>>>>>> Best,
>>>>>>
>>>>>> Rafa
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> On 09.04.2018 16:44, Martin Morgan wrote:
>>>>>>> I'll try to provide you with a pull request addressing issues.
>>>>>>> Martin
>>>>>>>
>>>>>>> On 04/09/2018 08:42 AM, campos wrote:
>>>>>>>> Dear devel team,
>>>>>>>>
>>>>>>>> I am still puzzled with the problems with mac compiling. I am
>>>>>>>> really lost and have no idea how to continue or how to be able
>>>>>>>> to check about this problems with my linux machine in order to
>>>>>>>> fix it faster. Could you please help me with that??
>>>>>>>>
>>>>>>>> Best,
>>>>>>>>
>>>>>>>> Rafael
>>>>>>>>
>>>>>>>>
>>>>>>>> On 05.04.2018 14:29, Shepherd, Lori wrote:
>>>>>>>>>
>>>>>>>>> In order for changes to be propagated a version bump in the
>>>>>>>>> DESCRIPTION file is needed. Please bump the version in the
>>>>>>>>> DESCRIPTION file to 2.7.2.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Lori Shepherd
>>>>>>>>>
>>>>>>>>> Bioconductor Core Team
>>>>>>>>>
>>>>>>>>> Roswell Park Cancer Institute
>>>>>>>>>
>>>>>>>>> Department of Biostatistics & Bioinformatics
>>>>>>>>>
>>>>>>>>> Elm & Carlton Streets
>>>>>>>>>
>>>>>>>>> Buffalo, New York 14263
>>>>>>>>>
>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>
>>>>>>>>> *From:* Bioc-devel <bioc-devel-bounces at r-project.org> on
>>>>>>>>> behalf of campos <campos at mpipz.mpg.de>
>>>>>>>>> *Sent:* Thursday, April 5, 2018 7:45:57 AM
>>>>>>>>> *To:* Morgan, Martin; bioc-devel
>>>>>>>>> *Subject:* Re: [Bioc-devel] vignette problems
>>>>>>>>> Hey Martin,
>>>>>>>>>
>>>>>>>>> I pushed new changes since last friday but in
>>>>>>>>> https://bioconductor.org/checkResults/3.7/bioc-LATEST/STAN/
>>>>>>>>> says that
>>>>>>>>> the last change date was friday. Any idea what is the problem?
>>>>>>>>>
>>>>>>>>> I have tried to fix the problems with memory and all you told me.
>>>>>>>>>
>>>>>>>>> Best,
>>>>>>>>>
>>>>>>>>> Rafael
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On 03.04.2018 17:06, Martin Morgan wrote:
>>>>>>>>> > Please use 'reply all' so that the mailing list remains
>>>>>>>>> engaged.
>>>>>>>>> >
>>>>>>>>> > Check out the release schedule
>>>>>>>>> >
>>>>>>>>> > http://bioconductor.org/developers/release-schedule/
>>>>>>>>> >
>>>>>>>>> > in particular
>>>>>>>>> >
>>>>>>>>> > Wednesday April 25
>>>>>>>>> >
>>>>>>>>> > - Deadline for packages passing ‘‘R CMD build’’ and ‘‘R CMD
>>>>>>>>> check’’
>>>>>>>>> > without errors or warnings.
>>>>>>>>> >
>>>>>>>>> > so you still have time to get your package in order.
>>>>>>>>> >
>>>>>>>>> > Using the same techniques as before, I still see valgrind
>>>>>>>>> problems,
>>>>>>>>> > the first being
>>>>>>>>> >
>>>>>>>>> > > hmm_fitted_poilog = fitHMM(trainRegions, hmm_poilog,
>>>>>>>>> > sizeFactors=sizeFactors, maxIters=10)
>>>>>>>>> > ==24916== Invalid write of size 4
>>>>>>>>> > ==24916== at 0x4BA93FD7:
>>>>>>>>> > TransitionMatrix::updateAuxiliaries(double**, double***,
>>>>>>>>> double*,
>>>>>>>>> > int*, int, int**, int, double, int) (TransitionMatrix.cpp:292)
>>>>>>>>> > ==24916== by 0x4BA77934: HMM::updateSampleAux(double***,
>>>>>>>>> int*, int,
>>>>>>>>> > double**, double**, double**, double***, double*, int*,
>>>>>>>>> int*, int*,
>>>>>>>>> > int**, double***, SEXPREC*, SEXPREC*, int, double, int, int,
>>>>>>>>> int)
>>>>>>>>> > (HMM.cpp:771)
>>>>>>>>> > ==24916== by 0x4BA7896D:
>>>>>>>>> HMM::BaumWelch[abi:cxx11](double***, int*,
>>>>>>>>> > int, int, int**, int*, int*, int*, int, int, int**, double***,
>>>>>>>>> > SEXPREC*, SEXPREC*, int, double, double, int, int)
>>>>>>>>> (HMM.cpp:1076)
>>>>>>>>> > ==24916== by 0x4BA8FEFD: RHMMFit (RWrapper.cpp:1494)
>>>>>>>>> > ==24916== by 0x4F2992D: R_doDotCall (dotcode.c:692)
>>>>>>>>> > ==24916== by 0x4F339D5: do_dotcall (dotcode.c:1252)
>>>>>>>>> > ==24916== by 0x4F81BA6: bcEval (eval.c:6771)
>>>>>>>>> > ==24916== by 0x4F6E963: Rf_eval (eval.c:624)
>>>>>>>>> > ==24916== by 0x4F71188: R_execClosure (eval.c:1764)
>>>>>>>>> > ==24916== by 0x4F70E7C: Rf_applyClosure (eval.c:1692)
>>>>>>>>> > ==24916== by 0x4F6F18B: Rf_eval (eval.c:747)
>>>>>>>>> > ==24916== by 0x4F74B12: do_set (eval.c:2774)
>>>>>>>>> > ==24916== Address 0x2e73a294 is 4 bytes inside a block of
>>>>>>>>> size 5 alloc'd
>>>>>>>>> > ==24916== at 0x4C2DB8F: malloc (in
>>>>>>>>> > /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
>>>>>>>>> > ==24916== by 0x4BA93FA6:
>>>>>>>>> > TransitionMatrix::updateAuxiliaries(double**, double***,
>>>>>>>>> double*,
>>>>>>>>> > int*, int, int**, int, double, int) (TransitionMatrix.cpp:289)
>>>>>>>>> > ==24916== by 0x4BA77934: HMM::updateSampleAux(double***,
>>>>>>>>> int*, int,
>>>>>>>>> > double**, double**, double**, double***, double*, int*,
>>>>>>>>> int*, int*,
>>>>>>>>> > int**, double***, SEXPREC*, SEXPREC*, int, double, int, int,
>>>>>>>>> int)
>>>>>>>>> > (HMM.cpp:771)
>>>>>>>>> > ==24916== by 0x4BA7896D:
>>>>>>>>> HMM::BaumWelch[abi:cxx11](double***, int*,
>>>>>>>>> > int, int, int**, int*, int*, int*, int, int, int**, double***,
>>>>>>>>> > SEXPREC*, SEXPREC*, int, double, double, int, int)
>>>>>>>>> (HMM.cpp:1076)
>>>>>>>>> > ==24916== by 0x4BA8FEFD: RHMMFit (RWrapper.cpp:1494)
>>>>>>>>> > ==24916== by 0x4F2992D: R_doDotCall (dotcode.c:692)
>>>>>>>>> > ==24916== by 0x4F339D5: do_dotcall (dotcode.c:1252)
>>>>>>>>> > ==24916== by 0x4F81BA6: bcEval (eval.c:6771)
>>>>>>>>> > ==24916== by 0x4F6E963: Rf_eval (eval.c:624)
>>>>>>>>> > ==24916== by 0x4F71188: R_execClosure (eval.c:1764)
>>>>>>>>> > ==24916== by 0x4F70E7C: Rf_applyClosure (eval.c:1692)
>>>>>>>>> > ==24916== by 0x4F6F18B: Rf_eval (eval.c:747)
>>>>>>>>> > ==24916==
>>>>>>>>> >
>>>>>>>>> > This seems to be the exact same code as in the problem that
>>>>>>>>> you fixed
>>>>>>>>> > at another location. Actually, I would guess that all of these
>>>>>>>>> >
>>>>>>>>> > grep --color -nH -e ")\*ncores+1" *
>>>>>>>>> > HMM.cpp:784: int *myStateBuckets =
>>>>>>>>> (int*)malloc(sizeof(int)*ncores+1);
>>>>>>>>> > MultivariateGaussian.cpp:295: int *myDimBuckets =
>>>>>>>>> > (int*)malloc(sizeof(int)*ncores+1);
>>>>>>>>> > MultivariateGaussian.cpp:475: int *myDimBuckets =
>>>>>>>>> > (int*)malloc(sizeof(int)*ncores+1);
>>>>>>>>> > TransitionMatrix.cpp:132: int *myStateBuckets =
>>>>>>>>> > (int*)malloc(sizeof(int)*ncores+1);
>>>>>>>>> > TransitionMatrix.cpp:289: int *myStateBuckets =
>>>>>>>>> > (int*)malloc(sizeof(int)*ncores+1);
>>>>>>>>> >
>>>>>>>>> > are the same problem. Also, usually code that has been
>>>>>>>>> copy/pasted
>>>>>>>>> > like this can instead be refactored to a single function
>>>>>>>>> call, so a
>>>>>>>>> > bug can be fixed in one place.
>>>>>>>>> >
>>>>>>>>> > I still see a number of compiler warnings, the first of
>>>>>>>>> which is
>>>>>>>>> >
>>>>>>>>> > STAN master$ R CMD INSTALL .
>>>>>>>>> > Bioconductor version 3.7 (BiocInstaller 1.29.5), ?biocLite
>>>>>>>>> for help
>>>>>>>>> > * installing to library
>>>>>>>>> > '/home/mtmorgan/R/x86_64-pc-linux-gnu-library/3.5-Bioc-3.7'
>>>>>>>>> > * installing *source* package 'STAN' ...
>>>>>>>>> > ** libs
>>>>>>>>> > g++ -I"/home/mtmorgan/bin/R-3-5-branch/include" -DNDEBUG
>>>>>>>>> > -I/usr/local/include -D_RDLL_ -fopenmp -fpic -g -O0 -Wall
>>>>>>>>> -pedantic
>>>>>>>>> > -c HMM.cpp -o HMM.o
>>>>>>>>> > HMM.cpp: In member function ‘virtual void
>>>>>>>>> > HMM::calcEmissionProbs(double***, double**, int*, int,
>>>>>>>>> int**, int*,
>>>>>>>>> > int*, int**, int, int, int*)’:
>>>>>>>>> > HMM.cpp:112:15: warning: unused variable ‘j’
>>>>>>>>> [-Wunused-variable]
>>>>>>>>> > int i,j,t,k;
>>>>>>>>> > ^
>>>>>>>>> > It really pays to clean these up; most are harmless, but
>>>>>>>>> they obscure
>>>>>>>>> > the more important warnings.
>>>>>>>>> >
>>>>>>>>> > Martin
>>>>>>>>> >
>>>>>>>>> >
>>>>>>>>> > On 04/03/2018 09:58 AM, campos wrote:
>>>>>>>>> >> Hi Martin,
>>>>>>>>> >>
>>>>>>>>> >> when I run now valgrind seems that there are no problems. I
>>>>>>>>> pushed
>>>>>>>>> >> yesterday the changes, was I still on time for the new
>>>>>>>>> release? We
>>>>>>>>> >> want to publish the changes and it would be really helpful
>>>>>>>>> if the
>>>>>>>>> >> package is running on Bioconductor.
>>>>>>>>> >>
>>>>>>>>> >> Thank you very much,
>>>>>>>>> >>
>>>>>>>>> >> Rafael
>>>>>>>>> >>
>>>>>>>>> >>
>>>>>>>>> >> On 02.04.2018 02:51, Martin Morgan wrote:
>>>>>>>>> >>>
>>>>>>>>> >>>
>>>>>>>>> >>> On 04/01/2018 08:06 PM, Martin Morgan wrote:
>>>>>>>>> >>>>
>>>>>>>>> >>>>
>>>>>>>>> >>>> On 04/01/2018 03:53 PM, campos wrote:
>>>>>>>>> >>>>> Dear Martin,
>>>>>>>>> >>>>>
>>>>>>>>> >>>>> I am trying to fix this problem but I am really lost...
>>>>>>>>> Do you
>>>>>>>>> >>>>> mean C++ code? Becasue there is no C code in the whole
>>>>>>>>> package. I
>>>>>>>>> >>>>> really don't know what the problem might be.
>>>>>>>>> >>>>
>>>>>>>>> >>>> Please keep the conversation on the bioc-devel mailing
>>>>>>>>> list, so
>>>>>>>>> >>>> that others can learn or help.
>>>>>>>>> >>>>
>>>>>>>>> >>>> I use Linux, not Mac, but C (which I used to mean your
>>>>>>>>> C++ code)
>>>>>>>>> >>>> errors often occur on all platforms but are only visible
>>>>>>>>> as a
>>>>>>>>> >>>> segfault on one. I created the vignette R code with
>>>>>>>>> >>>>
>>>>>>>>> >>>> cd vignettes
>>>>>>>>> >>>> R CMD Stangle STAN-knitr.Rmd
>>>>>>>>> >>>>
>>>>>>>>> >>>> This produces a file STAN-knitr.R. I then ran your R code
>>>>>>>>> with
>>>>>>>>> >>>> valgrind
>>>>>>>>> >>>>
>>>>>>>>> >>>> R -d valgrind -f STAN-knitr.R
>>>>>>>>> >>>>
>>>>>>>>> >>>> this runs much slower than without valgrind. The first error
>>>>>>>>> >>>> reported by valgrind was
>>>>>>>>> >>>>
>>>>>>>>> >>>>
>>>>>>>>> >>>> > ##
>>>>>>>>> >>>>
>>>>>>>>> ----STAN-PoiLog-----------------------------------------------------------
>>>>>>>>>
>>>>>>>>> >>>>
>>>>>>>>> >>>> > nStates = 10
>>>>>>>>> >>>> > hmm_poilog = initHMM(trainRegions, nStates,
>>>>>>>>> "PoissonLogNormal",
>>>>>>>>> >>>> sizeFactors)
>>>>>>>>> >>>> > hmm_fitted_poilog = fitHMM(trainRegions, hmm_poilog,
>>>>>>>>> >>>> sizeFactors=sizeFactors, maxIters=10)
>>>>>>>>> >>>> [1] 6
>>>>>>>>> >>>> ==22304== Invalid write of size 4
>>>>>>>>> >>>> ==22304== at 0x4B489316:
>>>>>>>>> HMM::BaumWelch[abi:cxx11](double***,
>>>>>>>>> >>>> int*, int, int, int**, int*, int*, int*, int, int, int**,
>>>>>>>>> >>>> double***, SEXPREC*, SEXPREC*, int, double, double, int,
>>>>>>>>> int)
>>>>>>>>> >>>> (HMM.cpp:998)
>>>>>>>>> >>>> ==22304== by 0x4B4A0EFF: RHMMFit (RWrapper.cpp:1494)
>>>>>>>>> >>>> ==22304== by 0x4F2992D: R_doDotCall (dotcode.c:692)
>>>>>>>>> >>>> ==22304== by 0x4F339D5: do_dotcall (dotcode.c:1252)
>>>>>>>>> >>>> ==22304== by 0x4F81BA6: bcEval (eval.c:6771)
>>>>>>>>> >>>> ==22304== by 0x4F6E963: Rf_eval (eval.c:624)
>>>>>>>>> >>>> ==22304== by 0x4F71188: R_execClosure (eval.c:1764)
>>>>>>>>> >>>> ==22304== by 0x4F70E7C: Rf_applyClosure (eval.c:1692)
>>>>>>>>> >>>> ==22304== by 0x4F6F18B: Rf_eval (eval.c:747)
>>>>>>>>> >>>> ==22304== by 0x4F74B12: do_set (eval.c:2774)
>>>>>>>>> >>>> ==22304== by 0x4F6EDF5: Rf_eval (eval.c:699)
>>>>>>>>> >>>> ==22304== by 0x4FB7BEE: Rf_ReplIteration (main.c:258)
>>>>>>>>> >>>> ==22304== Address 0x238b28f4 is 4 bytes inside a block
>>>>>>>>> of size 5
>>>>>>>>> >>>> alloc'd
>>>>>>>>> >>>> ==22304== at 0x4C2DB8F: malloc (in
>>>>>>>>> >>>> /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
>>>>>>>>> >>>> ==22304== by 0x4B4892E5:
>>>>>>>>> HMM::BaumWelch[abi:cxx11](double***,
>>>>>>>>> >>>> int*, int, int, int**, int*, int*, int*, int, int, int**,
>>>>>>>>> >>>> double***, SEXPREC*, SEXPREC*, int, double, double, int,
>>>>>>>>> int)
>>>>>>>>> >>>> (HMM.cpp:995)
>>>>>>>>> >>>> ==22304== by 0x4B4A0EFF: RHMMFit (RWrapper.cpp:1494)
>>>>>>>>> >>>> ==22304== by 0x4F2992D: R_doDotCall (dotcode.c:692)
>>>>>>>>> >>>> ==22304== by 0x4F339D5: do_dotcall (dotcode.c:1252)
>>>>>>>>> >>>> ==22304== by 0x4F81BA6: bcEval (eval.c:6771)
>>>>>>>>> >>>> ==22304== by 0x4F6E963: Rf_eval (eval.c:624)
>>>>>>>>> >>>> ==22304== by 0x4F71188: R_execClosure (eval.c:1764)
>>>>>>>>> >>>> ==22304== by 0x4F70E7C: Rf_applyClosure (eval.c:1692)
>>>>>>>>> >>>> ==22304== by 0x4F6F18B: Rf_eval (eval.c:747)
>>>>>>>>> >>>> ==22304== by 0x4F74B12: do_set (eval.c:2774)
>>>>>>>>> >>>> ==22304== by 0x4F6EDF5: Rf_eval (eval.c:699)
>>>>>>>>> >>>>
>>>>>>>>> >>>> 'Invalid write' suggests that you are writing after the
>>>>>>>>> end of
>>>>>>>>> >>>> memory that you'd allocated. I looked at the C code at
>>>>>>>>> the line
>>>>>>>>> >>>> where the error occurs as indicated in the stack trace,
>>>>>>>>> HMM.cpp:998
>>>>>>>>> >>>> which is the assigment myStateBucks[i] = 0 in the loop
>>>>>>>>> >>>>
>>>>>>>>> >>>> int *myStateBuckets =
>>>>>>>>> (int*)malloc(sizeof(int)*ncores+1);
>>>>>>>>> >>>> for(i=0; i<=ncores; i++)
>>>>>>>>> >>>> {
>>>>>>>>> >>>> myStateBuckets[i] = 0;
>>>>>>>>> >>>> }
>>>>>>>>> >>>>
>>>>>>>>> >>>> The argument to malloc (where he memory was allocated, at
>>>>>>>>> line 995)
>>>>>>>>> >>>> should be the number of bytes to allocate and it should
>>>>>>>>> have been
>>>>>>>>> >>>> memory for ncores + 1 'int'
>>>>>>>>> >>>>
>>>>>>>>> >>>> malloc(sizeof(int) * (ncores + 1))
>>>>>>>>> >>>>
>>>>>>>>> >>>> rather than what you wrote, which is memory for ncores
>>>>>>>>> ints plus 1
>>>>>>>>> >>>> byte.
>>>>>>>>> >>>>
>>>>>>>>> >>>> C++ code would avoid the need for such explicit memory
>>>>>>>>> management,
>>>>>>>>> >>>> e.g., using a vector from the standard template library
>>>>>>>>> >>>>
>>>>>>>>> >>>> std::vector<int> myStateBuckets(ncores);
>>>>>>>>> >>>
>>>>>>>>> >>> oops, std::vector<int> myStateBuckets(ncores + 1); !
>>>>>>>>> >>>>
>>>>>>>>> >>>> There were may other valgrind errors, but I do not know
>>>>>>>>> whether
>>>>>>>>> >>>> these are from similar programming errors, or a
>>>>>>>>> consequence of this
>>>>>>>>> >>>> one.
>>>>>>>>> >>>>
>>>>>>>>> >>>> Martin
>>>>>>>>> >>>>
>>>>>>>>> >>>>> Thanks,
>>>>>>>>> >>>>> Rafael
>>>>>>>>> >>>>>>
>>>>>>>>> >>>>>> On 03/29/2018 01:07 PM, campos wrote:
>>>>>>>>> >>>>>>> Dear bioc-devel team,
>>>>>>>>> >>>>>>>
>>>>>>>>> >>>>>>> I have made some changes in the package STAN and
>>>>>>>>> although it
>>>>>>>>> >>>>>>> seems to install correctly, I have problems with
>>>>>>>>> timeout and
>>>>>>>>> >>>>>>> error in windows... Could someone help me to improve
>>>>>>>>> the time?
>>>>>>>>> >>>>>>>
>>>>>>>>> >>>>>>>
>>>>>>>>> https://bioconductor.org/checkResults/3.7/bioc-LATEST/STAN/
>>>>>>>>> >>>>>>
>>>>>>>>> >>>>>> it looks like, with your most recent commit (at the top
>>>>>>>>> of the
>>>>>>>>> >>>>>> page, 'Snapshot Date', 'Last Commit', 'Last Changed
>>>>>>>>> Date'), the
>>>>>>>>> >>>>>> package built on Windows and Linux.
>>>>>>>>> >>>>>>
>>>>>>>>> >>>>>> There is a segfault on Mac, which is likely a
>>>>>>>>> programming error
>>>>>>>>> >>>>>> in your C code. It could be debugged perhaps using
>>>>>>>>> valgrind or
>>>>>>>>> >>>>>> similar tools, but the first step would be to isolate
>>>>>>>>> the code to
>>>>>>>>> >>>>>> something more easily reproduced than the full
>>>>>>>>> vignette. It would
>>>>>>>>> >>>>>> also help to clean up the C code so that it compiles
>>>>>>>>> without
>>>>>>>>> >>>>>> warnings with the -Wall -pedantic flags
>>>>>>>>> >>>>>>
>>>>>>>>> >>>>>> Martin
>>>>>>>>> >>>>>>
>>>>>>>>> >>>>>>>
>>>>>>>>> >>>>>>> Best,
>>>>>>>>> >>>>>>>
>>>>>>>>> >>>>>>> Rafael
>>>>>>>>> >>>>>>>
>>>>>>>>> >>>>>>>
>>>>>>>>> >>>>>>> On 28.03.2018 01:08, Martin Morgan wrote:
>>>>>>>>> >>>>>>>> When I try and install the version on the master
>>>>>>>>> branch of the
>>>>>>>>> >>>>>>>> Bioconductor git repository I get
>>>>>>>>> >>>>>>>>
>>>>>>>>> >>>>>>>> STAN master$ Rdev --vanilla CMD INSTALL .
>>>>>>>>> >>>>>>>> * installing to library
>>>>>>>>> >>>>>>>> ‘/home/mtmorgan/R/x86_64-pc-linux-gnu-library
>>>>>>>>> >>>>>>>> ...
>>>>>>>>> >>>>>>>> ** testing if installed package can be loaded
>>>>>>>>> >>>>>>>> Error: package or namespace load failed for 'STAN' in
>>>>>>>>> >>>>>>>> namespaceExport(ns, exports):
>>>>>>>>> >>>>>>>> undefined exports: viterbi2Gviz
>>>>>>>>> >>>>>>>>
>>>>>>>>> >>>>>>>>
>>>>>>>>> >>>>>>>> This comes about in a rather interesting way because
>>>>>>>>> the body
>>>>>>>>> >>>>>>>> of plotViterbi is not defined
>>>>>>>>> >>>>>>>>
>>>>>>>>> >>>>>>>> plotViterbi <- function(viterbi, regions, gen, chrom,
>>>>>>>>> from, to,
>>>>>>>>> >>>>>>>> statecols, col)
>>>>>>>>> >>>>>>>>
>>>>>>>>> >>>>>>>> #'
>>>>>>>>> >>>>>>>> ...
>>>>>>>>> >>>>>>>>
>>>>>>>>> >>>>>>>> Can you please commit a version of the package that
>>>>>>>>> installs?
>>>>>>>>> >>>>>>>>
>>>>>>>>> >>>>>>>> Martin
>>>>>>>>> >>>>>>>>
>>>>>>>>> >>>>>>>> On 03/27/2018 06:42 PM, campos wrote:
>>>>>>>>> >>>>>>>>> Dear bioc-devel team,
>>>>>>>>> >>>>>>>>>
>>>>>>>>> >>>>>>>>> I am developing the STAN packages and I am running into
>>>>>>>>> >>>>>>>>> problems when trying to build my package. The
>>>>>>>>> problem is the
>>>>>>>>> >>>>>>>>> following:
>>>>>>>>> >>>>>>>>>
>>>>>>>>> >>>>>>>>> Error in vignette_type(Outfile) :
>>>>>>>>> >>>>>>>>> Vignette product 'STAN.tex' does not have a known
>>>>>>>>> filename
>>>>>>>>> >>>>>>>>> extension ('NA')
>>>>>>>>> >>>>>>>>> ERROR: installing vignettes failed
>>>>>>>>> >>>>>>>>> * removing '/tmp/Rtmp925Iru/Rinst63471ff1efdc/STAN'
>>>>>>>>> >>>>>>>>> I tried to build the package in old versions (which
>>>>>>>>> they used
>>>>>>>>> >>>>>>>>> to work) and I run in other problems but in this
>>>>>>>>> case is:
>>>>>>>>> >>>>>>>>>
>>>>>>>>> >>>>>>>>> Error in texi2dvi(file = file, pdf = TRUE, clean =
>>>>>>>>> clean,
>>>>>>>>> >>>>>>>>> quiet = quiet, :
>>>>>>>>> >>>>>>>>> Running 'texi2dvi' on 'STAN.tex' failed.
>>>>>>>>> >>>>>>>>> LaTeX errors:
>>>>>>>>> >>>>>>>>> ! LaTeX Error: File `beramono.sty' not found.
>>>>>>>>> >>>>>>>>>
>>>>>>>>> >>>>>>>>> Type X to quit or <RETURN> to proceed,
>>>>>>>>> >>>>>>>>> or enter new name. (Default extension: sty)
>>>>>>>>> >>>>>>>>>
>>>>>>>>> >>>>>>>>> Could you help me with this problem?
>>>>>>>>> >>>>>>>>>
>>>>>>>>> >>>>>>>>> Thank you very much,
>>>>>>>>> >>>>>>>>>
>>>>>>>>> >>>>>>>>> Rafael
>>>>>>>>> >>>>>>>>>
>>>>>>>>> >>>>>>>>> _______________________________________________
>>>>>>>>> >>>>>>>>> Bioc-devel at r-project.org mailing list
>>>>>>>>> >>>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>>>>>> >>>>>>>>
>>>>>>>>> >>>>>>>>
>>>>>>>>> >>>>>>>> This email message may contain legally privileged and/or
>>>>>>>>> >>>>>>>> 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.
>>>>>>>>> >>>>>>>
>>>>>>>>> >>>>>>
>>>>>>>>> >>>>>>
>>>>>>>>> >>>>>> 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.
>>>>>>>>> >>>>>
>>>>>>>>> >>>>
>>>>>>>>> >>>>
>>>>>>>>> >>>> This email message may contain legally privileged
>>>>>>>>> >>>> and/or...{{dropped:2}}
>>>>>>>>> >>>>
>>>>>>>>> >>>> _______________________________________________
>>>>>>>>> >>>> Bioc-devel at r-project.org mailing list
>>>>>>>>> >>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>>>>>> >>>
>>>>>>>>> >>>
>>>>>>>>> >>> This email message may contain legally privileged and/or
>>>>>>>>> >>> 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.
>>>>>>>>> >>
>>>>>>>>> >
>>>>>>>>> >
>>>>>>>>> > 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.
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> Bioc-devel at r-project.org mailing list
>>>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>>>>>>
>>>>>>>>> This email message may contain legally privileged and/or
>>>>>>>>> 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.
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> 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.
>>>>>>
>>>>>
>>>>>
>>>>> 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.
>>>>
>>>
>>>
>>> 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.
>>
>
>
> 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.
>
More information about the Bioc-devel
mailing list