[Bioc-devel] vignette problems
Martin Morgan
martin.morgan at roswellpark.org
Tue Apr 24 16:03:54 CEST 2018
On 04/24/2018 09:42 AM, campos wrote:
> Hi Martin,
>
> thanks for your reply. I do not have vignette warnings, the warnings
> that I see are:
>
> MultivariateGaussianFactory.h:23:9: warning: control reaches end of non-void function [-Wreturn-type]
> BernoulliFactory.h:27:9: warning: control reaches end of non-void function [-Wreturn-type]
> PoissonFactory.h:24:9: warning: control reaches end of non-void function [-Wreturn-type]
> MultinomialFactory.h:24:9: warning: control reaches end of non-void function [-Wreturn-type]
> NegativeBinomialFactory.h:27:9: warning: control reaches end of non-void function [-Wreturn-type]
> PoissonLogNormalFactory.h:27:9: warning: control reaches end of non-void function [-Wreturn-type]
> RWrapper.cpp:742:5: warning: control reaches end of non-void function [-Wreturn-type]
> RWrapper.cpp:950:5: warning: control reaches end of non-void function [-Wreturn-type]
>
yes it looks like you tackled those with the commit
STAN/src master$ git log MultivariateGaussianFactory.h
commit c43b951db86e4c167356ce8b380f6b8429ae0754
Author: rfael0cm <rfael0cm at gmail.com>
Date: Tue Apr 24 13:52:13 2018 +0200
Update DESCRIPTION FILE 2.7.8
which has not built yet (it will be included in tonight's build, for
Wednesday's build report.
I think the change you made will silence the warning
--- a/src/MultivariateGaussianFactory.h
+++ b/src/MultivariateGaussianFactory.h
@@ -20,6 +20,7 @@ class MultivariateGaussianFactory : public EmissionFactory
{
return new MultivariateGaussian(emissionParams);
}
+ return NULL;
}
but I wonder whether this is correct? Will your code really work if
these functions return NULL? My sense actually is that the 'parallel'
argument is never used (it's always 0), and that the correct solution is
to remove it from the signature and to make the return value unconditional
--- a/src/MultivariateGaussianFactory.h
+++ b/src/MultivariateGaussianFactory.h
@@ -10,17 +10,13 @@
class MultivariateGaussianFactory : public EmissionFactory
{
public:
- EmissionFunction*
createEmissionFunction(ParamContainerEmissions *emissionParams, int
parallel)
+ EmissionFunction*
createEmissionFunction(ParamContainerEmissions *emissionParams)
{
if(DEBUG_MEMORY)
{
Rprintf("factory->create():");
}
- if(parallel == 0)
- {
- return new MultivariateGaussian(emissionParams);
- }
- return NULL;
+ return new MultivariateGaussian(emissionParams);
}
MultivariateGaussianFactory() {}
~MultivariateGaussianFactory() { }
This requires other changes in the code, to make the calling functions
consistent. I guess this is a 'feature' that was planned but never
implemented; it's usually better to keep such features out of the public
version of your software.
Martin
>
> On 24.04.2018 15:39, Martin Morgan wrote:
>> I don't see vignette warnings on the build report.
>>
>> You should address the simple namespace issue by adding
>>
>> importFrom("stats", "dnbinom", "kmeans", "optim", "ppois")
>>
>> to your NAMESPACE file.
>>
>> The compiler warnings are from the -Wall flag, which you can set by
>> creating a plain text file
>>
>> ~/.R/Makevars
>>
>> with the line
>>
>> CFLAGS = -Wall
>> CXXFLAGS = -Wall
>>
>> Martin
>>
>>
>> On 04/24/2018 05:49 AM, campos wrote:
>>> Dear Bio-dev,
>>>
>>> I have a quick question, for some reason I can reproduce the warnings
>>> that are stated in
>>> https://bioconductor.org/checkResults/3.7/bioc-LATEST/STAN/malbec2-checksrc.html
>>> on my linux machine. The check runs smoothly, any idea why so?
>>>
>>> Thank you again,
>>>
>>> Rafael
>>>
>>>
>>> On 11.04.2018 16:52, Martin Morgan wrote:
>>>>
>>>>
>>>> On 04/11/2018 10:47 AM, campos wrote:
>>>>> Hi Martin,
>>>>>
>>>>> when I run git status I get this:
>>>>>
>>>>> On branch master
>>>>> Your branch is up-to-date with 'origin/master'.
>>>>> nothing to commit, working directory clean
>>>>>
>>>>> shouldn't I see that my version in my machine is some commits behind?
>>>>>
>>>>> $git remote -v
>>>>> origin git at git.bioconductor.org:packages/STAN (fetch)
>>>>> origin git at git.bioconductor.org:packages/STAN (push)
>>>>
>>>> maybe your version is current; I have
>>>>
>>>> ~/b/git/STAN master$ git log --oneline -n10
>>>> 06dbdae Merge remote-tracking branch 'upstream/master'
>>>> 6e070d4 version 2.7.3
>>>> 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
>>>> 1c4f140 upgrade version 2.7.3
>>>>
>>>> if you don't, then I guess `git pull` or more pedantically `git
>>>> fetch origin; git merge origin/master master`.
>>>>
>>>> Martin
>>>>
>>>>>
>>>>> Thanks a lot,
>>>>>
>>>>> Rafa
>>>>>
>>>>>
>>>>> On 11.04.2018 16:43, Martin Morgan wrote:
>>>>>>
>>>>>>
>>>>>> On 04/11/2018 09:58 AM, campos wrote:
>>>>>>> Hi Martin,
>>>>>>>
>>>>>>> thank you very much for your time and effort!
>>>>>>>
>>>>>>> I pulled the branch to my computer updated the DESCRIPTION file
>>>>>>> and pushed the changes. That should be enough right?
>>>>>>
>>>>>> actually I seemed to have messed up the git commit, but I fixed it
>>>>>> from my end; you should git pull and not worry about pushing any
>>>>>> further commits for the moment.
>>>>>>
>>>>>>>
>>>>>>> Best,
>>>>>>>
>>>>>>> Rafa
>>>>>>>
>>>>>>> PS: If you ever stop by Cologne please let me know. I owe you a
>>>>>>> beer or two!
>>>>>>
>>>>>> tasty!
>>>>>>
>>>>>> Martin
>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On 10.04.2018 23:44, Martin Morgan wrote:
>>>>>>>> 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
>>>>>>>>>>>>>> >>>>>>>>
>>>>>>>>>>>>>> >>>>>>>>
>>>>>>>>>>>>>> >>>>>>>> This email message may contain legally privileged
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>>>>>>>>>>>>>> intended
>>>>>>>>>>>>>> >>>>>>>> recipient(s), or the employee or agent
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>>>>>>>>>>>>>> >>>>>>>> delivery of this message to the intended
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>>>>>>>>>>>>>> >>>>>>>
>>>>>>>>>>>>>> >>>>>>
>>>>>>>>>>>>>> >>>>>>
>>>>>>>>>>>>>> >>>>>> This email message may contain legally privileged
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>>>>>>>>>>>>>> >>>>
>>>>>>>>>>>>>> >>>>
>>>>>>>>>>>>>> >>>> This email message may contain legally privileged
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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
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>>>>>>>>>>>>>> recipient(s),
>>>>>>>>>>>>>> >>> or the employee or agent responsible for the delivery
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>>>>>>>>>>>>>> error, please
>>>>>>>>>>>>>> >>> notify the sender immediately by e-mail and delete
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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
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>>>>>>>>>>>>>> > you have received this message in error, please notify
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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
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>>>>>>>>>>>>>> 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.
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> 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
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>>>>>>>>>>>> you have received this message in error, please notify the
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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
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>>>>>>>>>> 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.
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> 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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>>>>>>>> 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.
>>>>>>>
>>>>>>
>>>>>>
>>>>>> 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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>>>>>> 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.
>>>>>>
>>>>>
>>>>
>>>>
>>>> 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
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>>>> 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.
>>>>
>>>
>>
>>
>> This email message may contain legally privileged and/or confidential
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