[Bioc-devel] vignette problems
campos
campos at mpipz.mpg.de
Sat Apr 21 12:49:04 CEST 2018
Hi Martin,
sorry to bother you again... I have been working on the void problem
warning this whole week with some other people and we couldn't come
along a proper solution... I read that some warnings might be accepted,
we have checked the package and it seems to work properly. Would that be
a possible warning to be ignored?
Thank you very much again,
Rafael
On 11.04.2018 16:52, Martin Morgan wrote:
>
>
> On 04/11/2018 10:47 AM, campos wrote:
>> 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?
>>
>> $git remote -v
>> origin git at git.bioconductor.org:packages/STAN (fetch)
>> origin git at git.bioconductor.org:packages/STAN (push)
>
> maybe your version is current; I have
>
> ~/b/git/STAN master$ git log --oneline -n10
> 06dbdae Merge remote-tracking branch 'upstream/master'
> 6e070d4 version 2.7.3
> 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
> 1c4f140 upgrade version 2.7.3
>
> if you don't, then I guess `git pull` or more pedantically `git fetch
> origin; git merge origin/master master`.
>
> Martin
>
>>
>> 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
>>>>>>>>>>> >>>>>>>>
>>>>>>>>>>> >>>>>>>>
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>>>>>>>>>>> >>>>>>>
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>>>>>>>>>>> >>>>>>
>>>>>>>>>>> >>>>>> This email message may contain legally privileged and/or
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>>>>>>>>>>> >>>>>
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>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>> This email message may contain legally privileged
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>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>> _______________________________________________
>>>>>>>>>>> >>>> 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
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>>>>>>>>>>> >>> or the employee or agent responsible for the delivery of
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>>>>>>>>>>> >>
>>>>>>>>>>> >
>>>>>>>>>>> >
>>>>>>>>>>> > This email message may contain legally privileged and/or
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>>>>>>>>>>>
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> 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
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>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
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>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> This email message may contain legally privileged and/or
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>>>>>>
>>>>>
>>>>>
>>>>> This email message may contain legally privileged and/or
>>>>> confidential information. If you are not the intended
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>>>>
>>>
>>>
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>>
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