[Bioc-devel] vignette problems
campos
campos at mpipz.mpg.de
Tue Apr 10 11:27:14 CEST 2018
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?
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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