[Bioc-devel] Package failed build on Windows - couldn't load related ExperimentHub dataset
Hervé Pagès
hp@ge@@on@g|thub @end|ng |rom gm@||@com
Fri Mar 26 18:25:32 CET 2021
On 3/26/21 10:01 AM, Murphy, Alan E wrote:
> Hi Hervé,
>
> I bumped the version again to get a new check run but unfortunately the
> first error I had on Windows has now happened on the Linux machine. I
> have no idea why this is happening?
Downloading the data to the local ExperimentHub cache seems quite
unreliable. Not sure why. What doesn't help is that a temporary cache is
used so the data needs to be re-downloaded each time. See my suggestion
in the review process on GitHub for how to maybe work around this.
>
> Also, the Windows run timed out again. With the two runs, has it been
> noted by other developers that the check is more stringent on time than
> that of the Linux and Mac? Or what could be causing this?
Well, the Windows machine tokay2 is a little bit old and not very fast.
What doesn't help is that it has to run everything (examples and tests)
twice, once in 32-bit mode and once in 64-bit mode. So yeah, the timeout
is not too surprising here. When I manually ran 'R CMD check' on tokay2
yesterday I noticed that the unit tests where taking a long time. So you
would need to manage to make the whole thing run a little bit faster.
But first I would try to use a persistent ExperimentHub cache. This
should improve speed on all the platforms. Let's discuss this on GitHub.
Thanks,
H.
>
> Kind regards,
> Alan.
> ------------------------------------------------------------------------
> *From:* Hervé Pagès <hpages.on.github using gmail.com>
> *Sent:* 26 March 2021 16:13
> *To:* Murphy, Alan E <a.murphy using imperial.ac.uk>; bioc-devel using r-project.org
> <bioc-devel using r-project.org>
> *Subject:* Re: [Bioc-devel] Package failed build on Windows - couldn't
> load related ExperimentHub dataset
> On 3/26/21 1:09 AM, Murphy, Alan E wrote:
>> Hey Hervé,
>>
>> Bumping the version did stop the error but now I'm getting time out
>> errors for both Mac and Windows. This is strange considering the code
>> didn't change and passed the mac checks last time without a timeout
>> issue. Is there much variability on these machines across R CMD Check
>> runs?
>
> There can be. These machines are very busy running the daily builds in
> addition to the SPB and the load can get quite high sometimes,
> especially between 6pm and 8am EST. It looks like these time outs
> happened during that window.
>
>> Also the run time on Windows when it timed out was 25 minutes
>> which is far higher than it takes to run the code locally on my mac.
>> Could something be astray here? Looking at the output of the Windows
>> test, it appears that the examples were run twice for some reason:
>
> This is because the Windows builders use the --merge-multiarch flag.
> Please refer to my previous email where I explained this.
>
> Best,
> H.
>
>>
>> Examples with CPU (user + system) or elapsed time > 5s
>> user system elapsed
>> generate.bootstrap.plots.for.transcriptome 44.78 0.51 46.71
>> add.res.to.merging.list 40.60 1.72 49.58
>> merged_ewce 36.39 0.83 39.62
>> generate.bootstrap.plots 24.03 1.32 26.50
>> ewce_expression_data 20.14 0.55 21.90
>> ewce.plot 16.09 0.36 17.42
>> controlled_geneset_enrichment 15.45 0.58 17.10
>> check.ewce.genelist.inputs 15.66 0.31 16.78
>> bootstrap.enrichment.test 15.13 0.47 16.53
>> fix.bad.mgi.symbols 9.13 0.31 10.40
>> filter.genes.without.1to1.homolog 7.53 0.21 8.03
>> prep.dendro 5.10 0.24 5.48
>> generate.celltype.data 4.82 0.13 5.17
>> drop.uninformative.genes 4.44 0.42 6.31
>> bin.specificity.into.quantiles 4.63 0.22 5.01
>> ** running examples for arch 'x64' ... [322s] OK
>> Examples with CPU (user + system) or elapsed time > 5s
>> user system elapsed
>> generate.bootstrap.plots.for.transcriptome 47.25 0.44 48.84
>> add.res.to.merging.list 41.17 1.89 49.72
>> merged_ewce 37.30 0.99 40.51
>> generate.bootstrap.plots 24.62 0.69 26.58
>> ewce_expression_data 20.64 0.64 22.58
>> controlled_geneset_enrichment 16.66 0.21 17.72
>> ewce.plot 16.06 0.47 17.41
>> check.ewce.genelist.inputs 15.95 0.40 17.16
>> bootstrap.enrichment.test 16.00 0.28 17.20
>> fix.bad.mgi.symbols 8.81 0.37 9.86
>> filter.genes.without.1to1.homolog 7.58 0.20 8.00
>> prep.dendro 5.11 0.06 5.33
>> generate.celltype.data 4.64 0.17 5.03
>> drop.uninformative.genes 4.34 0.25 6.11
>>
>>
>>
>> Kind regards,
>> Alan.
>> ------------------------------------------------------------------------
>> *From:* Hervé Pagès <hpages.on.github using gmail.com>
>> *Sent:* 25 March 2021 22:53
>> *To:* Murphy, Alan E <a.murphy using imperial.ac.uk>; bioc-devel using r-project.org
>> <bioc-devel using r-project.org>
>> *Subject:* Re: [Bioc-devel] Package failed build on Windows - couldn't
>> load related ExperimentHub dataset
>>
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>> Hi Alan,
>>
>> I just went on tokay2 and was able to manually run 'R CMD build' and 'R
>> CMD check' on EWCE and they produced clean output. See below.
>>
>> So I'm not sure what happened earlier with the SPB. Some sort of hiccup?
>> Can you bump the package version again? That will trigger another build
>> so we'll be able to see if that happens again.
>>
>> Thanks,
>> H.
>>
>> -----------------------------------------------------------------------
>>
>> Here is the output I got for 'R CMD build' and 'R CMD check' on tokay2.
>> Note that I didn't use the --merge-multiarch flag for 'R CMD check'
>> (like the automated builds normally do) so the examples and tests are
>> run only once (in 64-bit mode) instead of twice (in 32-bit and 64-bit
>> modes):
>>
>> PS C:\Users\biocbuild\bbs-3.13-bioc> .\R\bin\R CMD build
>> --keep-empty-dirs --no-resave-data EWCE
>> * checking for file 'EWCE/DESCRIPTION' ... OK
>> * preparing 'EWCE':
>> * checking DESCRIPTION meta-information ... OK
>> * installing the package to build vignettes
>> * creating vignettes ... OK
>> * checking for LF line-endings in source and make files and shell scripts
>> * checking for empty or unneeded directories
>> * building 'EWCE_0.99.6.tar.gz'
>>
>> PS C:\Users\biocbuild\bbs-3.13-bioc> .\R\bin\R CMD check --no-vignettes
>> EWCE_0.99.6.tar.gz
>> * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/EWCE.Rcheck'
>> * using R Under development (unstable) (2021-02-08 r79971)
>> * using platform: x86_64-w64-mingw32 (64-bit)
>> * using session charset: ISO8859-1
>> * using option '--no-vignettes'
>> * checking for file 'EWCE/DESCRIPTION' ... OK
>> * checking extension type ... Package
>> * this is package 'EWCE' version '0.99.6'
>> * package encoding: UTF-8
>> * checking package namespace information ... OK
>> * checking package dependencies ... OK
>> * checking if this is a source package ... OK
>> * checking if there is a namespace ... OK
>> * checking for executable files ... OK
>> * checking for hidden files and directories ... OK
>> * checking for portable file names ... OK
>> * checking whether package 'EWCE' can be installed ... OK
>> * checking installed package size ... OK
>> * checking package directory ... OK
>> * checking 'build' directory ... OK
>> * checking DESCRIPTION meta-information ... OK
>> * checking top-level files ... OK
>> * checking for left-over files ... OK
>> * checking index information ... OK
>> * checking package subdirectories ... OK
>> * checking R files for non-ASCII characters ... OK
>> * checking R files for syntax errors ... OK
>> * checking whether the package can be loaded ... OK
>> * checking whether the package can be loaded with stated dependencies ... OK
>> * checking whether the package can be unloaded cleanly ... OK
>> * checking whether the namespace can be loaded with stated dependencies
>> ... OK
>> * checking whether the namespace can be unloaded cleanly ... OK
>> * checking loading without being on the library search path ... OK
>> * checking dependencies in R code ... OK
>> * checking S3 generic/method consistency ... OK
>> * checking replacement functions ... OK
>> * checking foreign function calls ... OK
>> * checking R code for possible problems ... OK
>> * checking Rd files ... OK
>> * checking Rd metadata ... OK
>> * checking Rd cross-references ... OK
>> * checking for missing documentation entries ... OK
>> * checking for code/documentation mismatches ... OK
>> * checking Rd \usage sections ... OK
>> * checking Rd contents ... OK
>> * checking for unstated dependencies in examples ... OK
>> * checking installed files from 'inst/doc' ... OK
>> * checking files in 'vignettes' ... OK
>> * checking examples ...
>> * checking for unstated dependencies in 'tests' ... OK
>> * checking tests ...
>> Running 'testthat.R'
>> OK
>> * checking for unstated dependencies in vignettes ... OK
>> * checking package vignettes in 'inst/doc' ... OK
>> * checking running R code from vignettes ... SKIPPED
>> * checking re-building of vignette outputs ... SKIPPED
>> * checking PDF version of manual ... OK
>> * DONE
>>
>> Status: OK
>>
>> -----------------------------------------------------------------------
>>
>> On 3/25/21 12:27 AM, Murphy, Alan E wrote:
>>> Hi all,
>>>
>>> I am working on the development of [EWCE](https://github.com/NathanSkene/EWCE) which I am currently trying to get accepted to [Bioconductor](https://github.com/Bioconductor/Contributions/issues/1904#).
>>>
>>>
>>> Upon sumission checks, there still seems to be a Windows specific issue running EWCE: the run fails to load an ExperimentHub dataset in the vignette from my related data package [ewceData](https://github.com/neurogenomics/ewceData). I think the line causing the fail is:
>>>
>>>
>>> tt_alzh <- tt_alzh()
>>>
>>> which corresponds to the function containing (see utils.R in ewceData for more details):
>>>
>>> eh <- get_ExperimentHub()
>>> eh[["EH5373"]]
>>>
>>>
>>> Does anyone know what could be causing this issue? Again to note this fail only occurs on the Windows build and not the mac/linux.
>>>
>>> Kind regards,
>>>
>>> Alan.
>>>
>>> Alan Murphy
>>> Bioinformatician
>>> Neurogenomics lab
>>> UK Dementia Research Institute
>>> Imperial College London
>>>
>>> [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
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>>>
>>
>> --
>> Hervé Pagès
>>
>> Bioconductor Core Team
>> hpages.on.github using gmail.com
>
> --
> Hervé Pagès
>
> Bioconductor Core Team
> hpages.on.github using gmail.com
--
Hervé Pagès
Bioconductor Core Team
hpages.on.github using gmail.com
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