Hi Martin,
thanks for your reply. I do not have vignette warnings, the warnings
that I see are:
MultivariateGaussianFactory.h:23:9: warning: control reaches end of non-void
function [-Wreturn-type]
BernoulliFactory.h:27:9: warning: control reaches end of non-void function
[-Wreturn-type]
PoissonFactory.h:24:9: warning: control reaches end of non-void function
[-Wreturn-type]
MultinomialFactory.h:24:9: warning: control reaches end of non-void function
[-Wreturn-type]
NegativeBinomialFactory.h:27:9: warning: control reaches end of non-void
function [-Wreturn-type]
PoissonLogNormalFactory.h:27:9: warning: control reaches end of non-void
function [-Wreturn-type]
RWrapper.cpp:742:5: warning: control reaches end of non-void function
[-Wreturn-type]
RWrapper.cpp:950:5: warning: control reaches end of non-void function
[-Wreturn-type]
On 24.04.2018 15:39, Martin Morgan wrote:
> I don't see vignette warnings on the build report.
>
> You should address the simple namespace issue by adding
>
> � importFrom("stats", "dnbinom", "kmeans", "optim", "ppois")
>
> to your NAMESPACE file.
>
> The compiler warnings are from the -Wall flag, which you can set by
> creating a plain text file
>
> ~/.R/Makevars
>
> with the line
>
> � CFLAGS = -Wall
> � CXXFLAGS = -Wall
>
> Martin
>
>
> On 04/24/2018 05:49 AM, campos wrote:
>> Dear Bio-dev,
>>
>> I have a quick question, for some reason I can reproduce the warnings
>> that are stated in
>> https://bioconductor.org/checkResults/3.7/bioc-LATEST/STAN/malbec2-checksrc.html
>>
>> on my linux machine. The check runs smoothly, any idea why so?
>>
>> Thank you 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?
>>>>
>>>> ��$git remote -v
>>>> origin��� g...@git.bioconductor.org:packages/STAN (fetch)
>>>> origin��� g...@git.bioconductor.org:packages/STAN (push)
>>>
>>> maybe your version is current; I have
>>>
>>> ~/b/git/STAN master$ 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��� g...@git.bioconductor.org:packages/STAN (fetch)
>>>>>>> ��� origin��� g...@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-boun...@r-project.org> on
>>>>>>>>>>>>> behalf of campos <cam...@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@r-project.org mailing list
>>>>>>>>>>>>> >>>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>>>>>>>>>> >>>>>>>>
>>>>>>>>>>>>> >>>>>>>>
>>>>>>>>>>>>> >>>>>>>> This email message may contain legally privileged
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>>>>>>>>>>>>> intended
>>>>>>>>>>>>> >>>>>>>> recipient(s), or the employee or agent
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>>>>>>>>>>>>> >>>>>>>> delivery of this message to the intended
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>>>>>>>>>>>>> >>>>>>>> hereby notified that any disclosure, copying,
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>>>>>>>>>>>>> >>>>>>
>>>>>>>>>>>>> >>>>>> This email message may contain legally privileged
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>>>>>>>>>>>>> >>>> This email message may contain legally privileged
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>>>>>>>>>>>>> >>>>
>>>>>>>>>>>>> >>>> _______________________________________________
>>>>>>>>>>>>> >>>> Bioc-devel@r-project.org mailing list
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>>>>>>>>>>>>> >>>
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>>>>>>>>>>>>> >
>>>>>>>>>>>>> > This email message may contain legally privileged and/or
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>>>>>>>>>>>>> or the
>>>>>>>>>>>>> > employee or agent responsible for the delivery of this
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>>>>>>>>>>>>> Bioc-devel@r-project.org mailing list
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>>>>>>>>
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