[Bioc-devel] vignette problems

[campos]

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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