Re: [Bioc-devel] Wrong skipping of tests when builidng on Bioconductor and R CMD check timeout
Thank you very much for your effort!
Best regards and happy new year!
Jacopo
Il mar 26 dic 2023, 12:59 Kern, Lori ha
scritto:
> Sorry for the delay. These environment variables should be set now on the
> Single Package Builder.
>
> Lori Shepherd - Kern
>
> 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 Kern,
> Lori via Bioc-devel
> *Sent:* Friday, December 15, 2023 9:36 AM
> *To:* Jacopo Ronchi ; Hervé Pagès <
> hpages.on.git...@gmail.com>
> *Cc:* bioc-devel@r-project.org
> *Subject:* Re: [Bioc-devel] Wrong skipping of tests when builidng on
> Bioconductor and R CMD check timeout
>
> I can update the SPB to have that environment variable set. I will also
> cross check it with the current variables set on the daily builder.
> It may not be until next week that it is implemented.
>
> Cheers,
>
>
> Lori Shepherd - Kern
>
> 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 Jacopo
> Ronchi
> Sent: Friday, December 15, 2023 8:47 AM
> To: Herv�ag�
> Cc: bioc-devel@r-project.org
> Subject: Re: [Bioc-devel] Wrong skipping of tests when builidng on
> Bioconductor and R CMD check timeout
>
> Regarding the Renviron file i have seen on the GitHub repository of SPB
> that indeed it is not using the IS_BIOC_BUILD_MACHINE env variable. How
> should i do in order to pass the checks without errors for my package in
> submission?
>
> Kind regards,
> Jacopo
>
> Il mer 13 dic 2023, 00:48 Jacopo Ronchi ha
> scritto:
>
> > Dear Herv�>
> > Thank you very much for your answer. Regarding the issue that my package
> > encounters during the building on SPB i had the same doubt. Indeed when i
> > include that variable locally in my Renviron file everything works as
> > expected (tests that should be skipped on Bioconductor are indeed
> ignored).
> > So maybe the slight differences in variables between the two build
> systems
> > might be the answer.
> >
> > On the other hand, i did not consider the caching of resources used in
> > examples. Since i already use BiocFileCache in my package, i will extend
> > this also for other features used in examples! Thank you very much for
> this
> > very useful suggestion.
> >
> > Kind regards,
> > Jacopo
> >
> > Il mer 13 dic 2023, 00:00 Herv�ag� ha
> > scritto:
> >
> >> Hi Jacopo,
> >>
> >> testthat::skip_on_bioc() relies on the IS_BIOC_BUILD_MACHINE environment
> >> variable to know whether it's on a BioC build machine or not.
> >>
> >> This environment variable is defined during the daily build via the
> >> Renviron.bioc file. Note that a link to this file is provided on the
> >> individual build reports e.g. here
> >>
> https://secure-web.cisco.com/1VAUfQTzP732tzYFyWRl9R-VpUe0qcrj11ANCzhi1M7PXdmEUq8BM7_xAJMn24SuX7fWWohKPYZhB0230fNWhTyL4DmAVWLPvmLQrY5ekH9gk0wIeUU8p_IHNHwooLmCYzg1EM9sBSbHTBa-lYfH_5RxRsfe9G46Fzgh4qD9LOMpVZH1EVerXKPfVHgQIJIXjWIkiyjvKSPcnIEXFgTHXVrklHZnSW_X7ba5yCvjOLPEAsUhPpIdJdDbYUEhR37AlDIl7CI6ww6vt95xFIBwEpTv8AsSrGIUY7opOomIPbtZTZiiznEYRC6gZQPGmhUrd/https%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.19%2Fbioc-LATEST%2FBiobase%2F
> >> ("Renviron settings" link).
> >>
> >> Maybe this environment variable is not defined on the Single Package
> >> Builder (SPB)? The SPB is the build system used during the package
> >> submission process. It runs on the same machines as the daily builds
> but my
> >> understanding is that it uses a slightly different set of variables.
> Maybe
> >> Lori can shed some light?
> >>
> >> As for the timeout on merida1 (Intel Mac), have you considered using
> >> BiocFileCache to cache the data that you download in your examples? You
> >> might still get a timeout the next time 'R CMD check' will run on our
> build
> >> machines, but it should go significantly faster after that.
> >>
> >> Best,
> >>
> >> H.
> >> On 12/12/23 07:22, Jacopo Ronchi wrote:
> >>
> >> Dear Developers,
> >>
> >> I am currently in the process of submitting my package on Bioconductor
> and
> >> I am facing some issues during the R CMD check on the Bioconductor Build
> >> System. Since I was not able to find any answers to my doubts, I
> decided to
> >> ask for your help before doing anything wrong.
> >>
> >> The build report for my package is available here:
> http://secure-web.cisco.com/1Rk_soQiHKHVPFUyxQEVFg-vcGG0WAJR6XK9z24AVEnrYfyKPY9vQ4_mh_dSEWnq5yhsoMSsoBYGZdR9X6XGeGTieTjRz0eFyhxsZ6EwtJp5WanZk4hoMSYlCzTQlbWTrp0W0U3GNKSqDkKWI9JcB6yDgdJkYsz3_A3DTSPZ5utwV_dF7MrGbC9_ccpBq33AGenBIHH43zCquE-F0QDPTJI85Sufi4xzh9O0DjBTFaGekjHHCm2WVF406Ga6Ij_IBAQBNBO78-SU9THFiK386l4E_sv0N9hiMQM-6BU7wXBS8dtxYQfa7Z42RMzZ_6Rax/http%3A%2F%2Fbioconductor.org%2Fspb_reports%2FMIRit_buildreport_20231211095232.html
> >>
> >> In
Re: [Bioc-devel] Wrong skipping of tests when builidng on Bioconductor and R CMD check timeout
Sorry for the delay. These environment variables should be set now on the
Single Package Builder.
Lori Shepherd - Kern
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 Kern, Lori via
Bioc-devel
Sent: Friday, December 15, 2023 9:36 AM
To: Jacopo Ronchi ; Hervé Pagès
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Wrong skipping of tests when builidng on Bioconductor
and R CMD check timeout
I can update the SPB to have that environment variable set. I will also cross
check it with the current variables set on the daily builder.
It may not be until next week that it is implemented.
Cheers,
Lori Shepherd - Kern
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 Jacopo Ronchi
Sent: Friday, December 15, 2023 8:47 AM
To: Herv�ag�
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Wrong skipping of tests when builidng on Bioconductor
and R CMD check timeout
Regarding the Renviron file i have seen on the GitHub repository of SPB
that indeed it is not using the IS_BIOC_BUILD_MACHINE env variable. How
should i do in order to pass the checks without errors for my package in
submission?
Kind regards,
Jacopo
Il mer 13 dic 2023, 00:48 Jacopo Ronchi ha
scritto:
> Dear Herv�>
> Thank you very much for your answer. Regarding the issue that my package
> encounters during the building on SPB i had the same doubt. Indeed when i
> include that variable locally in my Renviron file everything works as
> expected (tests that should be skipped on Bioconductor are indeed ignored).
> So maybe the slight differences in variables between the two build systems
> might be the answer.
>
> On the other hand, i did not consider the caching of resources used in
> examples. Since i already use BiocFileCache in my package, i will extend
> this also for other features used in examples! Thank you very much for this
> very useful suggestion.
>
> Kind regards,
> Jacopo
>
> Il mer 13 dic 2023, 00:00 Herv�ag� ha
> scritto:
>
>> Hi Jacopo,
>>
>> testthat::skip_on_bioc() relies on the IS_BIOC_BUILD_MACHINE environment
>> variable to know whether it's on a BioC build machine or not.
>>
>> This environment variable is defined during the daily build via the
>> Renviron.bioc file. Note that a link to this file is provided on the
>> individual build reports e.g. here
>> https://secure-web.cisco.com/1VAUfQTzP732tzYFyWRl9R-VpUe0qcrj11ANCzhi1M7PXdmEUq8BM7_xAJMn24SuX7fWWohKPYZhB0230fNWhTyL4DmAVWLPvmLQrY5ekH9gk0wIeUU8p_IHNHwooLmCYzg1EM9sBSbHTBa-lYfH_5RxRsfe9G46Fzgh4qD9LOMpVZH1EVerXKPfVHgQIJIXjWIkiyjvKSPcnIEXFgTHXVrklHZnSW_X7ba5yCvjOLPEAsUhPpIdJdDbYUEhR37AlDIl7CI6ww6vt95xFIBwEpTv8AsSrGIUY7opOomIPbtZTZiiznEYRC6gZQPGmhUrd/https%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.19%2Fbioc-LATEST%2FBiobase%2F
>> ("Renviron settings" link).
>>
>> Maybe this environment variable is not defined on the Single Package
>> Builder (SPB)? The SPB is the build system used during the package
>> submission process. It runs on the same machines as the daily builds but my
>> understanding is that it uses a slightly different set of variables. Maybe
>> Lori can shed some light?
>>
>> As for the timeout on merida1 (Intel Mac), have you considered using
>> BiocFileCache to cache the data that you download in your examples? You
>> might still get a timeout the next time 'R CMD check' will run on our build
>> machines, but it should go significantly faster after that.
>>
>> Best,
>>
>> H.
>> On 12/12/23 07:22, Jacopo Ronchi wrote:
>>
>> Dear Developers,
>>
>> I am currently in the process of submitting my package on Bioconductor and
>> I am facing some issues during the R CMD check on the Bioconductor Build
>> System. Since I was not able to find any answers to my doubts, I decided to
>> ask for your help before doing anything wrong.
>>
>> The build report for my package is available
>> here:http://secure-web.cisco.com/1Rk_soQiHKHVPFUyxQEVFg-vcGG0WAJR6XK9z24AVEnrYfyKPY9vQ4_mh_dSEWnq5yhsoMSsoBYGZdR9X6XGeGTieTjRz0eFyhxsZ6EwtJp5WanZk4hoMSYlCzTQlbWTrp0W0U3GNKSqDkKWI9JcB6yDgdJkYsz3_A3DTSPZ5utwV_dF7MrGbC9_ccpBq33AGenBIHH43zCquE-F0QDPTJI85Sufi4xzh9O0DjBTFaGekjHHCm2WVF406Ga6Ij_IBAQBNBO78-SU9THFiK386l4E_sv0N9hiMQM-6BU7wXBS8dtxYQfa7Z42RMzZ_6Rax/http%3A%2F%2Fbioconductor.org%2Fspb_reports%2FMIRit_buildreport_20231211095232.html
>>
>> In particular, my package includes some functions where it accesses remote
>> resources. Therefore, I included some "skip_on_bioc()" chunks at the
>> beginning of these tests since I don't want my package to fail during the
>> build process because of occasional down times. However, when I look at the
>> build report, I notice that the relevant tests are not skipped.
>> Furthermore, other
Re: [Bioc-devel] Wrong skipping of tests when builidng on Bioconductor and R CMD check timeout
Great!
Thank you very much for this news!
Best regards,
Jacopo
Il ven 15 dic 2023, 15:36 Kern, Lori ha
scritto:
> I can update the SPB to have that environment variable set. I will also
> cross check it with the current variables set on the daily builder.
> It may not be until next week that it is implemented.
>
> Cheers,
>
> Lori Shepherd - Kern
>
> 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 Jacopo
> Ronchi
> *Sent:* Friday, December 15, 2023 8:47 AM
> *To:* Hervé Pagès
> *Cc:* bioc-devel@r-project.org
> *Subject:* Re: [Bioc-devel] Wrong skipping of tests when builidng on
> Bioconductor and R CMD check timeout
>
> Regarding the Renviron file i have seen on the GitHub repository of SPB
> that indeed it is not using the IS_BIOC_BUILD_MACHINE env variable. How
> should i do in order to pass the checks without errors for my package in
> submission?
>
> Kind regards,
> Jacopo
>
> Il mer 13 dic 2023, 00:48 Jacopo Ronchi ha
> scritto:
>
> > Dear Hervé,
> >
> > Thank you very much for your answer. Regarding the issue that my package
> > encounters during the building on SPB i had the same doubt. Indeed when i
> > include that variable locally in my Renviron file everything works as
> > expected (tests that should be skipped on Bioconductor are indeed
> ignored).
> > So maybe the slight differences in variables between the two build
> systems
> > might be the answer.
> >
> > On the other hand, i did not consider the caching of resources used in
> > examples. Since i already use BiocFileCache in my package, i will extend
> > this also for other features used in examples! Thank you very much for
> this
> > very useful suggestion.
> >
> > Kind regards,
> > Jacopo
> >
> > Il mer 13 dic 2023, 00:00 Hervé Pagès ha
> > scritto:
> >
> >> Hi Jacopo,
> >>
> >> testthat::skip_on_bioc() relies on the IS_BIOC_BUILD_MACHINE environment
> >> variable to know whether it's on a BioC build machine or not.
> >>
> >> This environment variable is defined during the daily build via the
> >> Renviron.bioc file. Note that a link to this file is provided on the
> >> individual build reports e.g. here
> >>
> https://secure-web.cisco.com/1VAUfQTzP732tzYFyWRl9R-VpUe0qcrj11ANCzhi1M7PXdmEUq8BM7_xAJMn24SuX7fWWohKPYZhB0230fNWhTyL4DmAVWLPvmLQrY5ekH9gk0wIeUU8p_IHNHwooLmCYzg1EM9sBSbHTBa-lYfH_5RxRsfe9G46Fzgh4qD9LOMpVZH1EVerXKPfVHgQIJIXjWIkiyjvKSPcnIEXFgTHXVrklHZnSW_X7ba5yCvjOLPEAsUhPpIdJdDbYUEhR37AlDIl7CI6ww6vt95xFIBwEpTv8AsSrGIUY7opOomIPbtZTZiiznEYRC6gZQPGmhUrd/https%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.19%2Fbioc-LATEST%2FBiobase%2F
> >> ("Renviron settings" link).
> >>
> >> Maybe this environment variable is not defined on the Single Package
> >> Builder (SPB)? The SPB is the build system used during the package
> >> submission process. It runs on the same machines as the daily builds
> but my
> >> understanding is that it uses a slightly different set of variables.
> Maybe
> >> Lori can shed some light?
> >>
> >> As for the timeout on merida1 (Intel Mac), have you considered using
> >> BiocFileCache to cache the data that you download in your examples? You
> >> might still get a timeout the next time 'R CMD check' will run on our
> build
> >> machines, but it should go significantly faster after that.
> >>
> >> Best,
> >>
> >> H.
> >> On 12/12/23 07:22, Jacopo Ronchi wrote:
> >>
> >> Dear Developers,
> >>
> >> I am currently in the process of submitting my package on Bioconductor
> and
> >> I am facing some issues during the R CMD check on the Bioconductor Build
> >> System. Since I was not able to find any answers to my doubts, I
> decided to
> >> ask for your help before doing anything wrong.
> >>
> >> The build report for my package is available here:
> http://secure-web.cisco.com/1Rk_soQiHKHVPFUyxQEVFg-vcGG0WAJR6XK9z24AVEnrYfyKPY9vQ4_mh_dSEWnq5yhsoMSsoBYGZdR9X6XGeGTieTjRz0eFyhxsZ6EwtJp5WanZk4hoMSYlCzTQlbWTrp0W0U3GNKSqDkKWI9JcB6yDgdJkYsz3_A3DTSPZ5utwV_dF7MrGbC9_ccpBq33AGenBIHH43zCquE-F0QDPTJI85Sufi4xzh9O0DjBTFaGekjHHCm2WVF406Ga6Ij_IBAQBNBO78-SU9THFiK386l4E_sv0N9hiMQM-6BU7wXBS8dtxYQfa7Z42RMzZ_6Rax/http%3A%2F%2Fbioconductor.org%2Fspb_reports%2FMIRit_buildreport_20231211095232.html
> >>
> >> In particular, my package includes some functions where it accesses
> remote
> >> resources. Therefore, I included some "skip_on_bioc()" chunks at the
> >> beginning of these tests since I don't want my package to fail during
> the
> >> build process because of occasional down times. However, when I look at
> the
> >> build report, I notice that the relevant tests are not skipped.
> >> Furthermore, other tests that should be run are instead skipped on
> CRAN. I
> >> am referring to these lines:
> >>
> >> Skipped tests (2)
> >>On CRAN (2): 'test-topological-integration.R:23:5',
> 'test-utils.R:20:5'
> >>
> >> Lastly, I have an error during R CMD
Re: [Bioc-devel] Wrong skipping of tests when builidng on Bioconductor and R CMD check timeout
I can update the SPB to have that environment variable set. I will also cross
check it with the current variables set on the daily builder.
It may not be until next week that it is implemented.
Cheers,
Lori Shepherd - Kern
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 Jacopo Ronchi
Sent: Friday, December 15, 2023 8:47 AM
To: Herv� Pag�s
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Wrong skipping of tests when builidng on Bioconductor
and R CMD check timeout
Regarding the Renviron file i have seen on the GitHub repository of SPB
that indeed it is not using the IS_BIOC_BUILD_MACHINE env variable. How
should i do in order to pass the checks without errors for my package in
submission?
Kind regards,
Jacopo
Il mer 13 dic 2023, 00:48 Jacopo Ronchi ha
scritto:
> Dear Herv�,
>
> Thank you very much for your answer. Regarding the issue that my package
> encounters during the building on SPB i had the same doubt. Indeed when i
> include that variable locally in my Renviron file everything works as
> expected (tests that should be skipped on Bioconductor are indeed ignored).
> So maybe the slight differences in variables between the two build systems
> might be the answer.
>
> On the other hand, i did not consider the caching of resources used in
> examples. Since i already use BiocFileCache in my package, i will extend
> this also for other features used in examples! Thank you very much for this
> very useful suggestion.
>
> Kind regards,
> Jacopo
>
> Il mer 13 dic 2023, 00:00 Herv� Pag�s ha
> scritto:
>
>> Hi Jacopo,
>>
>> testthat::skip_on_bioc() relies on the IS_BIOC_BUILD_MACHINE environment
>> variable to know whether it's on a BioC build machine or not.
>>
>> This environment variable is defined during the daily build via the
>> Renviron.bioc file. Note that a link to this file is provided on the
>> individual build reports e.g. here
>> https://secure-web.cisco.com/1VAUfQTzP732tzYFyWRl9R-VpUe0qcrj11ANCzhi1M7PXdmEUq8BM7_xAJMn24SuX7fWWohKPYZhB0230fNWhTyL4DmAVWLPvmLQrY5ekH9gk0wIeUU8p_IHNHwooLmCYzg1EM9sBSbHTBa-lYfH_5RxRsfe9G46Fzgh4qD9LOMpVZH1EVerXKPfVHgQIJIXjWIkiyjvKSPcnIEXFgTHXVrklHZnSW_X7ba5yCvjOLPEAsUhPpIdJdDbYUEhR37AlDIl7CI6ww6vt95xFIBwEpTv8AsSrGIUY7opOomIPbtZTZiiznEYRC6gZQPGmhUrd/https%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.19%2Fbioc-LATEST%2FBiobase%2F
>> ("Renviron settings" link).
>>
>> Maybe this environment variable is not defined on the Single Package
>> Builder (SPB)? The SPB is the build system used during the package
>> submission process. It runs on the same machines as the daily builds but my
>> understanding is that it uses a slightly different set of variables. Maybe
>> Lori can shed some light?
>>
>> As for the timeout on merida1 (Intel Mac), have you considered using
>> BiocFileCache to cache the data that you download in your examples? You
>> might still get a timeout the next time 'R CMD check' will run on our build
>> machines, but it should go significantly faster after that.
>>
>> Best,
>>
>> H.
>> On 12/12/23 07:22, Jacopo Ronchi wrote:
>>
>> Dear Developers,
>>
>> I am currently in the process of submitting my package on Bioconductor and
>> I am facing some issues during the R CMD check on the Bioconductor Build
>> System. Since I was not able to find any answers to my doubts, I decided to
>> ask for your help before doing anything wrong.
>>
>> The build report for my package is available
>> here:http://secure-web.cisco.com/1Rk_soQiHKHVPFUyxQEVFg-vcGG0WAJR6XK9z24AVEnrYfyKPY9vQ4_mh_dSEWnq5yhsoMSsoBYGZdR9X6XGeGTieTjRz0eFyhxsZ6EwtJp5WanZk4hoMSYlCzTQlbWTrp0W0U3GNKSqDkKWI9JcB6yDgdJkYsz3_A3DTSPZ5utwV_dF7MrGbC9_ccpBq33AGenBIHH43zCquE-F0QDPTJI85Sufi4xzh9O0DjBTFaGekjHHCm2WVF406Ga6Ij_IBAQBNBO78-SU9THFiK386l4E_sv0N9hiMQM-6BU7wXBS8dtxYQfa7Z42RMzZ_6Rax/http%3A%2F%2Fbioconductor.org%2Fspb_reports%2FMIRit_buildreport_20231211095232.html
>>
>> In particular, my package includes some functions where it accesses remote
>> resources. Therefore, I included some "skip_on_bioc()" chunks at the
>> beginning of these tests since I don't want my package to fail during the
>> build process because of occasional down times. However, when I look at the
>> build report, I notice that the relevant tests are not skipped.
>> Furthermore, other tests that should be run are instead skipped on CRAN. I
>> am referring to these lines:
>>
>> Skipped tests (2)
>>On CRAN (2): 'test-topological-integration.R:23:5', 'test-utils.R:20:5'
>>
>> Lastly, I have an error during R CMD check on macOS, and I really don't
>> know how to reduce the running time on this operating system. Currently, I
>> have reshaped the testing suite to reduce the time spent on unit tests.
>> However, on macOS, i guess that most of the time consumed is due to
>> examples. Nevertheless, the most time consuming functions retrieve
>> gene-sets
Re: [Bioc-devel] Wrong skipping of tests when builidng on Bioconductor and R CMD check timeout
Regarding the Renviron file i have seen on the GitHub repository of SPB
that indeed it is not using the IS_BIOC_BUILD_MACHINE env variable. How
should i do in order to pass the checks without errors for my package in
submission?
Kind regards,
Jacopo
Il mer 13 dic 2023, 00:48 Jacopo Ronchi ha
scritto:
> Dear Hervé,
>
> Thank you very much for your answer. Regarding the issue that my package
> encounters during the building on SPB i had the same doubt. Indeed when i
> include that variable locally in my Renviron file everything works as
> expected (tests that should be skipped on Bioconductor are indeed ignored).
> So maybe the slight differences in variables between the two build systems
> might be the answer.
>
> On the other hand, i did not consider the caching of resources used in
> examples. Since i already use BiocFileCache in my package, i will extend
> this also for other features used in examples! Thank you very much for this
> very useful suggestion.
>
> Kind regards,
> Jacopo
>
> Il mer 13 dic 2023, 00:00 Hervé Pagès ha
> scritto:
>
>> Hi Jacopo,
>>
>> testthat::skip_on_bioc() relies on the IS_BIOC_BUILD_MACHINE environment
>> variable to know whether it's on a BioC build machine or not.
>>
>> This environment variable is defined during the daily build via the
>> Renviron.bioc file. Note that a link to this file is provided on the
>> individual build reports e.g. here
>> https://bioconductor.org/checkResults/3.19/bioc-LATEST/Biobase/
>> ("Renviron settings" link).
>>
>> Maybe this environment variable is not defined on the Single Package
>> Builder (SPB)? The SPB is the build system used during the package
>> submission process. It runs on the same machines as the daily builds but my
>> understanding is that it uses a slightly different set of variables. Maybe
>> Lori can shed some light?
>>
>> As for the timeout on merida1 (Intel Mac), have you considered using
>> BiocFileCache to cache the data that you download in your examples? You
>> might still get a timeout the next time 'R CMD check' will run on our build
>> machines, but it should go significantly faster after that.
>>
>> Best,
>>
>> H.
>> On 12/12/23 07:22, Jacopo Ronchi wrote:
>>
>> Dear Developers,
>>
>> I am currently in the process of submitting my package on Bioconductor and
>> I am facing some issues during the R CMD check on the Bioconductor Build
>> System. Since I was not able to find any answers to my doubts, I decided to
>> ask for your help before doing anything wrong.
>>
>> The build report for my package is available
>> here:http://bioconductor.org/spb_reports/MIRit_buildreport_20231211095232.html
>>
>> In particular, my package includes some functions where it accesses remote
>> resources. Therefore, I included some "skip_on_bioc()" chunks at the
>> beginning of these tests since I don't want my package to fail during the
>> build process because of occasional down times. However, when I look at the
>> build report, I notice that the relevant tests are not skipped.
>> Furthermore, other tests that should be run are instead skipped on CRAN. I
>> am referring to these lines:
>>
>> Skipped tests (2)
>>On CRAN (2): 'test-topological-integration.R:23:5', 'test-utils.R:20:5'
>>
>> Lastly, I have an error during R CMD check on macOS, and I really don't
>> know how to reduce the running time on this operating system. Currently, I
>> have reshaped the testing suite to reduce the time spent on unit tests.
>> However, on macOS, i guess that most of the time consumed is due to
>> examples. Nevertheless, the most time consuming functions retrieve
>> gene-sets from external resources and I can't reduce the download size of
>> KEGG pathways, for example. What should I do?
>>
>> Sorry again for bothering you,
>> Best regards,
>> Jacopo
>>
>> [[alternative HTML version deleted]]
>>
>> ___bioc-de...@r-project.org
>> mailing listhttps://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>> --
>> Hervé Pagès
>>
>> Bioconductor Core teamhpages.on.git...@gmail.com
>>
>>
[[alternative HTML version deleted]]
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Re: [Bioc-devel] Wrong skipping of tests when builidng on Bioconductor and R CMD check timeout
Dear Hervé,
Thank you very much for your answer. Regarding the issue that my package
encounters during the building on SPB i had the same doubt. Indeed when i
include that variable locally in my Renviron file everything works as
expected (tests that should be skipped on Bioconductor are indeed ignored).
So maybe the slight differences in variables between the two build systems
might be the answer.
On the other hand, i did not consider the caching of resources used in
examples. Since i already use BiocFileCache in my package, i will extend
this also for other features used in examples! Thank you very much for this
very useful suggestion.
Kind regards,
Jacopo
Il mer 13 dic 2023, 00:00 Hervé Pagès ha
scritto:
> Hi Jacopo,
>
> testthat::skip_on_bioc() relies on the IS_BIOC_BUILD_MACHINE environment
> variable to know whether it's on a BioC build machine or not.
>
> This environment variable is defined during the daily build via the
> Renviron.bioc file. Note that a link to this file is provided on the
> individual build reports e.g. here
> https://bioconductor.org/checkResults/3.19/bioc-LATEST/Biobase/
> ("Renviron settings" link).
>
> Maybe this environment variable is not defined on the Single Package
> Builder (SPB)? The SPB is the build system used during the package
> submission process. It runs on the same machines as the daily builds but my
> understanding is that it uses a slightly different set of variables. Maybe
> Lori can shed some light?
>
> As for the timeout on merida1 (Intel Mac), have you considered using
> BiocFileCache to cache the data that you download in your examples? You
> might still get a timeout the next time 'R CMD check' will run on our build
> machines, but it should go significantly faster after that.
>
> Best,
>
> H.
> On 12/12/23 07:22, Jacopo Ronchi wrote:
>
> Dear Developers,
>
> I am currently in the process of submitting my package on Bioconductor and
> I am facing some issues during the R CMD check on the Bioconductor Build
> System. Since I was not able to find any answers to my doubts, I decided to
> ask for your help before doing anything wrong.
>
> The build report for my package is available
> here:http://bioconductor.org/spb_reports/MIRit_buildreport_20231211095232.html
>
> In particular, my package includes some functions where it accesses remote
> resources. Therefore, I included some "skip_on_bioc()" chunks at the
> beginning of these tests since I don't want my package to fail during the
> build process because of occasional down times. However, when I look at the
> build report, I notice that the relevant tests are not skipped.
> Furthermore, other tests that should be run are instead skipped on CRAN. I
> am referring to these lines:
>
> Skipped tests (2)
>On CRAN (2): 'test-topological-integration.R:23:5', 'test-utils.R:20:5'
>
> Lastly, I have an error during R CMD check on macOS, and I really don't
> know how to reduce the running time on this operating system. Currently, I
> have reshaped the testing suite to reduce the time spent on unit tests.
> However, on macOS, i guess that most of the time consumed is due to
> examples. Nevertheless, the most time consuming functions retrieve
> gene-sets from external resources and I can't reduce the download size of
> KEGG pathways, for example. What should I do?
>
> Sorry again for bothering you,
> Best regards,
> Jacopo
>
> [[alternative HTML version deleted]]
>
> ___bioc-de...@r-project.org
> mailing listhttps://stat.ethz.ch/mailman/listinfo/bioc-devel
>
> --
> Hervé Pagès
>
> Bioconductor Core teamhpages.on.git...@gmail.com
>
>
[[alternative HTML version deleted]]
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Re: [Bioc-devel] Wrong skipping of tests when builidng on Bioconductor and R CMD check timeout
Hi Jacopo,
testthat::skip_on_bioc() relies on the IS_BIOC_BUILD_MACHINE environment
variable to know whether it's on a BioC build machine or not.
This environment variable is defined during the daily build via the
Renviron.bioc file. Note that a link to this file is provided on the
individual build reports e.g. here
https://bioconductor.org/checkResults/3.19/bioc-LATEST/Biobase/
("Renviron settings" link).
Maybe this environment variable is not defined on the Single Package
Builder (SPB)? The SPB is the build system used during the package
submission process. It runs on the same machines as the daily builds but
my understanding is that it uses a slightly different set of variables.
Maybe Lori can shed some light?
As for the timeout on merida1 (Intel Mac), have you considered using
BiocFileCache to cache the data that you download in your examples? You
might still get a timeout the next time 'R CMD check' will run on our
build machines, but it should go significantly faster after that.
Best,
H.
On 12/12/23 07:22, Jacopo Ronchi wrote:
> Dear Developers,
>
> I am currently in the process of submitting my package on Bioconductor and
> I am facing some issues during the R CMD check on the Bioconductor Build
> System. Since I was not able to find any answers to my doubts, I decided to
> ask for your help before doing anything wrong.
>
> The build report for my package is available here:
> http://bioconductor.org/spb_reports/MIRit_buildreport_20231211095232.html
>
> In particular, my package includes some functions where it accesses remote
> resources. Therefore, I included some "skip_on_bioc()" chunks at the
> beginning of these tests since I don't want my package to fail during the
> build process because of occasional down times. However, when I look at the
> build report, I notice that the relevant tests are not skipped.
> Furthermore, other tests that should be run are instead skipped on CRAN. I
> am referring to these lines:
>
> Skipped tests (2)
> On CRAN (2): 'test-topological-integration.R:23:5', 'test-utils.R:20:5'
>
> Lastly, I have an error during R CMD check on macOS, and I really don't
> know how to reduce the running time on this operating system. Currently, I
> have reshaped the testing suite to reduce the time spent on unit tests.
> However, on macOS, i guess that most of the time consumed is due to
> examples. Nevertheless, the most time consuming functions retrieve
> gene-sets from external resources and I can't reduce the download size of
> KEGG pathways, for example. What should I do?
>
> Sorry again for bothering you,
> Best regards,
> Jacopo
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
Bioconductor Core Team
hpages.on.git...@gmail.com
[[alternative HTML version deleted]]
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[Bioc-devel] Wrong skipping of tests when builidng on Bioconductor and R CMD check timeout
Dear Developers, I am currently in the process of submitting my package on Bioconductor and I am facing some issues during the R CMD check on the Bioconductor Build System. Since I was not able to find any answers to my doubts, I decided to ask for your help before doing anything wrong. The build report for my package is available here: http://bioconductor.org/spb_reports/MIRit_buildreport_20231211095232.html In particular, my package includes some functions where it accesses remote resources. Therefore, I included some "skip_on_bioc()" chunks at the beginning of these tests since I don't want my package to fail during the build process because of occasional down times. However, when I look at the build report, I notice that the relevant tests are not skipped. Furthermore, other tests that should be run are instead skipped on CRAN. I am referring to these lines: Skipped tests (2) On CRAN (2): 'test-topological-integration.R:23:5', 'test-utils.R:20:5' Lastly, I have an error during R CMD check on macOS, and I really don't know how to reduce the running time on this operating system. Currently, I have reshaped the testing suite to reduce the time spent on unit tests. However, on macOS, i guess that most of the time consumed is due to examples. Nevertheless, the most time consuming functions retrieve gene-sets from external resources and I can't reduce the download size of KEGG pathways, for example. What should I do? Sorry again for bothering you, Best regards, Jacopo [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
