[Bioc-devel] vignette problems
campos
campos at mpipz.mpg.de
Tue Apr 24 16:16:17 CEST 2018
Hi Martin,
yeah, I have been wondering around the code these days looking for the
answer of that, I am the maintainer and not who developed the code... I
still couldn't reach the developer and ask about this, for the moment my
assumption is that whenever parallel == 0 (Which I also think is most of
the time this, but I found in the poissonLogNormalFactory.h another
statement in which it could be 1) it will return the right value if not
the NULL which is expected.
With this I want to get rid of the warnings in Linux and Windows and
pass the deadline which is tomorrow and have it updated on Bioconductor.
Once I can contact the developer maybe I can work in nicer code.
So, you think will pass the checks? so far I have not gotten any
warnings with your method.
Best,
Rafa
On 24.04.2018 16:03, Martin Morgan wrote:
>
>
> On 04/24/2018 09:42 AM, campos wrote:
>> 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]
>>
>
> yes it looks like you tackled those with the commit
>
> STAN/src master$ git log MultivariateGaussianFactory.h
> commit c43b951db86e4c167356ce8b380f6b8429ae0754
> Author: rfael0cm <rfael0cm at gmail.com>
> Date: Tue Apr 24 13:52:13 2018 +0200
>
> Update DESCRIPTION FILE 2.7.8
>
>
> which has not built yet (it will be included in tonight's build, for
> Wednesday's build report.
>
> I think the change you made will silence the warning
>
> --- a/src/MultivariateGaussianFactory.h
> +++ b/src/MultivariateGaussianFactory.h
> @@ -20,6 +20,7 @@ class MultivariateGaussianFactory : public
> EmissionFactory
> {
> return new MultivariateGaussian(emissionParams);
> }
> + return NULL;
> }
>
> but I wonder whether this is correct? Will your code really work if
> these functions return NULL? My sense actually is that the 'parallel'
> argument is never used (it's always 0), and that the correct solution
> is to remove it from the signature and to make the return value
> unconditional
>
> --- a/src/MultivariateGaussianFactory.h
> +++ b/src/MultivariateGaussianFactory.h
> @@ -10,17 +10,13 @@
> class MultivariateGaussianFactory : public EmissionFactory
> {
> public:
> - EmissionFunction*
> createEmissionFunction(ParamContainerEmissions *emissionParams, int
> parallel)
> + EmissionFunction*
> createEmissionFunction(ParamContainerEmissions *emissionParams)
> {
> if(DEBUG_MEMORY)
> {
> Rprintf("factory->create():");
> }
> - if(parallel == 0)
> - {
> - return new MultivariateGaussian(emissionParams);
> - }
> - return NULL;
> + return new MultivariateGaussian(emissionParams);
> }
> MultivariateGaussianFactory() {}
> ~MultivariateGaussianFactory() { }
>
> This requires other changes in the code, to make the calling functions
> consistent. I guess this is a 'feature' that was planned but never
> implemented; it's usually better to keep such features out of the
> public version of your software.
>
> Martin
>
>>
>> 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?
>>>>>>
>>>>>> $git remote -v
>>>>>> origin git at git.bioconductor.org:packages/STAN (fetch)
>>>>>> origin git at git.bioconductor.org:packages/STAN (push)
>>>>>
>>>>> maybe your version is current; I have
>>>>>
>>>>> ~/b/git/STAN master$ 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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>>>>>>>>>>>>>>> >>>>>>
>>>>>>>>>>>>>>> >>>>>> This email message may contain legally privileged
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>>>>>>>>>>>>>>> >>>> This email message may contain legally privileged
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>>>>>>>>>>>>>>> >>>>
>>>>>>>>>>>>>>> >>>> _______________________________________________
>>>>>>>>>>>>>>> >>>> Bioc-devel at r-project.org mailing list
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>>>>>>>>>>>>>>> >>>
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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 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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