[Bioc-devel] vignette problems
Martin Morgan
martin.morgan at roswellpark.org
Wed Apr 11 16:52:34 CEST 2018
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
>>>>>>>>>> >>>>>>>>
>>>>>>>>>> >>>>>>>>
>>>>>>>>>> >>>>>>>> This email message may contain legally privileged and/or
>>>>>>>>>> >>>>>>>> confidential information. If you are not the intended
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>>>>>>>>>> for the
>>>>>>>>>> >>>>>>>> delivery of this message to the intended
>>>>>>>>>> recipient(s), you are
>>>>>>>>>> >>>>>>>> hereby notified that any disclosure, copying,
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>>>>>>>>>> received
>>>>>>>>>> >>>>>>>> this message in error, please notify the sender
>>>>>>>>>> immediately by
>>>>>>>>>> >>>>>>>> e-mail and delete this email message from your
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>>>>>>>>>> >>>>>>>> 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),
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>>>>>>>>>> >>>>>> hereby notified that any disclosure, copying,
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>>>>>>>>>> >>>>>> this message in error, please notify the sender
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>>>>>>>>>> >>>>>
>>>>>>>>>> >>>>
>>>>>>>>>> >>>>
>>>>>>>>>> >>>> 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
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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
>>>>>>>>>> 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.
>>
>
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