Re: [Bioc-devel] Ask for help to debug the error on riesling1
Hi Martin,
Thank you for going so deep. I tried
R -d "valgrind --leak-check=full --track-origins=yes" -f plotInteractionData.R
to locate the exact line where initialed the possible leak.
Is there any other possibility that killed the process and did not leave any
error log information?
Jianhong.
From: Martin Morgan
Sent: Wednesday, April 7, 2021 2:16 PM
To: Jianhong Ou, Ph.D. ; Hervé Pagès
; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Ask for help to debug the error on riesling1
I followed these steps, more or less, to configure and use valgrind on the
Bioconductor docker image.
https://urldefense.com/v3/__https://gist.github.com/mtmorgan/77f9d92d81830eeb7f254809b445874d__;!!OToaGQ!-g840WABoFzxZ4_VS8wWp_YSW6KeHVFxX66mQcS2nGxeHwk8XlzjCnonGt7rnWeMU0g$
For this particular use I
- added the valgrind system dependency
- installed trackViewer and it's 'Suggests' dependencies in a standard R session
- made a git clone --depth 1
https://urldefense.com/v3/__https://git.bioconductor.org/packages/trackViewer__;!!OToaGQ!-g840WABoFzxZ4_VS8wWp_YSW6KeHVFxX66mQcS2nGxeHwk8XlzjCnonGt7rzc3RP4s$
- made an R script from the vignette via cd vignettes && R CMD Stangle...
- ran once with
root@8dd16a8006a1:/tmp/trackViewer/vignettes# R -f plotInteractionData.R
as a sanity check, then
root@8dd16a8006a1:/tmp/trackViewer/vignettes# R -d valgrind -f
plotInteractionData.R
This lead to a single suspicious valgrind message
> importGInteractions(file=hic, format="hic",
+ ranges=GRanges("22", IRanges(5000, 1)),
+ out = "GInteractions")
==29679== Conditional jump or move depends on uninitialised value(s)
==29679==at 0x48428EC: memset (in
/usr/lib/x86_64-linux-gnu/valgrind/vgpreload_memcheck-amd64-linux.so)
==29679==by 0x212D08FF: memset (string_fortified.h:71)
==29679==by 0x212D08FF: select_hits (Hits_class.c:324)
==29679==by 0x4944EB3: R_doDotCall (dotcode.c:614)
==29679==by 0x4945464: do_dotcall (dotcode.c:1281)
==29679==by 0x498AC35: bcEval (eval.c:7072)
==29679==by 0x4999DA7: Rf_eval (eval.c:727)
==29679==by 0x499BBDE: R_execClosure (eval.c:1897)
==29679==by 0x499CAD1: Rf_applyClosure (eval.c:1823)
==29679==by 0x4987DBD: bcEval (eval.c:7083)
==29679==by 0x4999DA7: Rf_eval (eval.c:727)
==29679==by 0x499BBDE: R_execClosure (eval.c:1897)
==29679==by 0x499CAD1: Rf_applyClosure (eval.c:1823)
==29679==
Hits_class.c:324 is in S4Vectors
if (nodup0) {
is_used = _new_CharAE(get_nnode(nRnode, "R"));
memset(is_used->elts, 0, is_used->_buflength);
}
I re-ran under gdb
root@8dd16a8006a1:/tmp/trackViewer/vignettes# R -d valgrind -f
plotInteractionData.R
...
(gdb) break Hits_class.c:324
(gdb) run
...
(gdb) continue
...
> importGInteractions(file=hic, format="hic",
+ ranges=GRanges("22", IRanges(5000, 1)),
+ out = "GInteractions")
Thread 1 "R" hit Breakpoint 1, select_hits (from=,
to=, nLnode=, nRnode=0x56071b51d5e8,
select=, nodup=) at Hits_class.c:327
327 in Hits_class.c
(gdb) p *is_used
$2 = {_buflength = 0, _nelt = 0, elts = 0x0}
I guess the complaint is about elts = 0x0, but I'm not really sure if this is
enough to cause a fault during package build -- it seems like the code writes
nothing nowhere, but ...
Martin Morgan
On 4/7/21, 8:08 AM, "Bioc-devel on behalf of Jianhong Ou, Ph.D."
wrote:
Hi Herv�,
Thank you for the information. I will try to figure out.
Jianhong.
From: Herv� Pag�s
Sent: Wednesday, April 7, 2021 1:54 AM
To: Jianhong Ou, Ph.D. ; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Ask for help to debug the error on riesling1
Hi Jianhong,
Memory leaks and other memory errors are bugs in native code that often
exist on all platforms but typically manifest themselves in different
ways depending on the platform where it runs. Running your code thru a
tool like Valgrind should reveal these problems even if you do this on a
non-Windows machine. See
https://urldefense.com/v3/__https://bioconductor.org/developers/how-to/c-debugging/__;!!OToaGQ!6X7J1i17XSPaKkNmZMcdEY24rEjchLfeQ8YTdhLB68dZII3WDxYfoPTTpGr2AOjQ4ds$
for more information.
Best,
H.
On 4/6/21 6:46 AM, Jianhong Ou, Ph.D. wrote:
> Hi,
>
> The trackViewer package got error on Windows Server since version 1.27.4.
I am totally lost to figure it out by myself. The current error message listed
in building system is:
>
>
> * creating vignettes ... ERROR
> --- re-building 'changeTracksStyles.Rmd' using rmarkdown
> --- finished re-building 'changeTracksStyles.Rmd'
>
> --- re-building 'dandelionPlot.Rmd' using rmarkdown
> --- finished re-building 'dandelionPlot.Rmd'
>
> --- re-building
Re: [Bioc-devel] Ask for help to debug the error on riesling1
I followed these steps, more or less, to configure and use valgrind on the
Bioconductor docker image.
https://gist.github.com/mtmorgan/77f9d92d81830eeb7f254809b445874d
For this particular use I
- added the valgrind system dependency
- installed trackViewer and it's 'Suggests' dependencies in a standard R session
- made a git clone --depth 1 https://git.bioconductor.org/packages/trackViewer
- made an R script from the vignette via cd vignettes && R CMD Stangle...
- ran once with
root@8dd16a8006a1:/tmp/trackViewer/vignettes# R -f plotInteractionData.R
as a sanity check, then
root@8dd16a8006a1:/tmp/trackViewer/vignettes# R -d valgrind -f
plotInteractionData.R
This lead to a single suspicious valgrind message
> importGInteractions(file=hic, format="hic",
+ ranges=GRanges("22", IRanges(5000, 1)),
+ out = "GInteractions")
==29679== Conditional jump or move depends on uninitialised value(s)
==29679==at 0x48428EC: memset (in
/usr/lib/x86_64-linux-gnu/valgrind/vgpreload_memcheck-amd64-linux.so)
==29679==by 0x212D08FF: memset (string_fortified.h:71)
==29679==by 0x212D08FF: select_hits (Hits_class.c:324)
==29679==by 0x4944EB3: R_doDotCall (dotcode.c:614)
==29679==by 0x4945464: do_dotcall (dotcode.c:1281)
==29679==by 0x498AC35: bcEval (eval.c:7072)
==29679==by 0x4999DA7: Rf_eval (eval.c:727)
==29679==by 0x499BBDE: R_execClosure (eval.c:1897)
==29679==by 0x499CAD1: Rf_applyClosure (eval.c:1823)
==29679==by 0x4987DBD: bcEval (eval.c:7083)
==29679==by 0x4999DA7: Rf_eval (eval.c:727)
==29679==by 0x499BBDE: R_execClosure (eval.c:1897)
==29679==by 0x499CAD1: Rf_applyClosure (eval.c:1823)
==29679==
Hits_class.c:324 is in S4Vectors
if (nodup0) {
is_used = _new_CharAE(get_nnode(nRnode, "R"));
memset(is_used->elts, 0, is_used->_buflength);
}
I re-ran under gdb
root@8dd16a8006a1:/tmp/trackViewer/vignettes# R -d valgrind -f
plotInteractionData.R
...
(gdb) break Hits_class.c:324
(gdb) run
...
(gdb) continue
...
> importGInteractions(file=hic, format="hic",
+ ranges=GRanges("22", IRanges(5000, 1)),
+ out = "GInteractions")
Thread 1 "R" hit Breakpoint 1, select_hits (from=,
to=, nLnode=, nRnode=0x56071b51d5e8,
select=, nodup=) at Hits_class.c:327
327 in Hits_class.c
(gdb) p *is_used
$2 = {_buflength = 0, _nelt = 0, elts = 0x0}
I guess the complaint is about elts = 0x0, but I'm not really sure if this is
enough to cause a fault during package build -- it seems like the code writes
nothing nowhere, but ...
Martin Morgan
On 4/7/21, 8:08 AM, "Bioc-devel on behalf of Jianhong Ou, Ph.D."
wrote:
Hi Herv�,
Thank you for the information. I will try to figure out.
Jianhong.
From: Herv� Pag�s
Sent: Wednesday, April 7, 2021 1:54 AM
To: Jianhong Ou, Ph.D. ; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Ask for help to debug the error on riesling1
Hi Jianhong,
Memory leaks and other memory errors are bugs in native code that often
exist on all platforms but typically manifest themselves in different
ways depending on the platform where it runs. Running your code thru a
tool like Valgrind should reveal these problems even if you do this on a
non-Windows machine. See
https://urldefense.com/v3/__https://bioconductor.org/developers/how-to/c-debugging/__;!!OToaGQ!6X7J1i17XSPaKkNmZMcdEY24rEjchLfeQ8YTdhLB68dZII3WDxYfoPTTpGr2AOjQ4ds$
for more information.
Best,
H.
On 4/6/21 6:46 AM, Jianhong Ou, Ph.D. wrote:
> Hi,
>
> The trackViewer package got error on Windows Server since version 1.27.4.
I am totally lost to figure it out by myself. The current error message listed
in building system is:
>
>
> * creating vignettes ... ERROR
> --- re-building 'changeTracksStyles.Rmd' using rmarkdown
> --- finished re-building 'changeTracksStyles.Rmd'
>
> --- re-building 'dandelionPlot.Rmd' using rmarkdown
> --- finished re-building 'dandelionPlot.Rmd'
>
> --- re-building 'lollipopPlot.Rmd' using rmarkdown
> --- finished re-building 'lollipopPlot.Rmd'
>
> --- re-building 'plotInteractionData.Rmd' using rmarkdown
>
> I suppose this is a memory leak error. But I don't have windows server to
repeat the error. What is the best way to fix the issue? Thank you in advance
for your help.
>
>
> Yours Sincerely,
>
> Jianhong Ou
>
> Email: jianhong...@duke.edu
> Bioinformatician II
> Department of Cell Biology
> Duke University School of Medicine
> Durham, NC, 27710
>
> Confidentiality Notice:\ This e-mail message, including ...{{dropped:12}}
>
> ___
> Bioc-devel@r-project.org mailing list
>
Re: [Bioc-devel] Ask for help to debug the error on riesling1
Hi Herv�,
Thank you for the information. I will try to figure out.
Jianhong.
From: Herv� Pag�s
Sent: Wednesday, April 7, 2021 1:54 AM
To: Jianhong Ou, Ph.D. ; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Ask for help to debug the error on riesling1
Hi Jianhong,
Memory leaks and other memory errors are bugs in native code that often
exist on all platforms but typically manifest themselves in different
ways depending on the platform where it runs. Running your code thru a
tool like Valgrind should reveal these problems even if you do this on a
non-Windows machine. See
https://urldefense.com/v3/__https://bioconductor.org/developers/how-to/c-debugging/__;!!OToaGQ!6X7J1i17XSPaKkNmZMcdEY24rEjchLfeQ8YTdhLB68dZII3WDxYfoPTTpGr2AOjQ4ds$
for more information.
Best,
H.
On 4/6/21 6:46 AM, Jianhong Ou, Ph.D. wrote:
> Hi,
>
> The trackViewer package got error on Windows Server since version 1.27.4. I
> am totally lost to figure it out by myself. The current error message listed
> in building system is:
>
>
> * creating vignettes ... ERROR
> --- re-building 'changeTracksStyles.Rmd' using rmarkdown
> --- finished re-building 'changeTracksStyles.Rmd'
>
> --- re-building 'dandelionPlot.Rmd' using rmarkdown
> --- finished re-building 'dandelionPlot.Rmd'
>
> --- re-building 'lollipopPlot.Rmd' using rmarkdown
> --- finished re-building 'lollipopPlot.Rmd'
>
> --- re-building 'plotInteractionData.Rmd' using rmarkdown
>
> I suppose this is a memory leak error. But I don't have windows server to
> repeat the error. What is the best way to fix the issue? Thank you in advance
> for your help.
>
>
> Yours Sincerely,
>
> Jianhong Ou
>
> Email: jianhong...@duke.edu
> Bioinformatician II
> Department of Cell Biology
> Duke University School of Medicine
> Durham, NC, 27710
>
> Confidentiality Notice:\ This e-mail message, including ...{{dropped:12}}
>
> ___
> Bioc-devel@r-project.org mailing list
> https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc-devel__;!!OToaGQ!6X7J1i17XSPaKkNmZMcdEY24rEjchLfeQ8YTdhLB68dZII3WDxYfoPTTpGr2_rFwouU$
>
--
Herv� Pag�s
Bioconductor Core Team
hpages.on.git...@gmail.com
[[alternative HTML version deleted]]
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Ask for help to debug the error on riesling1
Hi Jianhong,
Memory leaks and other memory errors are bugs in native code that often
exist on all platforms but typically manifest themselves in different
ways depending on the platform where it runs. Running your code thru a
tool like Valgrind should reveal these problems even if you do this on a
non-Windows machine. See
https://bioconductor.org/developers/how-to/c-debugging/
for more information.
Best,
H.
On 4/6/21 6:46 AM, Jianhong Ou, Ph.D. wrote:
Hi,
The trackViewer package got error on Windows Server since version 1.27.4. I am
totally lost to figure it out by myself. The current error message listed in
building system is:
* creating vignettes ... ERROR
--- re-building 'changeTracksStyles.Rmd' using rmarkdown
--- finished re-building 'changeTracksStyles.Rmd'
--- re-building 'dandelionPlot.Rmd' using rmarkdown
--- finished re-building 'dandelionPlot.Rmd'
--- re-building 'lollipopPlot.Rmd' using rmarkdown
--- finished re-building 'lollipopPlot.Rmd'
--- re-building 'plotInteractionData.Rmd' using rmarkdown
I suppose this is a memory leak error. But I don't have windows server to
repeat the error. What is the best way to fix the issue? Thank you in advance
for your help.
Yours Sincerely,
Jianhong Ou
Email: jianhong...@duke.edu
Bioinformatician II
Department of Cell Biology
Duke University School of Medicine
Durham, NC, 27710
Confidentiality Notice:\ This e-mail message, including ...{{dropped:12}}
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
Bioconductor Core Team
hpages.on.git...@gmail.com
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Ask for help to debug the error on riesling1
Hi,
The trackViewer package got error on Windows Server since version 1.27.4. I am
totally lost to figure it out by myself. The current error message listed in
building system is:
* creating vignettes ... ERROR
--- re-building 'changeTracksStyles.Rmd' using rmarkdown
--- finished re-building 'changeTracksStyles.Rmd'
--- re-building 'dandelionPlot.Rmd' using rmarkdown
--- finished re-building 'dandelionPlot.Rmd'
--- re-building 'lollipopPlot.Rmd' using rmarkdown
--- finished re-building 'lollipopPlot.Rmd'
--- re-building 'plotInteractionData.Rmd' using rmarkdown
I suppose this is a memory leak error. But I don't have windows server to
repeat the error. What is the best way to fix the issue? Thank you in advance
for your help.
Yours Sincerely,
Jianhong Ou
Email: jianhong...@duke.edu
Bioinformatician II
Department of Cell Biology
Duke University School of Medicine
Durham, NC, 27710
Confidentiality Notice:\ This e-mail message, including ...{{dropped:12}}
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
