[Bioc-devel] Package failed build on Windows - couldn't load related ExperimentHub dataset

Hi Herv?,

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:* Herv? Pag?s <hpages.on.github at gmail.com>
*Sent:* 26 March 2021 16:13
*To:* Murphy, Alan E <a.murphy at imperial.ac.uk>; bioc-devel at r-project.org 
<bioc-devel at 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 Herv?,

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:* Herv? Pag?s <hpages.on.github at gmail.com>
*Sent:* 25 March 2021 22:53
*To:* Murphy, Alan E <a.murphy at imperial.ac.uk>; bioc-devel at r-project.org 
<bioc-devel at 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

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-- 
Herv? Pag?s

Bioconductor Core Team
hpages.on.github at gmail.com
-- 
Herv? Pag?s

Bioconductor Core Team
hpages.on.github at gmail.com

Herv? Pag?s

Bioconductor Core Team
hpages.on.github at gmail.com

[Bioc-devel] Package failed build on Windows - couldn't load related ExperimentHub dataset

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