[Bioc-devel] Package update before october 23rd deadline and build errors [duplicated, wrong email address previous]

Pages, Herve hp@ge@ @end|ng |rom |redhutch@org
Tue Oct 27 00:37:48 CET 2020

Hi Giulia,

Don't know what warning you saw on yesterday's report but it seems that 
it's gone today:


Just to clarify, propagation is usually irreversible. This means that, 
since the latest version of the package (0.99.15) has already propagated 
for all platforms (as you can see on the package landing page 
https://bioconductor.org/packages/3.12/ISAnalytics), it is now available 
for download (via BiocManager::install()). And it will remain like that 
even if we see one of these intermittent errors or warnings on the 
report tomorrow or after tomorrow.


On 10/25/20 13:57, Giulia Pais wrote:
> Hello,
> we keep getting weird warning messages for check on windows, it's also 
> even more odd since we got yesterday a build report with no errors or 
> warnings but the build report for today gives an error on Windows Server 
> 2012 R2 Standard / x64 only. We can't understand what the warning is, 
> why does it happen only for tests and also why it doesn't happen 
> consistently (same lines of codes are run in examples in the 
> documentation).
> Could you give us further insight on the meaning of this warning? We are 
> not able to reproduce it.
> Also will our package be released for bioconductor 3.12?
> Thank you
> Il 21/10/2020 19:08, Pages, Herve ha scritto:
>> Hi Giulia,
>> Today's report is available. Unfortunately ISAnalytics tests are still
>> failing on Windows:
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_ISAnalytics_tokay1-2Dchecksrc.html&d=DwICaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=EtLEFyiJFQUn1VZ8ZmcVYiieNEboH1-SlzE9K5y0DH4&s=SyFSSVPLc4YwZzSVc5uHaDOXpUbJLctxyVKLbKbQYQk&e= 
>> Note that you have this warning at the beginning of the tests:
>>     > test_check("ISAnalytics")
>>     Warning message:
>>     In file(file, "rt") :
>>       file("") only supports open = "w+" and open = "w+b": using the 
>> former
>> Maybe it's relevant?
>> In any case, that warning should not be ignored as it is most likely
>> reporting a real problem.
>> Best,
>> H.
>> On 10/21/20 02:58, Giulia Pais wrote:
>>> Hello, bioconductor team,
>>> I'm one of the contributors for the package ISAnalytics. We pushed some
>>> changes we would like to be included in the release for bioconductor
>>> 3.12 a couple of days ago but the build report still refers to the older
>>> version, did we miss the deadline for updates or is it normal? Moreover,
>>> by taking a look at the build report for the older version we noticed it
>>> had failed on Windows, which is to us very odd, since we develop and
>>> check the package on windows locally and we also have github automated
>>> actions that perform the same checks on other machines and there were no
>>> errors or warnings. From what we can see from the report it seems a
>>> BiocParallel problem, could you give us feedback on this please? The
>>> link to the build report:
>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_ISAnalytics_&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=CHJeB1qsdWS04WzhReQyXwYrMCo0ZFIzgm8KFXf0dSU&s=gGAt_tpoNlVhB63K8IusN9oxHe9SQzGi6T3Drsx4jxU&e= 
>>> Thank you in advance,
>>> Giulia Pais
>>> _______________________________________________
>>> Bioc-devel using r-project.org mailing list
>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=CHJeB1qsdWS04WzhReQyXwYrMCo0ZFIzgm8KFXf0dSU&s=9yNBZH8vQVM9oEPd9kEepBSAQH0XcokumxvYXW_bYxA&e= 

Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages using fredhutch.org
Phone:  (206) 667-5791
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