Re: [Bioc-devel] check fails on arch 'i386'
Many thanks Kasper, this would be much appreciated.
Best,
Tim
On 18/10/19 12:58 am, Kasper Daniel Hansen wrote:
I see these packages may have something to do with mini. There is a a (very
old, nothing new) issue with the annotation objects in minfi where loading them
uses a _lot_ of ram. For a long time I couldn't understand it, but now I get
it. I should really fix this, and probably _very_soon. It won't have any real
user-visible changes (unless you're using the SNP functionality which is very
nice but not used by many people I think), but it will require a new set of
annotation packages.
Best,
Kasper
On Thu, Oct 17, 2019 at 4:08 AM Tim Peters
mailto:t.pet...@garvan.org.au>> wrote:
Hi Hervé (and Reka),
I am having much the same problem on tokay1 with DMRcate
(https://bioconductor.org/checkResults/3.10/bioc-LATEST/DMRcate/tokay1-checksrc.html).
I've gone through a number of iterations trying to minimise the amount
of memory run by the examples (including your suggestions such as using
GRanges as a container for everything in a CpGannotated object, and
restricting analysis to 100 CpG sites) but the memory allocation error
is persistent, failing to allocate a quite modest ~500Mb.
I suspect it's being caused by minfi::makeGenomicRatioSetFromMatrix()
which is called by cpg.annotate() and DMR.plot() - I started a thread
here around the time of the April release concerning the problem but it
wasn't responded to:
https://stat.ethz.ch/pipermail/bioc-devel/2019-April/015012.html
This leaves me in a bind as minfi::makeGenomicRatioSetFromMatrix() has
exactly the functionality cpg.annotate() and DMR.plot() needs, plus it
provides minimal code and I don't really want to reinvent the wheel here!
Would it be possible to waive the 32-bit Windows build for DMRcate?
Best,
Tim
On 15/10/19 4:34 am, Pages, Herve wrote:
> Hi Toth,
>
> Not clear to me what's going on but I kind of suspect this might have
> something to do with the use of data.table.
>
> A few things to keep in mind:
>
> - 'R CMD check' runs all the example in the same R session. This means
> that the outcome of the examples of a given man page can be affected by
> the examples from other man pages.
>
> - A process cannot allocate more than 3 Gb of memory on 32-bit Windows.
> There is no such limit on 64-bit Windows or on the other platforms we
> support (Linux and Mac). On these platforms the maximum amount of memory
> a process can allocate only depends on what's available on the system.
>
> - Generally speaking, sticking to the Bioconductor way of doing things
> (e.g use of GRanges objects instead of data.table objects, use of
> findOverlaps() instead of data.table::foverlaps()) will lead to faster
> code and reduced memory usage. Therefore I would strongly encourage you
> to consider switching to GRanges/findOverlaps() and to avoid the use of
> data.table in methrix.
>
> Best,
> H.
>
>
> On 10/11/19 09:36, Toth, Reka wrote:
>> Dear BioC developers,
>>
>> The most recent build of methrix fails on Tokay1 server:
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_spb-5Freports_methrix-5Fbuildreport-5F20191009174210.html=DwIF-g=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=doO3ej8vD58ZBQWVxkHTaCLk-xipbskav8uofJL2syI=zs3uDnFqyAl-hr_7StB3Yr-tGZW8VPfclbPY_JKtSt8=
>> The error message is the following:
>>
>> ** running examples for arch 'i386' ... ERROR
>> Running examples in 'methrix-Ex.R' failed
>> The error most likely occurred in:
>>
>>> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
>>> ### Name: get_region_summary
>>> ### Title: Extract and summarize methylation or coverage info by regions of
>>> ### interest
>>> ### Aliases: get_region_summary
>>>
>>> ### ** Examples
>>>
>>> data("methrix_data")
>>> get_region_summary(m = methrix_data, regions = data.table(chr = "chr21",
>>> start = 27867971, end = 27868103), type = "M", how = "mean")
>> -Checking for overlaps..
>> Error: cannot allocate vector of size 1.4 Gb
>> Execution halted
>>
>> I am a bit puzzled what the reasons could be, since it passed this step
>> during the previous builds and I didn’t change any of the functions in my
>> last commit.
>> When I run the check on our local Windows, I don’t get any error. We use a
>> very small dataset as example, it definitely should not use a vector of size
>> 1.4 Gb.
>>
>> I would appreciate every input or idea on how to tackle this error.
>> Thanks a lot!
>>
>> Best,
>> Reka
>>
>> Dr. Reka Toth
>> Computational Epigenomics Group
>> Division of Epigenomics and Cancer Risk Factors /C010
>> Postdoctoral Fellow
>>
>> German Cancer Research Center (DKFZ)
>> Foundation under Public Law
>> Im Neuenheimer Feld 280
>> 69120 Heidelberg
>> Germany
>>
>> r.t...@dkfz-heidelberg.de
>>
Re: [Bioc-devel] check fails on arch 'i386'
I see these packages may have something to do with mini. There is a a (very
old, nothing new) issue with the annotation objects in minfi where loading
them uses a _lot_ of ram. For a long time I couldn't understand it, but now
I get it. I should really fix this, and probably _very_soon. It won't have
any real user-visible changes (unless you're using the SNP functionality
which is very nice but not used by many people I think), but it will
require a new set of annotation packages.
Best,
Kasper
On Thu, Oct 17, 2019 at 4:08 AM Tim Peters wrote:
> Hi Hervé (and Reka),
>
> I am having much the same problem on tokay1 with DMRcate
> (
> https://bioconductor.org/checkResults/3.10/bioc-LATEST/DMRcate/tokay1-checksrc.html
> ).
>
>
> I've gone through a number of iterations trying to minimise the amount
> of memory run by the examples (including your suggestions such as using
> GRanges as a container for everything in a CpGannotated object, and
> restricting analysis to 100 CpG sites) but the memory allocation error
> is persistent, failing to allocate a quite modest ~500Mb.
>
> I suspect it's being caused by minfi::makeGenomicRatioSetFromMatrix()
> which is called by cpg.annotate() and DMR.plot() - I started a thread
> here around the time of the April release concerning the problem but it
> wasn't responded to:
>
> https://stat.ethz.ch/pipermail/bioc-devel/2019-April/015012.html
>
> This leaves me in a bind as minfi::makeGenomicRatioSetFromMatrix() has
> exactly the functionality cpg.annotate() and DMR.plot() needs, plus it
> provides minimal code and I don't really want to reinvent the wheel here!
>
> Would it be possible to waive the 32-bit Windows build for DMRcate?
>
> Best,
>
> Tim
>
> On 15/10/19 4:34 am, Pages, Herve wrote:
> > Hi Toth,
> >
> > Not clear to me what's going on but I kind of suspect this might have
> > something to do with the use of data.table.
> >
> > A few things to keep in mind:
> >
> > - 'R CMD check' runs all the example in the same R session. This means
> > that the outcome of the examples of a given man page can be affected by
> > the examples from other man pages.
> >
> > - A process cannot allocate more than 3 Gb of memory on 32-bit Windows.
> > There is no such limit on 64-bit Windows or on the other platforms we
> > support (Linux and Mac). On these platforms the maximum amount of memory
> > a process can allocate only depends on what's available on the system.
> >
> > - Generally speaking, sticking to the Bioconductor way of doing things
> > (e.g use of GRanges objects instead of data.table objects, use of
> > findOverlaps() instead of data.table::foverlaps()) will lead to faster
> > code and reduced memory usage. Therefore I would strongly encourage you
> > to consider switching to GRanges/findOverlaps() and to avoid the use of
> > data.table in methrix.
> >
> > Best,
> > H.
> >
> >
> > On 10/11/19 09:36, Toth, Reka wrote:
> >> Dear BioC developers,
> >>
> >> The most recent build of methrix fails on Tokay1 server:
> >>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_spb-5Freports_methrix-5Fbuildreport-5F20191009174210.html=DwIF-g=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=doO3ej8vD58ZBQWVxkHTaCLk-xipbskav8uofJL2syI=zs3uDnFqyAl-hr_7StB3Yr-tGZW8VPfclbPY_JKtSt8=
> >> The error message is the following:
> >>
> >> ** running examples for arch 'i386' ... ERROR
> >> Running examples in 'methrix-Ex.R' failed
> >> The error most likely occurred in:
> >>
> >>> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> >>> ### Name: get_region_summary
> >>> ### Title: Extract and summarize methylation or coverage info by
> regions of
> >>> ### interest
> >>> ### Aliases: get_region_summary
> >>>
> >>> ### ** Examples
> >>>
> >>> data("methrix_data")
> >>> get_region_summary(m = methrix_data, regions = data.table(chr =
> "chr21", start = 27867971, end = 27868103), type = "M", how = "mean")
> >> -Checking for overlaps..
> >> Error: cannot allocate vector of size 1.4 Gb
> >> Execution halted
> >>
> >> I am a bit puzzled what the reasons could be, since it passed this step
> during the previous builds and I didn’t change any of the functions in my
> last commit.
> >> When I run the check on our local Windows, I don’t get any error. We
> use a very small dataset as example, it definitely should not use a vector
> of size 1.4 Gb.
> >>
> >> I would appreciate every input or idea on how to tackle this error.
> >> Thanks a lot!
> >>
> >> Best,
> >> Reka
> >>
> >> Dr. Reka Toth
> >> Computational Epigenomics Group
> >> Division of Epigenomics and Cancer Risk Factors /C010
> >> Postdoctoral Fellow
> >>
> >> German Cancer Research Center (DKFZ)
> >> Foundation under Public Law
> >> Im Neuenheimer Feld 280
> >> 69120 Heidelberg
> >> Germany
> >>
> >> r.t...@dkfz-heidelberg.de
> >>
>
Re: [Bioc-devel] check fails on arch 'i386'
Hi Hervé (and Reka),
I am having much the same problem on tokay1 with DMRcate
(https://bioconductor.org/checkResults/3.10/bioc-LATEST/DMRcate/tokay1-checksrc.html).
I've gone through a number of iterations trying to minimise the amount
of memory run by the examples (including your suggestions such as using
GRanges as a container for everything in a CpGannotated object, and
restricting analysis to 100 CpG sites) but the memory allocation error
is persistent, failing to allocate a quite modest ~500Mb.
I suspect it's being caused by minfi::makeGenomicRatioSetFromMatrix()
which is called by cpg.annotate() and DMR.plot() - I started a thread
here around the time of the April release concerning the problem but it
wasn't responded to:
https://stat.ethz.ch/pipermail/bioc-devel/2019-April/015012.html
This leaves me in a bind as minfi::makeGenomicRatioSetFromMatrix() has
exactly the functionality cpg.annotate() and DMR.plot() needs, plus it
provides minimal code and I don't really want to reinvent the wheel here!
Would it be possible to waive the 32-bit Windows build for DMRcate?
Best,
Tim
On 15/10/19 4:34 am, Pages, Herve wrote:
Hi Toth,
Not clear to me what's going on but I kind of suspect this might have
something to do with the use of data.table.
A few things to keep in mind:
- 'R CMD check' runs all the example in the same R session. This means
that the outcome of the examples of a given man page can be affected by
the examples from other man pages.
- A process cannot allocate more than 3 Gb of memory on 32-bit Windows.
There is no such limit on 64-bit Windows or on the other platforms we
support (Linux and Mac). On these platforms the maximum amount of memory
a process can allocate only depends on what's available on the system.
- Generally speaking, sticking to the Bioconductor way of doing things
(e.g use of GRanges objects instead of data.table objects, use of
findOverlaps() instead of data.table::foverlaps()) will lead to faster
code and reduced memory usage. Therefore I would strongly encourage you
to consider switching to GRanges/findOverlaps() and to avoid the use of
data.table in methrix.
Best,
H.
On 10/11/19 09:36, Toth, Reka wrote:
Dear BioC developers,
The most recent build of methrix fails on Tokay1 server:
https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_spb-5Freports_methrix-5Fbuildreport-5F20191009174210.html=DwIF-g=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=doO3ej8vD58ZBQWVxkHTaCLk-xipbskav8uofJL2syI=zs3uDnFqyAl-hr_7StB3Yr-tGZW8VPfclbPY_JKtSt8=
The error message is the following:
** running examples for arch 'i386' ... ERROR
Running examples in 'methrix-Ex.R' failed
The error most likely occurred in:
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: get_region_summary
### Title: Extract and summarize methylation or coverage info by regions of
### interest
### Aliases: get_region_summary
### ** Examples
data("methrix_data")
get_region_summary(m = methrix_data, regions = data.table(chr = "chr21", start = 27867971, end =
27868103), type = "M", how = "mean")
-Checking for overlaps..
Error: cannot allocate vector of size 1.4 Gb
Execution halted
I am a bit puzzled what the reasons could be, since it passed this step during
the previous builds and I didn’t change any of the functions in my last commit.
When I run the check on our local Windows, I don’t get any error. We use a very
small dataset as example, it definitely should not use a vector of size 1.4 Gb.
I would appreciate every input or idea on how to tackle this error.
Thanks a lot!
Best,
Reka
Dr. Reka Toth
Computational Epigenomics Group
Division of Epigenomics and Cancer Risk Factors /C010
Postdoctoral Fellow
German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 280
69120 Heidelberg
Germany
r.t...@dkfz-heidelberg.de
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.dkfz.de=DwIF-g=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=doO3ej8vD58ZBQWVxkHTaCLk-xipbskav8uofJL2syI=U7YGBonX7WmBqfyEneCtEsuRUKl1fbTS6Esi3e9XGAI=
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--
===
Tim Peters, PhD
Bioinformatics Research Officer | Immunogenomics Laboratory | Immunology
Division
Garvan Institute of Medical Research
384 Victoria St., Darlinghurst, NSW, Australia 2010
E: t.pet...@garvan.org.au | W: http://www.garvan.org.au | P: +612 9295 8325
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Re: [Bioc-devel] check fails on arch 'i386'
Thank you Herve,
I finally was able to reproduce the error and solve it. You are right, it was
most probably due to the data.table package.
Interestingly, the problem occurs randomly, with different error messages
(sometimes it is complaining about negative vector size...). I will open an
issue for data.table, because on these small datasets it shouldn't happen that
it needs those big vector sizes.
Thanks again.
Best,
Reka
-Original Message-
From: Pages, Herve [mailto:hpa...@fredhutch.org]
Sent: Monday, October 14, 2019 7:34 PM
To: Toth, Reka; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] check fails on arch 'i386'
Hi Toth,
Not clear to me what's going on but I kind of suspect this might have
something to do with the use of data.table.
A few things to keep in mind:
- 'R CMD check' runs all the example in the same R session. This means
that the outcome of the examples of a given man page can be affected by
the examples from other man pages.
- A process cannot allocate more than 3 Gb of memory on 32-bit Windows.
There is no such limit on 64-bit Windows or on the other platforms we
support (Linux and Mac). On these platforms the maximum amount of memory
a process can allocate only depends on what's available on the system.
- Generally speaking, sticking to the Bioconductor way of doing things
(e.g use of GRanges objects instead of data.table objects, use of
findOverlaps() instead of data.table::foverlaps()) will lead to faster
code and reduced memory usage. Therefore I would strongly encourage you
to consider switching to GRanges/findOverlaps() and to avoid the use of
data.table in methrix.
Best,
H.
On 10/11/19 09:36, Toth, Reka wrote:
>
> Dear BioC developers,
>
> The most recent build of methrix fails on Tokay1 server:
> https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_spb-5Freports_methrix-5Fbuildreport-5F20191009174210.html=DwIF-g=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=doO3ej8vD58ZBQWVxkHTaCLk-xipbskav8uofJL2syI=zs3uDnFqyAl-hr_7StB3Yr-tGZW8VPfclbPY_JKtSt8=
> The error message is the following:
>
> ** running examples for arch 'i386' ... ERROR
> Running examples in 'methrix-Ex.R' failed
> The error most likely occurred in:
>
>> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
>> ### Name: get_region_summary
>> ### Title: Extract and summarize methylation or coverage info by regions of
>> ### interest
>> ### Aliases: get_region_summary
>>
>> ### ** Examples
>>
>> data("methrix_data")
>> get_region_summary(m = methrix_data, regions = data.table(chr = "chr21",
>> start = 27867971, end = 27868103), type = "M", how = "mean")
> -Checking for overlaps..
> Error: cannot allocate vector of size 1.4 Gb
> Execution halted
>
> I am a bit puzzled what the reasons could be, since it passed this step
> during the previous builds and I didn't change any of the functions in my
> last commit.
> When I run the check on our local Windows, I don't get any error. We use a
> very small dataset as example, it definitely should not use a vector of size
> 1.4 Gb.
>
> I would appreciate every input or idea on how to tackle this error.
> Thanks a lot!
>
> Best,
> Reka
>
> Dr. Reka Toth
> Computational Epigenomics Group
> Division of Epigenomics and Cancer Risk Factors /C010
> Postdoctoral Fellow
>
> German Cancer Research Center (DKFZ)
> Foundation under Public Law
> Im Neuenheimer Feld 280
> 69120 Heidelberg
> Germany
>
> r.t...@dkfz-heidelberg.de
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.dkfz.de=DwIF-g=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=doO3ej8vD58ZBQWVxkHTaCLk-xipbskav8uofJL2syI=U7YGBonX7WmBqfyEneCtEsuRUKl1fbTS6Esi3e9XGAI=
>
> ___
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>
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax:(206) 667-1319
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Re: [Bioc-devel] check fails on arch 'i386'
Hi Toth,
Not clear to me what's going on but I kind of suspect this might have
something to do with the use of data.table.
A few things to keep in mind:
- 'R CMD check' runs all the example in the same R session. This means
that the outcome of the examples of a given man page can be affected by
the examples from other man pages.
- A process cannot allocate more than 3 Gb of memory on 32-bit Windows.
There is no such limit on 64-bit Windows or on the other platforms we
support (Linux and Mac). On these platforms the maximum amount of memory
a process can allocate only depends on what's available on the system.
- Generally speaking, sticking to the Bioconductor way of doing things
(e.g use of GRanges objects instead of data.table objects, use of
findOverlaps() instead of data.table::foverlaps()) will lead to faster
code and reduced memory usage. Therefore I would strongly encourage you
to consider switching to GRanges/findOverlaps() and to avoid the use of
data.table in methrix.
Best,
H.
On 10/11/19 09:36, Toth, Reka wrote:
>
> Dear BioC developers,
>
> The most recent build of methrix fails on Tokay1 server:
> https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_spb-5Freports_methrix-5Fbuildreport-5F20191009174210.html=DwIF-g=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=doO3ej8vD58ZBQWVxkHTaCLk-xipbskav8uofJL2syI=zs3uDnFqyAl-hr_7StB3Yr-tGZW8VPfclbPY_JKtSt8=
> The error message is the following:
>
> ** running examples for arch 'i386' ... ERROR
> Running examples in 'methrix-Ex.R' failed
> The error most likely occurred in:
>
>> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
>> ### Name: get_region_summary
>> ### Title: Extract and summarize methylation or coverage info by regions of
>> ### interest
>> ### Aliases: get_region_summary
>>
>> ### ** Examples
>>
>> data("methrix_data")
>> get_region_summary(m = methrix_data, regions = data.table(chr = "chr21",
>> start = 27867971, end = 27868103), type = "M", how = "mean")
> -Checking for overlaps..
> Error: cannot allocate vector of size 1.4 Gb
> Execution halted
>
> I am a bit puzzled what the reasons could be, since it passed this step
> during the previous builds and I didn’t change any of the functions in my
> last commit.
> When I run the check on our local Windows, I don’t get any error. We use a
> very small dataset as example, it definitely should not use a vector of size
> 1.4 Gb.
>
> I would appreciate every input or idea on how to tackle this error.
> Thanks a lot!
>
> Best,
> Reka
>
> Dr. Reka Toth
> Computational Epigenomics Group
> Division of Epigenomics and Cancer Risk Factors /C010
> Postdoctoral Fellow
>
> German Cancer Research Center (DKFZ)
> Foundation under Public Law
> Im Neuenheimer Feld 280
> 69120 Heidelberg
> Germany
>
> r.t...@dkfz-heidelberg.de
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.dkfz.de=DwIF-g=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=doO3ej8vD58ZBQWVxkHTaCLk-xipbskav8uofJL2syI=U7YGBonX7WmBqfyEneCtEsuRUKl1fbTS6Esi3e9XGAI=
>
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>
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax:(206) 667-1319
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