[Bioc-devel] vignette problems
campos
campos at mpipz.mpg.de
Wed Apr 11 15:58:38 CEST 2018
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?
Best,
Rafa
PS: If you ever stop by Cologne please let me know. I owe you a beer or two!
On 10.04.2018 23:44, Martin Morgan wrote:
> Hi --
>
> I'm not sure what you mean; the 'devel' builld report does not include
> mac (the build system experienced problems with disk space last night,
> so the build did not complete)
>
> https://bioconductor.org/checkResults/devel/bioc-LATEST/STAN/
>
> and STAN failed in Release
>
> https://bioconductor.org/checkResults/release/bioc-LATEST/STAN/
>
>
> HOWEVER, I spent some time with your package. First, I compiled it
> with compiler flages -Wall -pedantic, which makes the compiler quite
> sensitive. I did this by creating, on my Linux, a file
>
> $ cat ~/.R/Makevars
> CFLAGS = -g -O0 -Wall -pedantic
> CXXFLAGS = -g -O0 -Wall -pedantic
>
> and then installing the package from the source directory
>
> STAN master$ rm -f src/*o && R CMD INSTALL .
>
> There were a number of minor issues (unused variables, incorrect
> printf formatting [and use of printf() rather than Rprintf()]) as well
> as somewhat more substantial problems (virtual destructors for
> polymorphic base classes); a few problems remain, of the form
>
> RWrapper.cpp:950:5: warning: control reaches end of non-void
> function [-Wreturn-type]
> }
>
> where the problem is obvious -- no return value if parallel != 0 --
> but also innocuous, since it seems from inspection that in fact this
> function is always invoked with parallel == 0
>
> HMM* createHMM(int parallel, int K, InitialProbability* initProb,
> TransitionMatrix* transMat, EmissionFunction** myEmissions)
> {
> if(parallel == 0)
> {
> return new HMM(K, initProb, transMat, myEmissions);
> }
> }
>
> You should fix these problems, e.g., by removing the parallel argument
> from the function and body. After cleaning up as best I could, I
> install the package again and ran the vignette through valgrind
>
> STAN master$ R CMD INSTALL .
> ...
> STAN master$ cd vignettes
> STAN/vignettes master$ R CMD Stangle STAN-knitr.Rnw
> STAN/vignettes master$ R CMD Stangle STAN-knitr.Rnw
> STAN/vignettes master$ R -d valgrind -f STAN-knitr.R
>
> leading to an about mismatched new[] / delete[] -- memory allocated by
> 'new x[]' must be deleted with 'delete[]', but the package code had
> simply 'delete'.
>
> With these changes, the vignette builds without segfaulting or
> valgrind errors on my machine, and on the Mac builder; I did not check
> the full build and check of the package.
>
> The changes are summarized in the following commits:
>
> STAN master$ git log --oneline
> a719f42 version bump
> b8e2123 make destructors for polymorhpic base classes virtual
> 18ac6ba mismatch new[] / delete[]
> 985768b restore EmissionFactory::createEmissionFunctionMixed
> 8b749db provide return value for non-void functions
> 26ca36e update poor printf statements
> 0bb83ab clear 'unused variable' -Wall -pedantic warnings
> a3b7666 remove vignette product STAN-knitr.R
>
> You should pull these down to your local git repository, e.g., for me
> I have
>
> STAN master$ git remote -v
> origin git at git.bioconductor.org:packages/STAN (fetch)
> origin git at git.bioconductor.org:packages/STAN (push)
>
> So I would
>
> STAN master$ git pull origin master
>
> to incorporate the changes.
>
> It would be good to port these changes to the RELEASE_3_6 branch;
> remember to bump the version of the RELEASE_3_6 branch to 2.6.1.
>
> Unfortunately, I pushed the changes after tonight's builds started, so
> the effect of the changes will not be reported until Thursday
> mid-morning, Eastern time, if the build system does not have problems.
>
> Martin
>
> On 04/10/2018 02:14 PM, campos wrote:
>> Hi Martin,
>>
>> it seems like mac is ok now. What has changed??
>>
>> Thank you very much,
>>
>> Rafael
>>
>>
>> On 10.04.2018 11:33, Martin Morgan wrote:
>>>
>>>
>>> On 04/10/2018 05:27 AM, campos wrote:
>>>> Hi Martin,
>>>>
>>>> Thank you very much, I am a bit concerned about the option of:
>>>>
>>>>
>>>> Last Changed Date: 2018-04-05 09:37:37 -0400 (Thu, 05 Apr 2018)
>>>>
>>>> I did a change yesterday and push it, why isn't it visible?
>>>
>>> Notice that at the top of the build report it says
>>>
>>> This page was generated on 2018-04-09 09:50:05 -0400 (Mon, 09 Apr
>>> 2018).
>>>
>>> Snapshot Date: 2018-04-08 16:45:28 -0400 (Sun, 08 Apr 2018)
>>>
>>> If you pushed after the snapshot date then your changes are not yet
>>> visible.
>>>
>>> Martin
>>>
>>>>
>>>> Best,
>>>>
>>>> Rafa
>>>>
>>>>
>>>>
>>>>
>>>> On 09.04.2018 16:44, Martin Morgan wrote:
>>>>> I'll try to provide you with a pull request addressing issues. Martin
>>>>>
>>>>> On 04/09/2018 08:42 AM, campos wrote:
>>>>>> Dear devel team,
>>>>>>
>>>>>> I am still puzzled with the problems with mac compiling. I am
>>>>>> really lost and have no idea how to continue or how to be able to
>>>>>> check about this problems with my linux machine in order to fix
>>>>>> it faster. Could you please help me with that??
>>>>>>
>>>>>> Best,
>>>>>>
>>>>>> Rafael
>>>>>>
>>>>>>
>>>>>> On 05.04.2018 14:29, Shepherd, Lori wrote:
>>>>>>>
>>>>>>> In order for changes to be propagated a version bump in the
>>>>>>> DESCRIPTION file is needed. Please bump the version in the
>>>>>>> DESCRIPTION file to 2.7.2.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Lori Shepherd
>>>>>>>
>>>>>>> Bioconductor Core Team
>>>>>>>
>>>>>>> Roswell Park Cancer Institute
>>>>>>>
>>>>>>> Department of Biostatistics & Bioinformatics
>>>>>>>
>>>>>>> Elm & Carlton Streets
>>>>>>>
>>>>>>> Buffalo, New York 14263
>>>>>>>
>>>>>>> ------------------------------------------------------------------------
>>>>>>>
>>>>>>> *From:* Bioc-devel <bioc-devel-bounces at r-project.org> on behalf
>>>>>>> of campos <campos at mpipz.mpg.de>
>>>>>>> *Sent:* Thursday, April 5, 2018 7:45:57 AM
>>>>>>> *To:* Morgan, Martin; bioc-devel
>>>>>>> *Subject:* Re: [Bioc-devel] vignette problems
>>>>>>> Hey Martin,
>>>>>>>
>>>>>>> I pushed new changes since last friday but in
>>>>>>> https://bioconductor.org/checkResults/3.7/bioc-LATEST/STAN/ says
>>>>>>> that
>>>>>>> the last change date was friday. Any idea what is the problem?
>>>>>>>
>>>>>>> I have tried to fix the problems with memory and all you told me.
>>>>>>>
>>>>>>> Best,
>>>>>>>
>>>>>>> Rafael
>>>>>>>
>>>>>>>
>>>>>>> On 03.04.2018 17:06, Martin Morgan wrote:
>>>>>>> > Please use 'reply all' so that the mailing list remains engaged.
>>>>>>> >
>>>>>>> > Check out the release schedule
>>>>>>> >
>>>>>>> > http://bioconductor.org/developers/release-schedule/
>>>>>>> >
>>>>>>> > in particular
>>>>>>> >
>>>>>>> > Wednesday April 25
>>>>>>> >
>>>>>>> > - Deadline for packages passing ‘‘R CMD build’’ and ‘‘R CMD
>>>>>>> check’’
>>>>>>> > without errors or warnings.
>>>>>>> >
>>>>>>> > so you still have time to get your package in order.
>>>>>>> >
>>>>>>> > Using the same techniques as before, I still see valgrind
>>>>>>> problems,
>>>>>>> > the first being
>>>>>>> >
>>>>>>> > > hmm_fitted_poilog = fitHMM(trainRegions, hmm_poilog,
>>>>>>> > sizeFactors=sizeFactors, maxIters=10)
>>>>>>> > ==24916== Invalid write of size 4
>>>>>>> > ==24916== at 0x4BA93FD7:
>>>>>>> > TransitionMatrix::updateAuxiliaries(double**, double***, double*,
>>>>>>> > int*, int, int**, int, double, int) (TransitionMatrix.cpp:292)
>>>>>>> > ==24916== by 0x4BA77934: HMM::updateSampleAux(double***,
>>>>>>> int*, int,
>>>>>>> > double**, double**, double**, double***, double*, int*, int*,
>>>>>>> int*,
>>>>>>> > int**, double***, SEXPREC*, SEXPREC*, int, double, int, int, int)
>>>>>>> > (HMM.cpp:771)
>>>>>>> > ==24916== by 0x4BA7896D:
>>>>>>> HMM::BaumWelch[abi:cxx11](double***, int*,
>>>>>>> > int, int, int**, int*, int*, int*, int, int, int**, double***,
>>>>>>> > SEXPREC*, SEXPREC*, int, double, double, int, int) (HMM.cpp:1076)
>>>>>>> > ==24916== by 0x4BA8FEFD: RHMMFit (RWrapper.cpp:1494)
>>>>>>> > ==24916== by 0x4F2992D: R_doDotCall (dotcode.c:692)
>>>>>>> > ==24916== by 0x4F339D5: do_dotcall (dotcode.c:1252)
>>>>>>> > ==24916== by 0x4F81BA6: bcEval (eval.c:6771)
>>>>>>> > ==24916== by 0x4F6E963: Rf_eval (eval.c:624)
>>>>>>> > ==24916== by 0x4F71188: R_execClosure (eval.c:1764)
>>>>>>> > ==24916== by 0x4F70E7C: Rf_applyClosure (eval.c:1692)
>>>>>>> > ==24916== by 0x4F6F18B: Rf_eval (eval.c:747)
>>>>>>> > ==24916== by 0x4F74B12: do_set (eval.c:2774)
>>>>>>> > ==24916== Address 0x2e73a294 is 4 bytes inside a block of
>>>>>>> size 5 alloc'd
>>>>>>> > ==24916== at 0x4C2DB8F: malloc (in
>>>>>>> > /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
>>>>>>> > ==24916== by 0x4BA93FA6:
>>>>>>> > TransitionMatrix::updateAuxiliaries(double**, double***, double*,
>>>>>>> > int*, int, int**, int, double, int) (TransitionMatrix.cpp:289)
>>>>>>> > ==24916== by 0x4BA77934: HMM::updateSampleAux(double***,
>>>>>>> int*, int,
>>>>>>> > double**, double**, double**, double***, double*, int*, int*,
>>>>>>> int*,
>>>>>>> > int**, double***, SEXPREC*, SEXPREC*, int, double, int, int, int)
>>>>>>> > (HMM.cpp:771)
>>>>>>> > ==24916== by 0x4BA7896D:
>>>>>>> HMM::BaumWelch[abi:cxx11](double***, int*,
>>>>>>> > int, int, int**, int*, int*, int*, int, int, int**, double***,
>>>>>>> > SEXPREC*, SEXPREC*, int, double, double, int, int) (HMM.cpp:1076)
>>>>>>> > ==24916== by 0x4BA8FEFD: RHMMFit (RWrapper.cpp:1494)
>>>>>>> > ==24916== by 0x4F2992D: R_doDotCall (dotcode.c:692)
>>>>>>> > ==24916== by 0x4F339D5: do_dotcall (dotcode.c:1252)
>>>>>>> > ==24916== by 0x4F81BA6: bcEval (eval.c:6771)
>>>>>>> > ==24916== by 0x4F6E963: Rf_eval (eval.c:624)
>>>>>>> > ==24916== by 0x4F71188: R_execClosure (eval.c:1764)
>>>>>>> > ==24916== by 0x4F70E7C: Rf_applyClosure (eval.c:1692)
>>>>>>> > ==24916== by 0x4F6F18B: Rf_eval (eval.c:747)
>>>>>>> > ==24916==
>>>>>>> >
>>>>>>> > This seems to be the exact same code as in the problem that
>>>>>>> you fixed
>>>>>>> > at another location. Actually, I would guess that all of these
>>>>>>> >
>>>>>>> > grep --color -nH -e ")\*ncores+1" *
>>>>>>> > HMM.cpp:784: int *myStateBuckets =
>>>>>>> (int*)malloc(sizeof(int)*ncores+1);
>>>>>>> > MultivariateGaussian.cpp:295: int *myDimBuckets =
>>>>>>> > (int*)malloc(sizeof(int)*ncores+1);
>>>>>>> > MultivariateGaussian.cpp:475: int *myDimBuckets =
>>>>>>> > (int*)malloc(sizeof(int)*ncores+1);
>>>>>>> > TransitionMatrix.cpp:132: int *myStateBuckets =
>>>>>>> > (int*)malloc(sizeof(int)*ncores+1);
>>>>>>> > TransitionMatrix.cpp:289: int *myStateBuckets =
>>>>>>> > (int*)malloc(sizeof(int)*ncores+1);
>>>>>>> >
>>>>>>> > are the same problem. Also, usually code that has been
>>>>>>> copy/pasted
>>>>>>> > like this can instead be refactored to a single function
>>>>>>> call, so a
>>>>>>> > bug can be fixed in one place.
>>>>>>> >
>>>>>>> > I still see a number of compiler warnings, the first of which is
>>>>>>> >
>>>>>>> > STAN master$ R CMD INSTALL .
>>>>>>> > Bioconductor version 3.7 (BiocInstaller 1.29.5), ?biocLite for
>>>>>>> help
>>>>>>> > * installing to library
>>>>>>> > '/home/mtmorgan/R/x86_64-pc-linux-gnu-library/3.5-Bioc-3.7'
>>>>>>> > * installing *source* package 'STAN' ...
>>>>>>> > ** libs
>>>>>>> > g++ -I"/home/mtmorgan/bin/R-3-5-branch/include" -DNDEBUG
>>>>>>> > -I/usr/local/include -D_RDLL_ -fopenmp -fpic -g -O0 -Wall
>>>>>>> -pedantic
>>>>>>> > -c HMM.cpp -o HMM.o
>>>>>>> > HMM.cpp: In member function ‘virtual void
>>>>>>> > HMM::calcEmissionProbs(double***, double**, int*, int, int**,
>>>>>>> int*,
>>>>>>> > int*, int**, int, int, int*)’:
>>>>>>> > HMM.cpp:112:15: warning: unused variable ‘j’ [-Wunused-variable]
>>>>>>> > int i,j,t,k;
>>>>>>> > ^
>>>>>>> > It really pays to clean these up; most are harmless, but they
>>>>>>> obscure
>>>>>>> > the more important warnings.
>>>>>>> >
>>>>>>> > Martin
>>>>>>> >
>>>>>>> >
>>>>>>> > On 04/03/2018 09:58 AM, campos wrote:
>>>>>>> >> Hi Martin,
>>>>>>> >>
>>>>>>> >> when I run now valgrind seems that there are no problems. I
>>>>>>> pushed
>>>>>>> >> yesterday the changes, was I still on time for the new
>>>>>>> release? We
>>>>>>> >> want to publish the changes and it would be really helpful if
>>>>>>> the
>>>>>>> >> package is running on Bioconductor.
>>>>>>> >>
>>>>>>> >> Thank you very much,
>>>>>>> >>
>>>>>>> >> Rafael
>>>>>>> >>
>>>>>>> >>
>>>>>>> >> On 02.04.2018 02:51, Martin Morgan wrote:
>>>>>>> >>>
>>>>>>> >>>
>>>>>>> >>> On 04/01/2018 08:06 PM, Martin Morgan wrote:
>>>>>>> >>>>
>>>>>>> >>>>
>>>>>>> >>>> On 04/01/2018 03:53 PM, campos wrote:
>>>>>>> >>>>> Dear Martin,
>>>>>>> >>>>>
>>>>>>> >>>>> I am trying to fix this problem but I am really lost... Do
>>>>>>> you
>>>>>>> >>>>> mean C++ code? Becasue there is no C code in the whole
>>>>>>> package. I
>>>>>>> >>>>> really don't know what the problem might be.
>>>>>>> >>>>
>>>>>>> >>>> Please keep the conversation on the bioc-devel mailing
>>>>>>> list, so
>>>>>>> >>>> that others can learn or help.
>>>>>>> >>>>
>>>>>>> >>>> I use Linux, not Mac, but C (which I used to mean your C++
>>>>>>> code)
>>>>>>> >>>> errors often occur on all platforms but are only visible as a
>>>>>>> >>>> segfault on one. I created the vignette R code with
>>>>>>> >>>>
>>>>>>> >>>> cd vignettes
>>>>>>> >>>> R CMD Stangle STAN-knitr.Rmd
>>>>>>> >>>>
>>>>>>> >>>> This produces a file STAN-knitr.R. I then ran your R code with
>>>>>>> >>>> valgrind
>>>>>>> >>>>
>>>>>>> >>>> R -d valgrind -f STAN-knitr.R
>>>>>>> >>>>
>>>>>>> >>>> this runs much slower than without valgrind. The first error
>>>>>>> >>>> reported by valgrind was
>>>>>>> >>>>
>>>>>>> >>>>
>>>>>>> >>>> > ##
>>>>>>> >>>>
>>>>>>> ----STAN-PoiLog-----------------------------------------------------------
>>>>>>>
>>>>>>> >>>>
>>>>>>> >>>> > nStates = 10
>>>>>>> >>>> > hmm_poilog = initHMM(trainRegions, nStates,
>>>>>>> "PoissonLogNormal",
>>>>>>> >>>> sizeFactors)
>>>>>>> >>>> > hmm_fitted_poilog = fitHMM(trainRegions, hmm_poilog,
>>>>>>> >>>> sizeFactors=sizeFactors, maxIters=10)
>>>>>>> >>>> [1] 6
>>>>>>> >>>> ==22304== Invalid write of size 4
>>>>>>> >>>> ==22304== at 0x4B489316:
>>>>>>> HMM::BaumWelch[abi:cxx11](double***,
>>>>>>> >>>> int*, int, int, int**, int*, int*, int*, int, int, int**,
>>>>>>> >>>> double***, SEXPREC*, SEXPREC*, int, double, double, int, int)
>>>>>>> >>>> (HMM.cpp:998)
>>>>>>> >>>> ==22304== by 0x4B4A0EFF: RHMMFit (RWrapper.cpp:1494)
>>>>>>> >>>> ==22304== by 0x4F2992D: R_doDotCall (dotcode.c:692)
>>>>>>> >>>> ==22304== by 0x4F339D5: do_dotcall (dotcode.c:1252)
>>>>>>> >>>> ==22304== by 0x4F81BA6: bcEval (eval.c:6771)
>>>>>>> >>>> ==22304== by 0x4F6E963: Rf_eval (eval.c:624)
>>>>>>> >>>> ==22304== by 0x4F71188: R_execClosure (eval.c:1764)
>>>>>>> >>>> ==22304== by 0x4F70E7C: Rf_applyClosure (eval.c:1692)
>>>>>>> >>>> ==22304== by 0x4F6F18B: Rf_eval (eval.c:747)
>>>>>>> >>>> ==22304== by 0x4F74B12: do_set (eval.c:2774)
>>>>>>> >>>> ==22304== by 0x4F6EDF5: Rf_eval (eval.c:699)
>>>>>>> >>>> ==22304== by 0x4FB7BEE: Rf_ReplIteration (main.c:258)
>>>>>>> >>>> ==22304== Address 0x238b28f4 is 4 bytes inside a block of
>>>>>>> size 5
>>>>>>> >>>> alloc'd
>>>>>>> >>>> ==22304== at 0x4C2DB8F: malloc (in
>>>>>>> >>>> /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
>>>>>>> >>>> ==22304== by 0x4B4892E5:
>>>>>>> HMM::BaumWelch[abi:cxx11](double***,
>>>>>>> >>>> int*, int, int, int**, int*, int*, int*, int, int, int**,
>>>>>>> >>>> double***, SEXPREC*, SEXPREC*, int, double, double, int, int)
>>>>>>> >>>> (HMM.cpp:995)
>>>>>>> >>>> ==22304== by 0x4B4A0EFF: RHMMFit (RWrapper.cpp:1494)
>>>>>>> >>>> ==22304== by 0x4F2992D: R_doDotCall (dotcode.c:692)
>>>>>>> >>>> ==22304== by 0x4F339D5: do_dotcall (dotcode.c:1252)
>>>>>>> >>>> ==22304== by 0x4F81BA6: bcEval (eval.c:6771)
>>>>>>> >>>> ==22304== by 0x4F6E963: Rf_eval (eval.c:624)
>>>>>>> >>>> ==22304== by 0x4F71188: R_execClosure (eval.c:1764)
>>>>>>> >>>> ==22304== by 0x4F70E7C: Rf_applyClosure (eval.c:1692)
>>>>>>> >>>> ==22304== by 0x4F6F18B: Rf_eval (eval.c:747)
>>>>>>> >>>> ==22304== by 0x4F74B12: do_set (eval.c:2774)
>>>>>>> >>>> ==22304== by 0x4F6EDF5: Rf_eval (eval.c:699)
>>>>>>> >>>>
>>>>>>> >>>> 'Invalid write' suggests that you are writing after the end of
>>>>>>> >>>> memory that you'd allocated. I looked at the C code at the
>>>>>>> line
>>>>>>> >>>> where the error occurs as indicated in the stack trace,
>>>>>>> HMM.cpp:998
>>>>>>> >>>> which is the assigment myStateBucks[i] = 0 in the loop
>>>>>>> >>>>
>>>>>>> >>>> int *myStateBuckets = (int*)malloc(sizeof(int)*ncores+1);
>>>>>>> >>>> for(i=0; i<=ncores; i++)
>>>>>>> >>>> {
>>>>>>> >>>> myStateBuckets[i] = 0;
>>>>>>> >>>> }
>>>>>>> >>>>
>>>>>>> >>>> The argument to malloc (where he memory was allocated, at
>>>>>>> line 995)
>>>>>>> >>>> should be the number of bytes to allocate and it should
>>>>>>> have been
>>>>>>> >>>> memory for ncores + 1 'int'
>>>>>>> >>>>
>>>>>>> >>>> malloc(sizeof(int) * (ncores + 1))
>>>>>>> >>>>
>>>>>>> >>>> rather than what you wrote, which is memory for ncores ints
>>>>>>> plus 1
>>>>>>> >>>> byte.
>>>>>>> >>>>
>>>>>>> >>>> C++ code would avoid the need for such explicit memory
>>>>>>> management,
>>>>>>> >>>> e.g., using a vector from the standard template library
>>>>>>> >>>>
>>>>>>> >>>> std::vector<int> myStateBuckets(ncores);
>>>>>>> >>>
>>>>>>> >>> oops, std::vector<int> myStateBuckets(ncores + 1); !
>>>>>>> >>>>
>>>>>>> >>>> There were may other valgrind errors, but I do not know
>>>>>>> whether
>>>>>>> >>>> these are from similar programming errors, or a consequence
>>>>>>> of this
>>>>>>> >>>> one.
>>>>>>> >>>>
>>>>>>> >>>> Martin
>>>>>>> >>>>
>>>>>>> >>>>> Thanks,
>>>>>>> >>>>> Rafael
>>>>>>> >>>>>>
>>>>>>> >>>>>> On 03/29/2018 01:07 PM, campos wrote:
>>>>>>> >>>>>>> Dear bioc-devel team,
>>>>>>> >>>>>>>
>>>>>>> >>>>>>> I have made some changes in the package STAN and
>>>>>>> although it
>>>>>>> >>>>>>> seems to install correctly, I have problems with timeout
>>>>>>> and
>>>>>>> >>>>>>> error in windows... Could someone help me to improve the
>>>>>>> time?
>>>>>>> >>>>>>>
>>>>>>> >>>>>>> https://bioconductor.org/checkResults/3.7/bioc-LATEST/STAN/
>>>>>>> >>>>>>
>>>>>>> >>>>>> it looks like, with your most recent commit (at the top
>>>>>>> of the
>>>>>>> >>>>>> page, 'Snapshot Date', 'Last Commit', 'Last Changed
>>>>>>> Date'), the
>>>>>>> >>>>>> package built on Windows and Linux.
>>>>>>> >>>>>>
>>>>>>> >>>>>> There is a segfault on Mac, which is likely a programming
>>>>>>> error
>>>>>>> >>>>>> in your C code. It could be debugged perhaps using
>>>>>>> valgrind or
>>>>>>> >>>>>> similar tools, but the first step would be to isolate the
>>>>>>> code to
>>>>>>> >>>>>> something more easily reproduced than the full vignette.
>>>>>>> It would
>>>>>>> >>>>>> also help to clean up the C code so that it compiles without
>>>>>>> >>>>>> warnings with the -Wall -pedantic flags
>>>>>>> >>>>>>
>>>>>>> >>>>>> Martin
>>>>>>> >>>>>>
>>>>>>> >>>>>>>
>>>>>>> >>>>>>> Best,
>>>>>>> >>>>>>>
>>>>>>> >>>>>>> Rafael
>>>>>>> >>>>>>>
>>>>>>> >>>>>>>
>>>>>>> >>>>>>> On 28.03.2018 01:08, Martin Morgan wrote:
>>>>>>> >>>>>>>> When I try and install the version on the master branch
>>>>>>> of the
>>>>>>> >>>>>>>> Bioconductor git repository I get
>>>>>>> >>>>>>>>
>>>>>>> >>>>>>>> STAN master$ Rdev --vanilla CMD INSTALL .
>>>>>>> >>>>>>>> * installing to library
>>>>>>> >>>>>>>> ‘/home/mtmorgan/R/x86_64-pc-linux-gnu-library
>>>>>>> >>>>>>>> ...
>>>>>>> >>>>>>>> ** testing if installed package can be loaded
>>>>>>> >>>>>>>> Error: package or namespace load failed for 'STAN' in
>>>>>>> >>>>>>>> namespaceExport(ns, exports):
>>>>>>> >>>>>>>> undefined exports: viterbi2Gviz
>>>>>>> >>>>>>>>
>>>>>>> >>>>>>>>
>>>>>>> >>>>>>>> This comes about in a rather interesting way because
>>>>>>> the body
>>>>>>> >>>>>>>> of plotViterbi is not defined
>>>>>>> >>>>>>>>
>>>>>>> >>>>>>>> plotViterbi <- function(viterbi, regions, gen, chrom,
>>>>>>> from, to,
>>>>>>> >>>>>>>> statecols, col)
>>>>>>> >>>>>>>>
>>>>>>> >>>>>>>> #'
>>>>>>> >>>>>>>> ...
>>>>>>> >>>>>>>>
>>>>>>> >>>>>>>> Can you please commit a version of the package that
>>>>>>> installs?
>>>>>>> >>>>>>>>
>>>>>>> >>>>>>>> Martin
>>>>>>> >>>>>>>>
>>>>>>> >>>>>>>> On 03/27/2018 06:42 PM, campos wrote:
>>>>>>> >>>>>>>>> Dear bioc-devel team,
>>>>>>> >>>>>>>>>
>>>>>>> >>>>>>>>> I am developing the STAN packages and I am running into
>>>>>>> >>>>>>>>> problems when trying to build my package. The problem
>>>>>>> is the
>>>>>>> >>>>>>>>> following:
>>>>>>> >>>>>>>>>
>>>>>>> >>>>>>>>> Error in vignette_type(Outfile) :
>>>>>>> >>>>>>>>> Vignette product 'STAN.tex' does not have a known
>>>>>>> filename
>>>>>>> >>>>>>>>> extension ('NA')
>>>>>>> >>>>>>>>> ERROR: installing vignettes failed
>>>>>>> >>>>>>>>> * removing '/tmp/Rtmp925Iru/Rinst63471ff1efdc/STAN'
>>>>>>> >>>>>>>>> I tried to build the package in old versions (which
>>>>>>> they used
>>>>>>> >>>>>>>>> to work) and I run in other problems but in this case is:
>>>>>>> >>>>>>>>>
>>>>>>> >>>>>>>>> Error in texi2dvi(file = file, pdf = TRUE, clean = clean,
>>>>>>> >>>>>>>>> quiet = quiet, :
>>>>>>> >>>>>>>>> Running 'texi2dvi' on 'STAN.tex' failed.
>>>>>>> >>>>>>>>> LaTeX errors:
>>>>>>> >>>>>>>>> ! LaTeX Error: File `beramono.sty' not found.
>>>>>>> >>>>>>>>>
>>>>>>> >>>>>>>>> Type X to quit or <RETURN> to proceed,
>>>>>>> >>>>>>>>> or enter new name. (Default extension: sty)
>>>>>>> >>>>>>>>>
>>>>>>> >>>>>>>>> Could you help me with this problem?
>>>>>>> >>>>>>>>>
>>>>>>> >>>>>>>>> Thank you very much,
>>>>>>> >>>>>>>>>
>>>>>>> >>>>>>>>> Rafael
>>>>>>> >>>>>>>>>
>>>>>>> >>>>>>>>> _______________________________________________
>>>>>>> >>>>>>>>> Bioc-devel at r-project.org mailing list
>>>>>>> >>>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>>>> >>>>>>>>
>>>>>>> >>>>>>>>
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>>>>>>> >>>>>>
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>>>>>>> Thank you.
>>>>>>> >>>>>
>>>>>>> >>>>
>>>>>>> >>>>
>>>>>>> >>>> This email message may contain legally privileged
>>>>>>> >>>> and/or...{{dropped:2}}
>>>>>>> >>>>
>>>>>>> >>>> _______________________________________________
>>>>>>> >>>> Bioc-devel at r-project.org mailing list
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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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>>>>>>> message
>>>>>>> >>> is prohibited. If you have received this message in error,
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>>>>>>> >>
>>>>>>> >
>>>>>>> >
>>>>>>> > 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
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>>>>>>> prohibited. If
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>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Bioc-devel at r-project.org mailing list
>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>>>>
>>>>>>> This email message may contain legally privileged and/or
>>>>>>> confidential information. If you are not the intended
>>>>>>> recipient(s), or the employee or agent responsible for the
>>>>>>> delivery of this message to the intended recipient(s), you are
>>>>>>> hereby notified that any disclosure, copying, distribution, or
>>>>>>> use of this email message is prohibited. If you have received
>>>>>>> this message in error, please notify the sender immediately by
>>>>>>> e-mail and delete this email message from your computer. Thank you.
>>>>>>
>>>>>
>>>>>
>>>>> This email message may contain legally privileged and/or
>>>>> confidential information. If you are not the intended
>>>>> recipient(s), or the employee or agent responsible for the
>>>>> delivery of this message to the intended recipient(s), you are
>>>>> hereby notified that any disclosure, copying, distribution, or use
>>>>> of this email message is prohibited. If you have received this
>>>>> message in error, please notify the sender immediately by e-mail
>>>>> and delete this email message from your computer. Thank you.
>>>>
>>>
>>>
>>> This email message may contain legally privileged and/or
>>> confidential information. If you are not the intended recipient(s),
>>> or the employee or agent responsible for the delivery of this
>>> message to the intended recipient(s), you are hereby notified that
>>> any disclosure, copying, distribution, or use of this email message
>>> is prohibited. If you have received this message in error, please
>>> notify the sender immediately by e-mail and delete this email
>>> message from your computer. Thank you.
>>
>
>
> This email message may contain legally privileged and/or confidential
> information. If you are not the intended recipient(s), or the
> employee or agent responsible for the delivery of this message to the
> intended recipient(s), you are hereby notified that any disclosure,
> copying, distribution, or use of this email message is prohibited. If
> you have received this message in error, please notify the sender
> immediately by e-mail and delete this email message from your
> computer. Thank you.
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