Re: [Bioc-devel] DMRcate: TIMEOUT

2017-05-31 Thread Tim Peters 
Thanks Martin and Sean, found the culprit. It's DSS::DMLtest(). Looks 
like it takes much longer under the new version. I should be able to 
attenuate the vignette input considerably so hopefully it will now beat 
the timeout.

For R/3.3.3, on a bsseq object with 5000 CpG sites, DMLtest() under 
DSS_2.14.0 takes roughly 4 seconds:

 > system.time(DSSres <- DMLtest(obj_bsseq, group1=sampnames[1:3], 
group2=sampnames[4:6], smoothing=FALSE))
Estimating dispersion for each CpG site, this will take a while ...
user  system elapsed
   3.724   0.017   3.738
 > sessionInfo()
R version 3.3.3 (2017-03-06)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS release 6.8 (Final)

locale:
  [1] LC_CTYPE=en_US.iso885915 LC_NUMERIC=C
  [3] LC_TIME=en_US.iso885915 LC_COLLATE=en_US.iso885915
  [5] LC_MONETARY=en_US.iso885915 LC_MESSAGES=en_US.iso885915
  [7] LC_PAPER=en_US.iso885915 LC_NAME=C
  [9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C

attached base packages:
  [1] splines   parallel  stats4stats graphics  grDevices utils
  [8] datasets  methods   base

other attached packages:
  [1] DSS_2.14.0 bsseq_1.10.0
  [3] limma_3.30.13  SummarizedExperiment_1.4.0
  [5] Biobase_2.34.0 DMRcatedata_1.10.1
  [7] GenomicRanges_1.26.4   GenomeInfoDb_1.10.3
  [9] IRanges_2.8.2  S4Vectors_0.12.2
[11] BiocGenerics_0.20.0

loaded via a namespace (and not attached):
  [1] Rcpp_0.12.11   XVector_0.14.1 zlibbioc_1.20.0 munsell_0.4.3
  [5] colorspace_1.3-2   lattice_0.20-35plyr_1.8.4 tools_3.3.3
  [9] grid_3.3.3 data.table_1.10.4  R.oo_1.21.0 gtools_3.5.0
[13] matrixStats_0.52.2 permute_0.9-4  Matrix_1.2-10 R.utils_2.5.0
[17] bitops_1.0-6   RCurl_1.95-4.8 R.methodsS3_1.7.1 scales_0.4.1
[21] locfit_1.5-9.1


And under R/3.4.0 under DSS_2.16.0 it takes 108 seconds:


 > system.time(DSSres <- DMLtest(obj_bsseq, group1=sampnames[1:3], 
group2=sampnames[4:6], smoothing=FALSE))
Estimating dispersion for each CpG site, this will take a while ...
user  system elapsed
108.305   0.184 108.596
 > sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.0
LAPACK: /usr/lib/lapack/liblapack.so.3.0

locale:
  [1] LC_CTYPE=en_AU.UTF-8   LC_NUMERIC=C LC_TIME=en_AU.UTF-8
LC_COLLATE=en_AU.UTF-8 LC_MONETARY=en_AU.UTF-8
  [6] LC_MESSAGES=en_AU.UTF-8LC_PAPER=en_AU.UTF-8 
LC_NAME=C  LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C

attached base packages:
  [1] splines   parallel  stats4stats graphics  grDevices 
utils datasets  methods   base

other attached packages:
  [1] DSS_2.16.0 bsseq_1.12.1 SummarizedExperiment_1.6.2 
DelayedArray_0.2.4 matrixStats_0.52.2
  [6] Biobase_2.36.2 DMRcatedata_1.12.0 
GenomicRanges_1.28.3   GenomeInfoDb_1.12.1 IRanges_2.10.2
[11] S4Vectors_0.14.2   BiocGenerics_0.22.0

loaded via a namespace (and not attached):
  [1] Rcpp_0.12.11XVector_0.16.0 zlibbioc_1.22.0 
munsell_0.4.3 colorspace_1.3-2lattice_0.20-35
  [7] plyr_1.8.4  tools_3.4.0 grid_3.4.0  
data.table_1.10.4 R.oo_1.21.0 gtools_3.5.0
[13] permute_0.9-4   Matrix_1.2-10 GenomeInfoDbData_0.99.0 
R.utils_2.5.0 bitops_1.0-6RCurl_1.95-4.8
[19] limma_3.32.2compiler_3.4.0 R.methodsS3_1.7.1   
scales_0.4.1 locfit_1.5-9.1


Thanks for your recommendations, I should be fine from here on.

Cheers,

Tim


On 31/05/17 21:36, Martin Morgan wrote:
> On 05/31/2017 06:18 AM, Sean Davis wrote:
>> Hi, Tim.
>>
>> Have you tried building the vignette independently, separate from the
>> package build process? Doing so might give you some hints about which 
>> code
>> blocks are the culprits.
>
> Also
>
> > Stangle("DMRcate.Rnw")
> Writing to file DMRcate.R
> > source("DMRcate.R", echo=TRUE, max=Inf)
>
> to generate the R code and process it.
>
> Martin
>
>>
>> Sean
>>
>>
>> On Wed, May 31, 2017 at 1:24 AM, Tim Peters  
>> wrote:
>>
>>> Hi bioc,
>>>
>>> Recently, under R/3.4.0, the newest version of DMRcate is taking 47mins
>>> to build on my local machine and I am getting TIMEOUTs on the build on
>>> the checkResults page
>>> http://master.bioconductor.org/checkResults/3.5/bioc-
>>> LATEST/DMRcate/malbec2-buildsrc.html.
>>> I have not made any changes to the attached data package or routines
>>> that warrant this increase in time. The vignette building in particular
>>> takes up the bulk of the time and this is where the build hangs.
>>> Building the same source on R/3.3.3 only takes 4mins 53secs by 
>>> comparison.
>>>
>>> Screendump below. Can someone provide an insight into what they 
>>> think is
>>> happening here?
>>>
>>> timpet@clark-lab:~/Documents$ time R CMD build DMRcate
>>> *

Re: [Bioc-devel] DMRcate: TIMEOUT

2017-05-31 Thread Martin Morgan 

On 05/31/2017 06:18 AM, Sean Davis wrote:

Hi, Tim.

Have you tried building the vignette independently, separate from the
package build process? Doing so might give you some hints about which code
blocks are the culprits.


Also

> Stangle("DMRcate.Rnw")
Writing to file DMRcate.R
> source("DMRcate.R", echo=TRUE, max=Inf)

to generate the R code and process it.

Martin



Sean


On Wed, May 31, 2017 at 1:24 AM, Tim Peters  wrote:


Hi bioc,

Recently, under R/3.4.0, the newest version of DMRcate is taking 47mins
to build on my local machine and I am getting TIMEOUTs on the build on
the checkResults page
http://master.bioconductor.org/checkResults/3.5/bioc-
LATEST/DMRcate/malbec2-buildsrc.html.
I have not made any changes to the attached data package or routines
that warrant this increase in time. The vignette building in particular
takes up the bulk of the time and this is where the build hangs.
Building the same source on R/3.3.3 only takes 4mins 53secs by comparison.

Screendump below. Can someone provide an insight into what they think is
happening here?

timpet@clark-lab:~/Documents$ time R CMD build DMRcate
* checking for file ‘DMRcate/DESCRIPTION’ ... OK
* preparing ‘DMRcate’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building ‘DMRcate_1.12.1.tar.gz’


real47m33.472s
user46m55.023s
sys0m4.647s
timpet@clark-lab:~/Documents$ R -e "sessionInfo()"

R version 3.4.0 (2017-04-21) -- "You Stupid Darkness"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

  > sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.0
LAPACK: /usr/lib/lapack/liblapack.so.3.0

locale:
   [1] LC_CTYPE=en_AU.UTF-8   LC_NUMERIC=C
   [3] LC_TIME=en_AU.UTF-8LC_COLLATE=en_AU.UTF-8
   [5] LC_MONETARY=en_AU.UTF-8LC_MESSAGES=en_AU.UTF-8
   [7] LC_PAPER=en_AU.UTF-8   LC_NAME=C
   [9] LC_ADDRESS=C   LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats graphics  grDevices utils datasets  methods base

loaded via a namespace (and not attached):
[1] compiler_3.4.0

Best,
Tim

--
Tim Peters, PhD

Bioinformatics Research Officer | Epigenetics Research Laboratory |
Genomics and Epigenetics Division

Garvan Institute of Medical Research

384 Victoria St., Darlinghurst, NSW, Australia 2010

Tel: +61 (2) 9295 8319


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Re: [Bioc-devel] DMRcate: TIMEOUT

2017-05-31 Thread Sean Davis 
Hi, Tim.

Have you tried building the vignette independently, separate from the
package build process? Doing so might give you some hints about which code
blocks are the culprits.

Sean


On Wed, May 31, 2017 at 1:24 AM, Tim Peters  wrote:

> Hi bioc,
>
> Recently, under R/3.4.0, the newest version of DMRcate is taking 47mins
> to build on my local machine and I am getting TIMEOUTs on the build on
> the checkResults page
> http://master.bioconductor.org/checkResults/3.5/bioc-
> LATEST/DMRcate/malbec2-buildsrc.html.
> I have not made any changes to the attached data package or routines
> that warrant this increase in time. The vignette building in particular
> takes up the bulk of the time and this is where the build hangs.
> Building the same source on R/3.3.3 only takes 4mins 53secs by comparison.
>
> Screendump below. Can someone provide an insight into what they think is
> happening here?
>
> timpet@clark-lab:~/Documents$ time R CMD build DMRcate
> * checking for file ‘DMRcate/DESCRIPTION’ ... OK
> * preparing ‘DMRcate’:
> * checking DESCRIPTION meta-information ... OK
> * installing the package to build vignettes
> * creating vignettes ... OK
> * checking for LF line-endings in source and make files
> * checking for empty or unneeded directories
> * building ‘DMRcate_1.12.1.tar.gz’
>
>
> real47m33.472s
> user46m55.023s
> sys0m4.647s
> timpet@clark-lab:~/Documents$ R -e "sessionInfo()"
>
> R version 3.4.0 (2017-04-21) -- "You Stupid Darkness"
> Copyright (C) 2017 The R Foundation for Statistical Computing
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
>
>Natural language support but running in an English locale
>
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
>
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
>
>  > sessionInfo()
> R version 3.4.0 (2017-04-21)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Ubuntu 14.04.5 LTS
>
> Matrix products: default
> BLAS: /usr/lib/libblas/libblas.so.3.0
> LAPACK: /usr/lib/lapack/liblapack.so.3.0
>
> locale:
>   [1] LC_CTYPE=en_AU.UTF-8   LC_NUMERIC=C
>   [3] LC_TIME=en_AU.UTF-8LC_COLLATE=en_AU.UTF-8
>   [5] LC_MONETARY=en_AU.UTF-8LC_MESSAGES=en_AU.UTF-8
>   [7] LC_PAPER=en_AU.UTF-8   LC_NAME=C
>   [9] LC_ADDRESS=C   LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics  grDevices utils datasets  methods base
>
> loaded via a namespace (and not attached):
> [1] compiler_3.4.0
>
> Best,
> Tim
>
> --
> Tim Peters, PhD
>
> Bioinformatics Research Officer | Epigenetics Research Laboratory |
> Genomics and Epigenetics Division
>
> Garvan Institute of Medical Research
>
> 384 Victoria St., Darlinghurst, NSW, Australia 2010
>
> Tel: +61 (2) 9295 8319
>
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel




-- 
Sean Davis, MD, PhD
Center for Cancer Research
National Cancer Institute
National Institutes of Health
Bethesda, MD 20892
https://seandavi.github.io/
https://twitter.com/seandavis12

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