[Bioc-devel] vignette problems
campos
campos at mpipz.mpg.de
Tue Apr 10 20:14:12 CEST 2018
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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