[Bioc-devel] vignette problems

[Martin Morgan]

On 04/11/2018 09:58 AM, campos wrote:
> Hi Martin,
> 
> thank you very much for your time and effort!
> 
> I pulled the branch to my computer updated the DESCRIPTION file and 
> pushed the changes. That should be enough right?

actually I seemed to have messed up the git commit, but I fixed it from 
my end; you should git pull and not worry about pushing any further 
commits for the moment.

> 
> Best,
> 
> Rafa
> 
> PS: If you ever stop by Cologne please let me know. I owe you a beer or 
> two!

tasty!

Martin

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


This email message may contain legally privileged and/or...{{dropped:2}}