Re: [Bioc-devel] vignette problems

[Martin Morgan]

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 <rfael...@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 g...@git.bioconductor.org:packages/STAN (fetch)
origin g...@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 g...@git.bioconductor.org:packages/STAN (fetch)
    origin g...@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-boun...@r-project.org> on 
behalf of campos <cam...@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
>>>>>>>>>
>>>>>>>>> _______________________________________________
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>>>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>>>>>
>>>>>>>>
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>>>>>>
>>>>>>
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>>>>
>>>>
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