Re: [R-pkg-devel] Package valgrind problem I can't solve: Direction?

2017-11-05 Thread Peter Dunn 
Impossible or not… it just happened (unless I am being really stupid, which is 
entirely possible, indeed probable).  I confirmed again this morning: After 
rebuilding (R CMD build) and checking (R CMD check) without any errors, I used 
rhub and the command line again:


Running valgrind at the command line, I get this error:

==5097== Conditional jump or move depends on uninitialised value(s)
==5097==at 0x1118F61FB: smallp_ (in 
/Users/pdunn2/Library/R/3.4/library/tweedie/libs/tweedie.so)

…when I am here:

$ pwd
/Users/pdunn2/Documents/Research/Rpackages/tweedie/tweedie-debug/CRAN-update/tweedie.Rcheck



In rhub:

check_with_valgrind("tweedie")

gives:

── 0 errors ✔ | 0 warnings ✔ | 0 notes ✔
─  Done with R CMD check
─  Saving artifacts

…when I am here:

> getwd()
[1] 
"/Users/pdunn2/Documents/Research/Rpackages/tweedie/tweedie-debug/CRAN-update"




I will take this to mean that there really is no problem… and put this down to 
things I don’t understand and “experience”.

Thanks for everyone’s help.

P.

From: Iñaki Úcar 
Date: Friday, 3 November 2017 at 7:45 pm
To: Peter Dunn 
Cc: "r-package-devel@r-project.org" 
Subject: Re: [R-pkg-devel] Package valgrind problem I can't solve: Direction?

2017-11-03 6:01 GMT+01:00 Peter Dunn :
> Iñaki and all
>
> Well, thanks for pointers to rhub. Wonderful. Moving things to github, but
> have to go home now…
>
> So, when I download CRAN code, initialise w and lambda (which workled for
> Iñaki), and run
>
> rhub::check_with_valgrind()
>
> on the code, I get no errors
> (https://builder.r-hub.io/status/tweedie_2.2.5.tar.gz-c8873979fcf84b4f8a0a4d5a47175f63).
>
>
> But running
>
> R -d "valgrind --tool=memcheck --leak-check=full --track-origins=yes"
> --vanilla < tweedie-Ex.R
>
> from the command line *still* gives me errors about “Conditional jump or
> move depends on uninitialised value(s)” in the subroutine smallp”.

That's impossible. Did you rebuild and reinstall the package after
making those changes?

Iñaki



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Re: [R-pkg-devel] Package valgrind problem I can't solve: Direction?

2017-11-05 Thread Iñaki Úcar 
2017-11-06 0:09 GMT+01:00 Peter Dunn :
> Impossible or not… it just happened (unless I am being really stupid, which
> is entirely possible, indeed probable). I confirmed again this morning:
> After rebuilding (R CMD build) and checking (R CMD check) without any
> errors, I used rhub and the command line again:
>
>
> Running valgrind at the command line, I get this error:
>
> ==5097== Conditional jump or move depends on uninitialised value(s)
> ==5097== at 0x1118F61FB: smallp_ (in
> /Users/pdunn2/Library/R/3.4/library/tweedie/libs/tweedie.so)

What I meant is that, if you run the script in tweedie.Rcheck from the
command line, Rscript uses your *installed* version of tweedie, not
the tarball you built with R CMD build. So if you didn't run R CMD
INSTALL, Rscript is running an old version without any fix, hence the
disagreement with R CMD check.

Iñaki

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Re: [R-pkg-devel] Package valgrind problem I can't solve: Direction?

2017-11-05 Thread Peter Dunn 
“unless I am being really stupid”

Lucky for that caveat. Feeling rather stupid for this late effort.

Thanks so much.  Help greatly appreciated.

P.



On 6/Nov/17, 9:51 am, "Iñaki Úcar"  wrote:

2017-11-06 0:09 GMT+01:00 Peter Dunn :
> Impossible or not… it just happened (unless I am being really stupid, 
which
> is entirely possible, indeed probable). I confirmed again this morning:
> After rebuilding (R CMD build) and checking (R CMD check) without any
> errors, I used rhub and the command line again:
>
>
> Running valgrind at the command line, I get this error:
>
> ==5097== Conditional jump or move depends on uninitialised value(s)
> ==5097== at 0x1118F61FB: smallp_ (in
> /Users/pdunn2/Library/R/3.4/library/tweedie/libs/tweedie.so)

What I meant is that, if you run the script in tweedie.Rcheck from the
command line, Rscript uses your *installed* version of tweedie, not
the tarball you built with R CMD build. So if you didn't run R CMD
INSTALL, Rscript is running an old version without any fix, hence the
disagreement with R CMD check.

Iñaki



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Re: [R-pkg-devel] Package valgrind problem I can't solve: Direction?

2017-11-05 Thread Merlise Clyde, Ph.D. 
Peter,

I ran into similar problems with using valgrind to check  my package  BAS

From my understanding using valgrind with rhub does not run the same checks as

R -d "valgrind --tool=memcheck --leak-check=full" --vanilla < mypkg-Ex.R


see https://github.com/r-hub/rhub/issues/23
which might explain why it will run without errors there but the CRAN check 
will flag errors/warnings.  (perhaps someone else can confirm)


best,
Merlise


Merlise A Clyde
Professor & Chair Department of Statistical Science
Duke University
http://stat.duke.edu/~clyde

cl...@duke.edu
919 681 8440




On Nov 5, 2017, at 7:05 PM, Peter Dunn 
mailto:pdu...@usc.edu.au>> wrote:

“unless I am being really stupid”

Lucky for that caveat. Feeling rather stupid for this late effort.

Thanks so much.  Help greatly appreciated.

P.



On 6/Nov/17, 9:51 am, "Iñaki Úcar" 
mailto:i.uca...@gmail.com>> wrote:

   2017-11-06 0:09 GMT+01:00 Peter Dunn 
mailto:pdu...@usc.edu.au>>:
Impossible or not… it just happened (unless I am being really stupid, which
is entirely possible, indeed probable). I confirmed again this morning:
After rebuilding (R CMD build) and checking (R CMD check) without any
errors, I used rhub and the command line again:


Running valgrind at the command line, I get this error:

==5097== Conditional jump or move depends on uninitialised value(s)
==5097== at 0x1118F61FB: smallp_ (in
/Users/pdunn2/Library/R/3.4/library/tweedie/libs/tweedie.so)

   What I meant is that, if you run the script in tweedie.Rcheck from the
   command line, Rscript uses your *installed* version of tweedie, not
   the tarball you built with R CMD build. So if you didn't run R CMD
   INSTALL, Rscript is running an old version without any fix, hence the
   disagreement with R CMD check.

   Iñaki



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CRICOS Provider No: 01595D
Please consider the environment before printing this email.
This email is confidential. If received in error, please delete it from your 
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