[Bioc-devel] vignette problems

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

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