[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 17:13:53 CET 2021
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
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