[Bioc-devel] vignette problems

Martin Morgan martin.morgan at roswellpark.org
Mon Apr 2 02:51:04 CEST 2018 


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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