Re: [Bioc-devel] Help for Error "Maximal Number of DLLs reached..."

2018-03-21 Thread Yuan Tian 
Thanks guys for your kind help! I would follow your tips and try to fix
these issues.

It's indeed quite hard to maintain it, luckily in past two years I made it.
It's indeed the right time to cut down some unnecessary packages and make
it easier to be maintained.

Thanks for your help! ^_^

Best
Yuan Tian

On Thu, Mar 22, 2018 at 12:14 AM Hervé Pagès  wrote:

> Hi,
>
> On 03/21/2018 07:32 AM, Martin Morgan wrote:
> >
> >
> > On 03/21/2018 10:14 AM, Henrik Bengtsson wrote:
> >> A few quick comments:
> >>
> >> * I don't think the limit was hardened in R 3.4.0; maybe you started to
> >> experience it sound then because more dependent packages started to
> >> rely on
> >> more DLLs?
> >>
> >> * The limit is OS/platform specific so it's not that R core is
> >> unwilling to
> >> fix this - I think they havejust tried to find a safe limit that work
> >> everywhere. Having said this...
> >>
> >> * It'll be less restrictive by default in R 3.5.0: from it's NEWS "The
> >> maximum number of DLLs that can be loaded into R e.g. via dyn.load() has
> >> been increased up to 614 when the OS limit on the number of open files
> >> allows"
> >>
> >> * R.utils::gcDLLs() will attempt to unregister possibly stray DLLs
> >> remaining after unloading packages. So unloading packages and gcDLLs()
> >> may
> >> provide you with a workaround until R 3.5.0 is in place (possibly also
> >> even
> >> after).
> >>
> >> See
> >>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_HenrikBengtsson_Wishlist-2Dfor-2DR_issues_29=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=p2zu7G8IjcYJfFGXTvJAlITWCwrBG0zBH72Htgm6go8=7UNVEDPfEm1j53ksGc7naLgnieltNzOnbv4lPUQh4Jk=
> >> for
> >> "random" notes and references to this problem.
> >>
> >>
> >> On Wed, Mar 21, 2018, 04:10 Yuan Tian 
> wrote:
> >>
> >>> Hello Guys:
> >>>
> >>> I encountered an error like "maximal number of dlls reached...". I am
> >>> maintaining ChAMP package now, which integrated many other packages
> >>> in my
> >>> research field. I have not updated this package in past 2 months but
> >>> suddenly this error happens.
> >>>
> >>> Currently, I think I know the reason is since R 3.4.X, numbers of
> >>> DLLs in
> >>> default R session was set 100. I have tested that using a newly
> >>> started R
> >>> 3.4.4 to install and load ChAMP package, *it works smoothly*, after
> >>> loading, I checked DLL loaded with function getLoadedDLLs(), then I see
> >>> ChAMP used 95 Dlls. I know it's a lot, but some of them are loaded by
> >>> ChAMP's relying packages but itself. *However, ChAMP cannot pass
> >>> Bioconductor check, thus I suspect Bioconductor checking system does
> NOT
> >>> start a new R session for each package right? Which means it's not
> >>> 100 DLLs
> >>> allocated for each package?*
> >
> > ChAMP is passing BiocCheck in release, where R is 3.4.x ?
> >
> >
> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_release_bioc-2DLATEST_ChAMP_malbec1-2Dchecksrc.html=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=p2zu7G8IjcYJfFGXTvJAlITWCwrBG0zBH72Htgm6go8=_B73-e5Y2XkRdvs7ssHGb6DAdSnMmG30eE_Ywu1W7iQ=
>
> mmmh, this is a stale page. Not sure what it's doing here. Will
> investigate.
>
> Today's "true" results are here:
>
>http://bioconductor.org/checkResults/release/bioc-LATEST/ChAMP/
>
> Note that you can't get to the stale page by following links from
> the report's main page:
>
>http://bioconductor.org/checkResults/release/bioc-LATEST/
>
> >
> >
> > Each package is built and tested in a separate process. Vignettes are
> > actually built in a single process (by R, not Bioconductor) so multiple
> > vignettes could load a higher number of DLLs.
>
> Also just to clarify: the build machines don't use any special settings
> to limit the nb of DLLs. They use whatever R uses by default.
>
> >
> >>>
> >>> Currently, I have told my users to modify R environment to allow their
> R
> >>> session with more DLLs. It works but only on users computer, not
> >>> Bioconductor checking system.
>
> Note that, in release (with R 3.4.4), the max DLL error happens at
> the end of an install:
>
>  > biocLite("ChAMP")
> BioC_mirror: https://bioconductor.org
> Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.3 (2017-11-30).
> Installing package(s) ‘ChAMP’
> trying URL
> '
> https://bioconductor.org/packages/3.6/bioc/src/contrib/ChAMP_2.9.10.tar.gz
> '
> Content type 'application/x-gzip' length 15513863 bytes (14.8 MB)
> ==
> downloaded 14.8 MB
>
> * installing *source* package ‘ChAMP’ ...
> ** R
> ** inst
> ** preparing package for lazy loading
> Warning: replacing previous import ‘igraph::edges’ by ‘graph::edges’
> when loading ‘FEM’
> Warning: replacing previous import ‘igraph::intersection’ by
> ‘graph::intersection’ when loading ‘FEM’
> Warning: replacing previous import ‘igraph::degree’ by

Re: [Bioc-devel] Help for Error "Maximal Number of DLLs reached..."

2018-03-21 Thread Hervé Pagès 

Hi,

On 03/21/2018 07:32 AM, Martin Morgan wrote:



On 03/21/2018 10:14 AM, Henrik Bengtsson wrote:

A few quick comments:

* I don't think the limit was hardened in R 3.4.0; maybe you started to
experience it sound then because more dependent packages started to 
rely on

more DLLs?

* The limit is OS/platform specific so it's not that R core is 
unwilling to

fix this - I think they havejust tried to find a safe limit that work
everywhere. Having said this...

* It'll be less restrictive by default in R 3.5.0: from it's NEWS "The
maximum number of DLLs that can be loaded into R e.g. via dyn.load() has
been increased up to 614 when the OS limit on the number of open files
allows"

* R.utils::gcDLLs() will attempt to unregister possibly stray DLLs
remaining after unloading packages. So unloading packages and gcDLLs() 
may
provide you with a workaround until R 3.5.0 is in place (possibly also 
even

after).

See 
https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_HenrikBengtsson_Wishlist-2Dfor-2DR_issues_29=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=p2zu7G8IjcYJfFGXTvJAlITWCwrBG0zBH72Htgm6go8=7UNVEDPfEm1j53ksGc7naLgnieltNzOnbv4lPUQh4Jk= 
for

"random" notes and references to this problem.


On Wed, Mar 21, 2018, 04:10 Yuan Tian  wrote:


Hello Guys:

I encountered an error like "maximal number of dlls reached...". I am
maintaining ChAMP package now, which integrated many other packages 
in my

research field. I have not updated this package in past 2 months but
suddenly this error happens.

Currently, I think I know the reason is since R 3.4.X, numbers of 
DLLs in
default R session was set 100. I have tested that using a newly 
started R

3.4.4 to install and load ChAMP package, *it works smoothly*, after
loading, I checked DLL loaded with function getLoadedDLLs(), then I see
ChAMP used 95 Dlls. I know it's a lot, but some of them are loaded by
ChAMP's relying packages but itself. *However, ChAMP cannot pass
Bioconductor check, thus I suspect Bioconductor checking system does NOT
start a new R session for each package right? Which means it's not 
100 DLLs

allocated for each package?*


ChAMP is passing BiocCheck in release, where R is 3.4.x ?

https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_release_bioc-2DLATEST_ChAMP_malbec1-2Dchecksrc.html=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=p2zu7G8IjcYJfFGXTvJAlITWCwrBG0zBH72Htgm6go8=_B73-e5Y2XkRdvs7ssHGb6DAdSnMmG30eE_Ywu1W7iQ= 


mmmh, this is a stale page. Not sure what it's doing here. Will
investigate.

Today's "true" results are here:

  http://bioconductor.org/checkResults/release/bioc-LATEST/ChAMP/

Note that you can't get to the stale page by following links from
the report's main page:

  http://bioconductor.org/checkResults/release/bioc-LATEST/




Each package is built and tested in a separate process. Vignettes are 
actually built in a single process (by R, not Bioconductor) so multiple 
vignettes could load a higher number of DLLs.


Also just to clarify: the build machines don't use any special settings
to limit the nb of DLLs. They use whatever R uses by default.





Currently, I have told my users to modify R environment to allow their R
session with more DLLs. It works but only on users computer, not
Bioconductor checking system.


Note that, in release (with R 3.4.4), the max DLL error happens at
the end of an install:

> biocLite("ChAMP")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.3 (2017-11-30).
Installing package(s) ‘ChAMP’
trying URL 
'https://bioconductor.org/packages/3.6/bioc/src/contrib/ChAMP_2.9.10.tar.gz'

Content type 'application/x-gzip' length 15513863 bytes (14.8 MB)
==
downloaded 14.8 MB

* installing *source* package ‘ChAMP’ ...
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘igraph::edges’ by ‘graph::edges’ 
when loading ‘FEM’
Warning: replacing previous import ‘igraph::intersection’ by 
‘graph::intersection’ when loading ‘FEM’
Warning: replacing previous import ‘igraph::degree’ by ‘graph::degree’ 
when loading ‘FEM’
Warning: replacing previous import ‘igraph::union’ by ‘graph::union’ 
when loading ‘FEM’
Warning: replacing previous import ‘limma::plotMA’ by 
‘BiocGenerics::plotMA’ when loading ‘FEM’
Warning: replacing previous import ‘Matrix::colSums’ by 
‘BiocGenerics::colSums’ when loading ‘FEM’
Warning: replacing previous import ‘Matrix::colMeans’ by 
‘BiocGenerics::colMeans’ when loading ‘FEM’
Warning: replacing previous import ‘Matrix::rowMeans’ by 
‘BiocGenerics::rowMeans’ when loading ‘FEM’
Warning: replacing previous import ‘Matrix::rowSums’ by 
‘BiocGenerics::rowSums’ when loading ‘FEM’
Warning: replacing previous import ‘Matrix::which’ by 
‘BiocGenerics::which’ when loading ‘FEM’
Warning: replacing previous import ‘igraph::normalize’ by

Re: [Bioc-devel] Help for Error "Maximal Number of DLLs reached..."

2018-03-21 Thread Martin Morgan 



On 03/21/2018 10:14 AM, Henrik Bengtsson wrote:

A few quick comments:

* I don't think the limit was hardened in R 3.4.0; maybe you started to
experience it sound then because more dependent packages started to rely on
more DLLs?

* The limit is OS/platform specific so it's not that R core is unwilling to
fix this - I think they havejust tried to find a safe limit that work
everywhere. Having said this...

* It'll be less restrictive by default in R 3.5.0: from it's NEWS "The
maximum number of DLLs that can be loaded into R e.g. via dyn.load() has
been increased up to 614 when the OS limit on the number of open files
allows"

* R.utils::gcDLLs() will attempt to unregister possibly stray DLLs
remaining after unloading packages. So unloading packages and gcDLLs() may
provide you with a workaround until R 3.5.0 is in place (possibly also even
after).

See https://github.com/HenrikBengtsson/Wishlist-for-R/issues/29 for
"random" notes and references to this problem.


On Wed, Mar 21, 2018, 04:10 Yuan Tian  wrote:


Hello Guys:

I encountered an error like "maximal number of dlls reached...". I am
maintaining ChAMP package now, which integrated many other packages in my
research field. I have not updated this package in past 2 months but
suddenly this error happens.

Currently, I think I know the reason is since R 3.4.X, numbers of DLLs in
default R session was set 100. I have tested that using a newly started R
3.4.4 to install and load ChAMP package, *it works smoothly*, after
loading, I checked DLL loaded with function getLoadedDLLs(), then I see
ChAMP used 95 Dlls. I know it's a lot, but some of them are loaded by
ChAMP's relying packages but itself. *However, ChAMP cannot pass
Bioconductor check, thus I suspect Bioconductor checking system does NOT
start a new R session for each package right? Which means it's not 100 DLLs
allocated for each package?*


ChAMP is passing BiocCheck in release, where R is 3.4.x ?

http://bioconductor.org/checkResults/release/bioc-LATEST/ChAMP/malbec1-checksrc.html

Each package is built and tested in a separate process. Vignettes are 
actually built in a single process (by R, not Bioconductor) so multiple 
vignettes could load a higher number of DLLs.




Currently, I have told my users to modify R environment to allow their R
session with more DLLs. It works but only on users computer, not
Bioconductor checking system. Thus I think I have to reduce dlls used by
current package right? Like removing some relying packages or function. *My
another question is how many DLLs is allowed by Bioconductor check? I think
it's less than 100. But I don't know I should cut it into 80 or 60 or even
50 dlls used.*

It's really disappointing that I need to modify quite a lot of code, and
even could hurt some key functionality of the package. Thus here I am
seeking your help and suggestions here.


Frankly, I think a package with so many dependencies cannot be 
maintained -- a change in any one of those packages could break your 
package (e.g., by changing their own dependencies to include additional 
DLLs!), and it must be virtually impossible to get sufficient test 
coverage to be confident that these problems will be detected before the 
package is made available to the user. It is time to consider a more 
modular design focusing on essential features.


Martin



Best
Yuan Tian

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[Bioc-devel] Help for Error "Maximal Number of DLLs reached..."

2018-03-21 Thread Yuan Tian 
Hello Guys:

I encountered an error like "maximal number of dlls reached...". I am
maintaining ChAMP package now, which integrated many other packages in my
research field. I have not updated this package in past 2 months but
suddenly this error happens.

Currently, I think I know the reason is since R 3.4.X, numbers of DLLs in
default R session was set 100. I have tested that using a newly started R
3.4.4 to install and load ChAMP package, *it works smoothly*, after
loading, I checked DLL loaded with function getLoadedDLLs(), then I see
ChAMP used 95 Dlls. I know it's a lot, but some of them are loaded by
ChAMP's relying packages but itself. *However, ChAMP cannot pass
Bioconductor check, thus I suspect Bioconductor checking system does NOT
start a new R session for each package right? Which means it's not 100 DLLs
allocated for each package?*

Currently, I have told my users to modify R environment to allow their R
session with more DLLs. It works but only on users computer, not
Bioconductor checking system. Thus I think I have to reduce dlls used by
current package right? Like removing some relying packages or function. *My
another question is how many DLLs is allowed by Bioconductor check? I think
it's less than 100. But I don't know I should cut it into 80 or 60 or even
50 dlls used.*

It's really disappointing that I need to modify quite a lot of code, and
even could hurt some key functionality of the package. Thus here I am
seeking your help and suggestions here.

Best
Yuan Tian

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel