[Bioc-devel] vignette problems
Martin Morgan
martin.morgan at roswellpark.org
Tue Apr 10 23:44:52 CEST 2018
Hi --
I'm not sure what you mean; the 'devel' builld report does not include
mac (the build system experienced problems with disk space last night,
so the build did not complete)
https://bioconductor.org/checkResults/devel/bioc-LATEST/STAN/
and STAN failed in Release
https://bioconductor.org/checkResults/release/bioc-LATEST/STAN/
HOWEVER, I spent some time with your package. First, I compiled it with
compiler flages -Wall -pedantic, which makes the compiler quite
sensitive. I did this by creating, on my Linux, a file
$ cat ~/.R/Makevars
CFLAGS = -g -O0 -Wall -pedantic
CXXFLAGS = -g -O0 -Wall -pedantic
and then installing the package from the source directory
STAN master$ rm -f src/*o && R CMD INSTALL .
There were a number of minor issues (unused variables, incorrect printf
formatting [and use of printf() rather than Rprintf()]) as well as
somewhat more substantial problems (virtual destructors for polymorphic
base classes); a few problems remain, of the form
RWrapper.cpp:950:5: warning: control reaches end of non-void
function [-Wreturn-type]
}
where the problem is obvious -- no return value if parallel != 0 -- but
also innocuous, since it seems from inspection that in fact this
function is always invoked with parallel == 0
HMM* createHMM(int parallel, int K, InitialProbability* initProb,
TransitionMatrix* transMat, EmissionFunction** myEmissions)
{
if(parallel == 0)
{
return new HMM(K, initProb, transMat, myEmissions);
}
}
You should fix these problems, e.g., by removing the parallel argument
from the function and body. After cleaning up as best I could, I install
the package again and ran the vignette through valgrind
STAN master$ R CMD INSTALL .
...
STAN master$ cd vignettes
STAN/vignettes master$ R CMD Stangle STAN-knitr.Rnw
STAN/vignettes master$ R CMD Stangle STAN-knitr.Rnw
STAN/vignettes master$ R -d valgrind -f STAN-knitr.R
leading to an about mismatched new[] / delete[] -- memory allocated by
'new x[]' must be deleted with 'delete[]', but the package code had
simply 'delete'.
With these changes, the vignette builds without segfaulting or valgrind
errors on my machine, and on the Mac builder; I did not check the full
build and check of the package.
The changes are summarized in the following commits:
STAN master$ git log --oneline
a719f42 version bump
b8e2123 make destructors for polymorhpic base classes virtual
18ac6ba mismatch new[] / delete[]
985768b restore EmissionFactory::createEmissionFunctionMixed
8b749db provide return value for non-void functions
26ca36e update poor printf statements
0bb83ab clear 'unused variable' -Wall -pedantic warnings
a3b7666 remove vignette product STAN-knitr.R
You should pull these down to your local git repository, e.g., for me I have
STAN master$ git remote -v
origin git at git.bioconductor.org:packages/STAN (fetch)
origin git at git.bioconductor.org:packages/STAN (push)
So I would
STAN master$ git pull origin master
to incorporate the changes.
It would be good to port these changes to the RELEASE_3_6 branch;
remember to bump the version of the RELEASE_3_6 branch to 2.6.1.
Unfortunately, I pushed the changes after tonight's builds started, so
the effect of the changes will not be reported until Thursday
mid-morning, Eastern time, if the build system does not have problems.
Martin
On 04/10/2018 02:14 PM, campos wrote:
> 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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>>>>>> >>
>>>>>> >
>>>>>> >
>>>>>> > This email message may contain legally privileged and/or
>>>>>> confidential
>>>>>> > information. If you are not the intended recipient(s), or the
>>>>>> > employee or agent responsible for the delivery of this message
>>>>>> to the
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>>>>>> > immediately by e-mail and delete this email message from your
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>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioc-devel at r-project.org mailing list
>>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>>>
>>>>>> This email message may contain legally privileged and/or
>>>>>> confidential information. If you are not the intended
>>>>>> recipient(s), or the employee or agent responsible for the
>>>>>> delivery of this message to the intended recipient(s), you are
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>>>>>
>>>>
>>>>
>>>> This email message may contain legally privileged and/or
>>>> confidential information. If you are not the intended recipient(s),
>>>> or the employee or agent responsible for the delivery of this
>>>> message to the intended recipient(s), you are hereby notified that
>>>> any disclosure, copying, distribution, or use of this email message
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>>>> notify the sender immediately by e-mail and delete this email
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>>>
>>
>>
>> This email message may contain legally privileged and/or confidential
>> information. If you are not the intended recipient(s), or the
>> employee or agent responsible for the delivery of this message to the
>> intended recipient(s), you are hereby notified that any disclosure,
>> copying, distribution, or use of this email message is prohibited. If
>> you have received this message in error, please notify the sender
>> immediately by e-mail and delete this email message from your
>> computer. Thank you.
>
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