Re: [Bioc-devel] Package update before october 23rd deadline and build errors [duplicated, wrong email address previous]
Hi Giulia,
Don't know what warning you saw on yesterday's report but it seems that
it's gone today:
https://bioconductor.org/checkResults/3.12/bioc-LATEST/ISAnalytics/
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.
Best,
H.
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=DwICaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=EtLEFyiJFQUn1VZ8ZmcVYiieNEboH1-SlzE9K5y0DH4=SyFSSVPLc4YwZzSVc5uHaDOXpUbJLctxyVKLbKbQYQk=
>>
>>
>> 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_=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=CHJeB1qsdWS04WzhReQyXwYrMCo0ZFIzgm8KFXf0dSU=gGAt_tpoNlVhB63K8IusN9oxHe9SQzGi6T3Drsx4jxU=
>>>
>>>
>>>
>>> Thank you in advance,
>>>
>>> Giulia Pais
>>>
>>> ___
>>> Bioc-devel@r-project.org mailing list
>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=CHJeB1qsdWS04WzhReQyXwYrMCo0ZFIzgm8KFXf0dSU=9yNBZH8vQVM9oEPd9kEepBSAQH0XcokumxvYXW_bYxA=
>>>
>>>
>>>
--
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: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax:(206) 667-1319
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Re: [Bioc-devel] Package update before october 23rd deadline and build errors [duplicated, wrong email address previous]
Giula,
Provided your package has been accepted by a reviewer, it will be released
as part of Bioconductor 3.12, as long as it satisfies the other
requirements, which includes some deadlines for when it is supposed to pass
check without errors.
In general, around release, there are a lot of changes to a lot of
packages. When you get an error from the build system, I suggest looking
closely at the error and also see if other packages are affected.
Unfortunately, sometimes things break on the build system which leads to
100s or 1000s of packages failing at the same time. For this reason, it is
sometimes useful to look at the Dashboard:
http://www.bioconductor.org/dashboard/
Today you can see ~20 packages failing build, ~70 failing installation and
~70 failing check (rough numbers across platforms). Nothing seems to be
amiss with windows.
Today you have a warning on one windows platform which suggests there is
something wrong with IRanges on that platform,
If you see occasional failures (errors), there could be many reasons
including internet access, memory overflow and failure to write to disk.
Its hard to know what you're suffering from without knowing your package.
On Sun, Oct 25, 2020 at 9:57 PM 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://bioconductor.org/checkResults/devel/bioc-LATEST/ISAnalytics/tokay1-checksrc.html
> >
> > 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_=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=CHJeB1qsdWS04WzhReQyXwYrMCo0ZFIzgm8KFXf0dSU=gGAt_tpoNlVhB63K8IusN9oxHe9SQzGi6T3Drsx4jxU=
> >>
> >> Thank you in advance,
> >>
> >> Giulia Pais
> >>
> >> ___
> >> Bioc-devel@r-project.org mailing list
> >>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=CHJeB1qsdWS04WzhReQyXwYrMCo0ZFIzgm8KFXf0dSU=9yNBZH8vQVM9oEPd9kEepBSAQH0XcokumxvYXW_bYxA=
> >>
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
--
Best,
Kasper
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Re: [Bioc-devel] Package update before october 23rd deadline and build errors [duplicated, wrong email address previous]
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://bioconductor.org/checkResults/devel/bioc-LATEST/ISAnalytics/tokay1-checksrc.html
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_=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=CHJeB1qsdWS04WzhReQyXwYrMCo0ZFIzgm8KFXf0dSU=gGAt_tpoNlVhB63K8IusN9oxHe9SQzGi6T3Drsx4jxU=
Thank you in advance,
Giulia Pais
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Re: [Bioc-devel] Package update before october 23rd deadline and build errors [duplicated, wrong email address previous]
Hi Giulia,
Today's report is available. Unfortunately ISAnalytics tests are still
failing on Windows:
https://bioconductor.org/checkResults/devel/bioc-LATEST/ISAnalytics/tokay1-checksrc.html
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_=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=CHJeB1qsdWS04WzhReQyXwYrMCo0ZFIzgm8KFXf0dSU=gGAt_tpoNlVhB63K8IusN9oxHe9SQzGi6T3Drsx4jxU=
>
>
> Thank you in advance,
>
> Giulia Pais
>
> ___
> Bioc-devel@r-project.org mailing list
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=CHJeB1qsdWS04WzhReQyXwYrMCo0ZFIzgm8KFXf0dSU=9yNBZH8vQVM9oEPd9kEepBSAQH0XcokumxvYXW_bYxA=
>
>
--
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: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax:(206) 667-1319
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Re: [Bioc-devel] Package update before october 23rd deadline and build errors [duplicated, wrong email address previous]
Hi Lori, thanks for your reply, unfortunately the problem persists, same as the previous build it appears to have issues with BiocParallel that we don't have both on local machines and github actions server machines. What should we do? Thank you Il 21/10/2020 14:33, Kern, Lori ha scritto: > We are sorry for the inconvenience.� There was an issue generating the > build report, again.� We hope to have it resolved and have the new > build report posted later today.� I do see the 0.99.13 updates in our > git repository so they were pushed up and should be reflected in the > next posted build report. > Please see if the issues clear up on the next build report otherwise > we can investigate further if there is an issue with the BiocParallel > implementation. > > Lori Shepherd > > Bioconductor Core Team > > Roswell Park Comprehensive Cancer Center > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > > > *From:* Bioc-devel on behalf of > Giulia Pais > *Sent:* Wednesday, October 21, 2020 5:58 AM > *To:* bioc-devel@r-project.org > *Subject:* [Bioc-devel] Package update before october 23rd deadline > and build errors [duplicated, wrong email address previous] > 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: > http://secure-web.cisco.com/1zHzlluYonVKy4ELoeCYul0uSR_LsrM-vATHafqCNWVC9GInGrIBBBUFD5evQqHGxEq3urvQtUqxFyRWZKHpwbQ8NV_UQoFsgnSGWJn6jay5_Vh89KT0OA7y8PNREUH-tSKNv34NZMyW6TGTUyOX0hHdYvwKx014kLa5Jtq9tcBtUzNwL_kaT94QNsgn2OdTriktDiI_jMdN_FKV4qtbdP1yTM_FG6NtIox4l8sLKzC5oB3cgvTG9dXqbQ-6K1iVRaz2ml_Prw6T0M-3Ye_A6Lck77kjUxwBKVXSc31mH3vpOiR4-PJBKlk8oXUn3Z15v/http%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2FISAnalytics%2F > > Thank you in advance, > > Giulia Pais > > ___ > Bioc-devel@r-project.org mailing list > https://secure-web.cisco.com/13zn0ely3HlLpozIs-qHy1js8Mi-OmANT3Cl7A72-MML9cpPyjxJp2WMuYvCIwmT7R-hwG_qxD13paKEwm9Obd3l3G7MkGILTmsrp2YiT4Zk4WzRBVh8b8I1WrfneDJ1KQJxsTLoa8h1VsiajJqiwkaZoL5ScfJ7BftT2ZAfBZr-cNAaZPpMwQpO7GS_5jEIFO0dIe7flKrJ1oSg_zf3yxdzwSXUWtddWYSGPwrbB5mU0xzHmVsxiLk2JRvsxf0sCPv8q1MaOJotii9fVcATKGtlKDOryUNYXq52di1RizZHPPzdEdi32oxGSIUwcucgK/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel > > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the employee > or agent responsible for the delivery of this message to the intended > recipient(s), you are hereby notified that any disclosure, copying, > distribution, or use of this email message is prohibited. If you have > received this message in error, please notify the sender immediately > by e-mail and delete this email message from your computer. Thank you. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Package update before october 23rd deadline and build errors [duplicated, wrong email address previous]
We are sorry for the inconvenience. There was an issue generating the build report, again. We hope to have it resolved and have the new build report posted later today. I do see the 0.99.13 updates in our git repository so they were pushed up and should be reflected in the next posted build report. Please see if the issues clear up on the next build report otherwise we can investigate further if there is an issue with the BiocParallel implementation. Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel on behalf of Giulia Pais Sent: Wednesday, October 21, 2020 5:58 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] Package update before october 23rd deadline and build errors [duplicated, wrong email address previous] 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: http://secure-web.cisco.com/1zHzlluYonVKy4ELoeCYul0uSR_LsrM-vATHafqCNWVC9GInGrIBBBUFD5evQqHGxEq3urvQtUqxFyRWZKHpwbQ8NV_UQoFsgnSGWJn6jay5_Vh89KT0OA7y8PNREUH-tSKNv34NZMyW6TGTUyOX0hHdYvwKx014kLa5Jtq9tcBtUzNwL_kaT94QNsgn2OdTriktDiI_jMdN_FKV4qtbdP1yTM_FG6NtIox4l8sLKzC5oB3cgvTG9dXqbQ-6K1iVRaz2ml_Prw6T0M-3Ye_A6Lck77kjUxwBKVXSc31mH3vpOiR4-PJBKlk8oXUn3Z15v/http%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2FISAnalytics%2F Thank you in advance, Giulia Pais ___ Bioc-devel@r-project.org mailing list https://secure-web.cisco.com/13zn0ely3HlLpozIs-qHy1js8Mi-OmANT3Cl7A72-MML9cpPyjxJp2WMuYvCIwmT7R-hwG_qxD13paKEwm9Obd3l3G7MkGILTmsrp2YiT4Zk4WzRBVh8b8I1WrfneDJ1KQJxsTLoa8h1VsiajJqiwkaZoL5ScfJ7BftT2ZAfBZr-cNAaZPpMwQpO7GS_5jEIFO0dIe7flKrJ1oSg_zf3yxdzwSXUWtddWYSGPwrbB5mU0xzHmVsxiLk2JRvsxf0sCPv8q1MaOJotii9fVcATKGtlKDOryUNYXq52di1RizZHPPzdEdi32oxGSIUwcucgK/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
