[Bioc-devel] vignette problems
Martin Morgan
martin.morgan at roswellpark.org
Tue Apr 10 11:33:26 CEST 2018
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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