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://bioconductor.org/checkResults/devel/bioc-LATEST/ISAnalytics/ Thank you in advance, Giulia Pais
[Bioc-devel] Package update before october 23rd deadline and build errors [duplicated, wrong email address previous]
9 messages · Shepherd, Lori, Hervé Pagès, Giulia Pais +1 more
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 <bioc-devel-bounces at r-project.org> on behalf of Giulia Pais <giuliapais1 at gmail.com>
Sent: Wednesday, October 21, 2020 5:58 AM
To: bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: [Bioc-devel] Package update before october 23rd deadline and build errors [duplicated, wrong email address previous]
Sent: Wednesday, October 21, 2020 5:58 AM
To: bioc-devel at r-project.org <bioc-devel at 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 at 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.
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 <bioc-devel-bounces at r-project.org> on behalf of Giulia Pais <giuliapais1 at gmail.com> *Sent:* Wednesday, October 21, 2020 5:58 AM *To:* bioc-devel at r-project.org <bioc-devel at 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
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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_&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=CHJeB1qsdWS04WzhReQyXwYrMCo0ZFIzgm8KFXf0dSU&s=gGAt_tpoNlVhB63K8IusN9oxHe9SQzGi6T3Drsx4jxU&e= Thank you in advance, Giulia Pais
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Herv? Pag?s 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 at fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319
4 days later
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_&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=CHJeB1qsdWS04WzhReQyXwYrMCo0ZFIzgm8KFXf0dSU&s=gGAt_tpoNlVhB63K8IusN9oxHe9SQzGi6T3Drsx4jxU&e= Thank you in advance, Giulia Pais
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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 <giuliapais1 at gmail.com> 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:
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
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Best, Kasper [[alternative HTML version deleted]]
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&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
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Herv? Pag?s 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 at fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319