[Bioc-devel] pwrEWAS package: Error in CHECK during checkResults on Windows

[Pages, Herve]

Hi Stefan,

It looks like a connectivity issue, likely a transient one. I would just 
wait and see if it goes away in the next days.

Thanks for keeping a close eye on the build results for your package.

Best,
H.

On 10/23/19 11:20, Graw, Stefan H wrote:
> Dear devel team,
> 
> My package "pwrEWAS" produced an error (see below) during checkResults in CHECK on the windows server. I previously had an OK and did not change anything. Should I just wait for the next build or how can I fix this issue?
> 
> Thanks,
> Stefan
> 
> 
> 
> ** running examples for arch 'x64' ... ERROR
> Running examples in 'pwrEWAS-Ex.R' failed
> The error most likely occurred in:
> 
>> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
>> ### Name: pwrEWAS
>> ### Title: pwrEWAS - A computationally efficient tool for comprehensive
>> ###   power estimation in EWAS
>> ### Aliases: pwrEWAS
>> ### Keywords: DNAm microarray power
>>
>> ### ** Examples
>>
>> outDelta <- pwrEWAS(minTotSampleSize = 10,
> +     maxTotSampleSize = 20,
> +     SampleSizeSteps = 10,
> +     NcntPer = 0.5,
> +     targetDelta = c(0.2, 0.5),
> +     J = 1000,
> +     targetDmCpGs = 10,
> +     tissueType = "Adult (PBMC)",
> +     detectionLimit = 0.01,
> +     DMmethod = "limma",
> +     FDRcritVal = 0.05,
> +     core = 2,
> +     sims = 30)
> Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\RtmpIhL8JZ/BiocFileCache
> Warning: download failed
>    web resource path: 'https://urldefense.proofpoint.com/v2/url?u=https-3A__experimenthub.bioconductor.org_metadata_experimenthub.sqlite3&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=4IVJ68WGWUI9QgCUkQl_JPz4iddilcl4o3MlQ7Tfkqw&s=dwyzUba3xBdIO4kUqbc_AcBCsbI4oX3-0_mn46VpJ84&e= '
>    local file path: 'C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\RtmpIhL8JZ/BiocFileCache/1e987801b42_experimenthub.sqlite3'
>    reason: Timeout was reached: [experimenthub.bioconductor.org] Connection timed out after 10014 milliseconds
> Warning: bfcadd() failed; resource removed
>    rid: BFC1
>    fpath: 'https://urldefense.proofpoint.com/v2/url?u=https-3A__experimenthub.bioconductor.org_metadata_experimenthub.sqlite3&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=4IVJ68WGWUI9QgCUkQl_JPz4iddilcl4o3MlQ7Tfkqw&s=dwyzUba3xBdIO4kUqbc_AcBCsbI4oX3-0_mn46VpJ84&e= '
>    reason: download failed
> Error in .util_download(x, rid[i], proxy, config, "bfcadd()", ...) :
>    bfcadd() failed; see warnings()
> Calls: pwrEWAS ... .create_cache -> .updateHubDB -> bfcadd -> bfcadd -> .util_download
> Execution halted
> 
> 
>  From https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_checkResults_3.10_bioc-2DLATEST_pwrEWAS_tokay1-2Dchecksrc.html&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=4IVJ68WGWUI9QgCUkQl_JPz4iddilcl4o3MlQ7Tfkqw&s=OLr1C0h-Ctwe-4W21Dp_kNsWRD_yoM0ro64ZTsVKgAQ&e=
> 
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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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