Dear All, I have noticed that on the latest build report, a package I maintain, OncoSimulR (http://bioconductor.org/checkResults/devel/bioc-LATEST/OncoSimulR/veracruz1-buildsrc.html), has status timeout on veracruz1. Package building stalls during creation of the vignette (that is not happening in the malbec1 ---linux--- build). I have noticed that this same pattern (timeout with build stopped when creating the vignette in veracruz1 but not in malbec1) seems to affect other packages (http://bioconductor.org/checkResults/devel/bioc-LATEST/index.html#show=timeout). Is there anything we should do? Just looking at the log I do not know how to proceed. Thanks, R. -- Ramon Diaz-Uriarte Department of Biochemistry, Lab B-25 Facultad de Medicina Universidad Aut?noma de Madrid Arzobispo Morcillo, 4 28029 Madrid Spain Phone: +34-91-497-2412 Email: rdiaz02 at gmail.com ramon.diaz at iib.uam.es http://ligarto.org/rdiaz
[Bioc-devel] BioC 3.6: timeouts on veracruz1 (OS X)
3 messages · Martin Morgan, Ramon Diaz-Uriarte
On 10/12/2017 07:08 AM, Ramon Diaz-Uriarte wrote:
Dear All, I have noticed that on the latest build report, a package I maintain, OncoSimulR (http://bioconductor.org/checkResults/devel/bioc-LATEST/OncoSimulR/veracruz1-buildsrc.html),
I wonder if it is this issue https://github.com/Bioconductor/BiocParallel/issues/67 which would occur if your vignette has parallel code (using 'fork' processed via parallel::mclapply or indirectly via BiocParallel::MulticoreParam() / doParallel etc.) If so then the best strategy is to wait for an upstream fix. Martin
has status timeout on veracruz1. Package building stalls during creation of the vignette (that is not happening in the malbec1 ---linux--- build). I have noticed that this same pattern (timeout with build stopped when creating the vignette in veracruz1 but not in malbec1) seems to affect other packages (http://bioconductor.org/checkResults/devel/bioc-LATEST/index.html#show=timeout). Is there anything we should do? Just looking at the log I do not know how to proceed. Thanks, R. -- Ramon Diaz-Uriarte Department of Biochemistry, Lab B-25 Facultad de Medicina Universidad Aut?noma de Madrid Arzobispo Morcillo, 4 28029 Madrid Spain Phone: +34-91-497-2412 Email: rdiaz02 at gmail.com ramon.diaz at iib.uam.es http://ligarto.org/rdiaz
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Dear Martin,
On Fri, 13-October-2017, at 12:27:31, Martin Morgan <martin.morgan at roswellpark.org> wrote:
On 10/12/2017 07:08 AM, Ramon Diaz-Uriarte wrote:
Dear All, I have noticed that on the latest build report, a package I maintain, OncoSimulR (http://bioconductor.org/checkResults/devel/bioc-LATEST/OncoSimulR/veracruz1-buildsrc.html),
I wonder if it is this issue https://github.com/Bioconductor/BiocParallel/issues/67 which would occur if your vignette has parallel code (using 'fork' processed via parallel::mclapply or indirectly via BiocParallel::MulticoreParam() / doParallel etc.)
Yes! I have both explicit calls to mclapply and implicit ones (functions that call functions that call mclapply) in the vignette.
If so then the best strategy is to wait for an upstream fix.
OK. Thank you. Best, R.
Martin
has status timeout on veracruz1. Package building stalls during creation of the vignette (that is not happening in the malbec1 ---linux--- build). I have noticed that this same pattern (timeout with build stopped when creating the vignette in veracruz1 but not in malbec1) seems to affect other packages (http://bioconductor.org/checkResults/devel/bioc-LATEST/index.html#show=timeout). Is there anything we should do? Just looking at the log I do not know how to proceed. Thanks, R. -- Ramon Diaz-Uriarte Department of Biochemistry, Lab B-25 Facultad de Medicina Universidad Aut?noma de Madrid Arzobispo Morcillo, 4 28029 Madrid Spain Phone: +34-91-497-2412 Email: rdiaz02 at gmail.com ramon.diaz at iib.uam.es http://ligarto.org/rdiaz
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Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Aut?noma de Madrid
Arzobispo Morcillo, 4
28029 Madrid
Spain
Phone: +34-91-497-2412
Email: rdiaz02 at gmail.com
ramon.diaz at iib.uam.es
http://ligarto.org/rdiaz