Dear Bioconductor community, One of the oldest requirements of Bioconductor is a vignette with some executed code. Recently I found some packages that do not have examples for some functions and vignettes with executed code in the current release while they did some versions ago. The vignette was replaced with a link to resources outside the Bioconductor repository. These resources might not be in sync with the released code of the package or might not work. Users, as I did, might get confused if code linked from the vignette does not work or is not found in the package. This is possible because submitted packages need to pass all checks specified by R CMD check and by BioCheck() in the BiocCheck package. However, once accepted, checks are no longer done with BiocCheck() and just with R CMD check. I think it would be desirable to keep the initial high quality of the packages after the peer review and with the BiocCheck. If authors need to move their code to a book they can use the book infrastructure set up by Bioconductor too. Perhaps Bioconductor checks on existing packages could use the same version of BiocCheck that was initially used or some specific tests to ensure that documentation is not dismissed. I would appreciate your thoughts on this. Best, Llu?s
[Bioc-devel] Packages removing documentation
4 messages · Lluís Revilla, Shepherd, Lori
Thank you. I agree packages should maintain the high integrity that they were accepted with. For now if you find these packages please let us know their name by sending an email to maintainer at bioconductor.org and we will reach out to notify them they are not in Bioconductor standards and will get a warning to fix or we will consider deprecating. We would like to run BiocCheck but our current resources do not allow for that. We will look into some other options for trying to run BiocCheck on the current Bioconductor packages for at least status checks. Hopefully we can find a way to identify these types of packages without increasing the build resource load. 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 <bioc-devel-bounces at r-project.org> on behalf of Llu?s Revilla <lluis.revilla at gmail.com>
Sent: Monday, August 1, 2022 5:36 PM
To: bioc-devel <bioc-devel at r-project.org>
Subject: [Bioc-devel] Packages removing documentation
Sent: Monday, August 1, 2022 5:36 PM
To: bioc-devel <bioc-devel at r-project.org>
Subject: [Bioc-devel] Packages removing documentation
Dear Bioconductor community, One of the oldest requirements of Bioconductor is a vignette with some executed code. Recently I found some packages that do not have examples for some functions and vignettes with executed code in the current release while they did some versions ago. The vignette was replaced with a link to resources outside the Bioconductor repository. These resources might not be in sync with the released code of the package or might not work. Users, as I did, might get confused if code linked from the vignette does not work or is not found in the package. This is possible because submitted packages need to pass all checks specified by R CMD check and by BioCheck() in the BiocCheck package. However, once accepted, checks are no longer done with BiocCheck() and just with R CMD check. I think it would be desirable to keep the initial high quality of the packages after the peer review and with the BiocCheck. If authors need to move their code to a book they can use the book infrastructure set up by Bioconductor too. Perhaps Bioconductor checks on existing packages could use the same version of BiocCheck that was initially used or some specific tests to ensure that documentation is not dismissed. I would appreciate your thoughts on this. Best, Llu?s _______________________________________________ Bioc-devel at r-project.org mailing list https://secure-web.cisco.com/1Bp9IWsmviNqtOXHZ8gQHEN2itJq-bl9sZVS3MlFqyqvm1ZUu_ETpQJ8E-kMwnkpHMw1wQ1jvRfZtcX47aEKiC-NeK9LKh_EqowOHdf6xg9D6BusJI6T19FILEzgFk43YumLMXkNcCK_pr5WLn1gnw9SjAysgQccaW2L1r8wBp7DLdxH1vsMzx_-bpYzxze13pD8CC4BiH379f56RX07mkreVsMmm9HJZmUXllPZioNdw3vzkVRsGSk_bsYhq9VLMJUMbFJLI62oalZJlnTVibPl5_vqRx85wdrx1kxQNsUcXZHnteaBD4mzTjmrEMw0C/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, Many thanks for your quick response. I think the requirements for new packages are great but I'm not sure all these standards can be applied to older packages: The new requirements in BiocCheck might result in warnings and errors to many packages. For instance, new submitted packages are required to remove files such as .Rproj or the .github folder [1, 2], which some older packages have (including mine). There was a discussion about these files a couple of years ago in the community-bioc slack and more recently to allow the inclusion of these files [3, 4, 5] Older packages might not have vignettes with executed code, which might be difficult for maintainers to now rewrite the vignettes. I don't know enough about the resources of Bioconductor to propose a good solution. But I think lower BiocChecks frequency than current checks, such as once every 3 months or at similar frequencies, would allow Bioconductor to detect those issues while not imposing too much burden on the Bioconductor resources. However, a faster and lighter approach might be using static analysis on the packages: grep or specific tools such as https://github.com/ropensci-review-tools/pkgstats. Cheers, Llu?s [1]: https://bioconductor.org/packages/release/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#bad-file-check [2]: https://github.com/Bioconductor/Contributions/issues/2658#issuecomment-1121182390 [3]: https://community-bioc.slack.com/archives/C6MVC96AZ/p1604600559030500 [4]: https://community-bioc.slack.com/archives/C6MVC96AZ/p1649041312699229 [5]: https://community-bioc.slack.com/archives/C6MVC96AZ/p1621466394001900 and subsequent messages
On Tue, 2 Aug 2022 at 13:22, Kern, Lori <Lori.Shepherd at roswellpark.org> wrote:
Thank you. I agree packages should maintain the high integrity that they were accepted with. For now if you find these packages please let us know their name by sending an email to maintainer at bioconductor.org and we will reach out to notify them they are not in Bioconductor standards and will get a warning to fix or we will consider deprecating. We would like to run BiocCheck but our current resources do not allow for that. We will look into some other options for trying to run BiocCheck on the current Bioconductor packages for at least status checks. Hopefully we can find a way to identify these types of packages without increasing the build resource load. 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 <bioc-devel-bounces at r-project.org> on behalf of Llu?s Revilla <lluis.revilla at gmail.com> Sent: Monday, August 1, 2022 5:36 PM To: bioc-devel <bioc-devel at r-project.org> Subject: [Bioc-devel] Packages removing documentation Dear Bioconductor community, One of the oldest requirements of Bioconductor is a vignette with some executed code. Recently I found some packages that do not have examples for some functions and vignettes with executed code in the current release while they did some versions ago. The vignette was replaced with a link to resources outside the Bioconductor repository. These resources might not be in sync with the released code of the package or might not work. Users, as I did, might get confused if code linked from the vignette does not work or is not found in the package. This is possible because submitted packages need to pass all checks specified by R CMD check and by BioCheck() in the BiocCheck package. However, once accepted, checks are no longer done with BiocCheck() and just with R CMD check. I think it would be desirable to keep the initial high quality of the packages after the peer review and with the BiocCheck. If authors need to move their code to a book they can use the book infrastructure set up by Bioconductor too. Perhaps Bioconductor checks on existing packages could use the same version of BiocCheck that was initially used or some specific tests to ensure that documentation is not dismissed. I would appreciate your thoughts on this. Best, Llu?s _______________________________________________ Bioc-devel at r-project.org mailing list https://secure-web.cisco.com/1Bp9IWsmviNqtOXHZ8gQHEN2itJq-bl9sZVS3MlFqyqvm1ZUu_ETpQJ8E-kMwnkpHMw1wQ1jvRfZtcX47aEKiC-NeK9LKh_EqowOHdf6xg9D6BusJI6T19FILEzgFk43YumLMXkNcCK_pr5WLn1gnw9SjAysgQccaW2L1r8wBp7DLdxH1vsMzx_-bpYzxze13pD8CC4BiH379f56RX07mkreVsMmm9HJZmUXllPZioNdw3vzkVRsGSk_bsYhq9VLMJUMbFJLI62oalZJlnTVibPl5_vqRx85wdrx1kxQNsUcXZHnteaBD4mzTjmrEMw0C/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.
Yes I was thinking along the same lines. Run once every few weeks to get a snapshot of how packages do on BiocCheck and slowly try to get maintainers to clean up those results. Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263
From: Llu?s Revilla <lluis.revilla at gmail.com>
Sent: Tuesday, August 2, 2022 9:08 AM
To: Kern, Lori <Lori.Shepherd at RoswellPark.org>
Cc: bioc-devel <bioc-devel at r-project.org>
Subject: Re: [Bioc-devel] Packages removing documentation
Sent: Tuesday, August 2, 2022 9:08 AM
To: Kern, Lori <Lori.Shepherd at RoswellPark.org>
Cc: bioc-devel <bioc-devel at r-project.org>
Subject: Re: [Bioc-devel] Packages removing documentation
Hi Lori, Many thanks for your quick response. I think the requirements for new packages are great but I'm not sure all these standards can be applied to older packages: The new requirements in BiocCheck might result in warnings and errors to many packages. For instance, new submitted packages are required to remove files such as .Rproj or the .github folder [1, 2], which some older packages have (including mine). There was a discussion about these files a couple of years ago in the community-bioc slack and more recently to allow the inclusion of these files [3, 4, 5] Older packages might not have vignettes with executed code, which might be difficult for maintainers to now rewrite the vignettes. I don't know enough about the resources of Bioconductor to propose a good solution. But I think lower BiocChecks frequency than current checks, such as once every 3 months or at similar frequencies, would allow Bioconductor to detect those issues while not imposing too much burden on the Bioconductor resources. However, a faster and lighter approach might be using static analysis on the packages: grep or specific tools such as https://secure-web.cisco.com/1R557UXDvqcXWXGd1Dmm73gkoF3ahbnvTzreZGbmPl1ECO5EKI6bycTqP2g3T8LdpEuSvPQD01IfvJCaeafjfjmoC0pHNiClqjtKbsud0slV3COJ-0SwVJqG4wz-IgBDtXMLeziiLfpTcncgaJiPYDmfUOsOXyCzn6Yd2GQJA06fMAhnjF_drUjSPdnSmvtIxxLQN02KZWGJoQ44AnYpiYHSgcMm23bpfaIBxK64jr-KuAeH0IpaTraip0nfVWsK0kAQcPja9O1_1P9d3bu8Hqsfl4-NjPEqIfPlTavT--fxSHwsXOgK0MdHayp8SdpoR/https%3A%2F%2Fgithub.com%2Fropensci-review-tools%2Fpkgstats Cheers, Llu?s [1]: https://secure-web.cisco.com/1a_0YmVnu1GsjtpN64fdr9ReKL8y7kvZMHKR8qpYBn5HgXrWtm5E5WfR7y_y2C8g1K0MLqzB2Wx72YP-A__2F7jWgrcpXEbhi7KS4H6Z-Y0YP3NlLQKWu844zMQ9jrQ3uYcH6kcr8HPvR_mSoo1Sho6wRWn5PNH9FIX42r-fPE-KXnBknAwOhsBw3Y3_lasNFyMcxa32gEG5P4CFeVNDB-xdtOy57SrG97UVBxwaBt3Na3NMb2djINlSirreD312cl7TwUvkMXE7caB1LX5VYaRy3NdInpp6K1GKxbEX_YBbfnwHTSEbz-V3q4wbapkay/https%3A%2F%2Fbioconductor.org%2Fpackages%2Frelease%2Fbioc%2Fvignettes%2FBiocCheck%2Finst%2Fdoc%2FBiocCheck.html%23bad-file-check [2]: https://secure-web.cisco.com/1Ccb2CHRSAmwZvpozxv1vJJRGKiuClEftczI6PoRWHwynswHD15Ube0O7f5yGQD2xEFX1kuk2SB7zdSx_IQ1ep0hwoRuHt72SOV_rCER6LD_T5nFpTqhZJ8-1usM3ENqGbqjOUphghqrWXchfyGrZ2zQ2_uFRoRab_1fzCPPkqlRSyc1VJbxQ4dEiNFfU5f4zHleD2oCGGnoTY6AUVGY_BIk4efWSBbPcMzxcOXxzHejGS7sLMRyY6KiB-w72t7MbtV6oS97x0i3XZvViLe0JIGx15M2RYozJcLyWcD_L-_gSAFGMHJYB-nb-aon_a-BK/https%3A%2F%2Fgithub.com%2FBioconductor%2FContributions%2Fissues%2F2658%23issuecomment-1121182390 [3]: https://secure-web.cisco.com/13KOi4VHL3o9Qdtvv2ePVVuAVKGS_Xhh52g__0PKj7ciXYEdt4joapalxqqZO5cK7IzHxOmcuUpI-Dm8DxX0Ki74y4yNMXTEyDwryXMKdf_9tV1X9D6b-Tbch5kwbQzBzlnmJlU1h0FMKC0DcqGrrPuSddn4xqvH8nZlct_-DXfkgnqLDyrzivlFGjaIjcqJ3414ekY3RFDX9hVIjvLuluQMxt09m3HGLDSP7VnuBksOO3RlEB1Ak319Fc2KTAeyptoRdB6vOVGyNdCM-OSrQ0gS3PYsoBzzeypGbW0fVOv81FNB-ji_qkzQaUYwrTzvz/https%3A%2F%2Fcommunity-bioc.slack.com%2Farchives%2FC6MVC96AZ%2Fp1604600559030500 [4]: https://secure-web.cisco.com/1kSs36-mDRQ4H-_n-mBfn5U-MGzivcYMwNRwuZiWQvpx3Ad5ND31J-iyC5Eq-dx4CE5phFz6l6oNVIDNX7K4uKD1MpW3Z0EWzlbMTlfi8HU3_lhfey3UIl37OpdWItn-Nwdco4uIj4g4L8Hovt2UA0F1E568jyGa7p65UKMwvoaAkpFgzaupcqTIK13kGjVa6LCpInj2zFfgNmLhsSEPosaJwTo_0FZjkpibWs793ktX1tOnOTDbLAK18Qp7b46Emin97J-S6RTWMFiX1Qdjswxr0uQLtu4WRu8vWcjlu5vJofWsTzdL8b4d-_Mb7SxLE/https%3A%2F%2Fcommunity-bioc.slack.com%2Farchives%2FC6MVC96AZ%2Fp1649041312699229 [5]: https://secure-web.cisco.com/1Hr59KpkdDTN0Xfel1CSvfsLH8p9Aw1n--dbFWgCgNqwL2Ic87FKByIFGEJfSnPWi7UJQ3Yx1R8MtIi15GT8VFaLT82FZi9S-CVfINQszKAVJ_LKMKz33xv_VCu_EELTs0wk24pCpzvi08xInBClFTDPn3t9sPH2S0WSQDYQVpI-w0W9YT6YSMH3Yvgmn2pmBJ0HcRVRyiWvj5JHSPdQWbtb3celIvb3EXQfrO-6zQ6xLnv8SlWZd17Yv6429ZDiWjxoEQwWLPxBpk7fKEQJJo3VLuVbXJN30xfPFCE5fL3fGPoSVisIdALi0133ESBWC/https%3A%2F%2Fcommunity-bioc.slack.com%2Farchives%2FC6MVC96AZ%2Fp1621466394001900 and subsequent messages On Tue, 2 Aug 2022 at 13:22, Kern, Lori <Lori.Shepherd at roswellpark.org> wrote: > > Thank you. > > I agree packages should maintain the high integrity that they were accepted with. For now if you find these packages please let us know their name by sending an email to maintainer at bioconductor.org and we will reach out to notify them they are not in Bioconductor standards and will get a warning to fix or we will consider deprecating. > > We would like to run BiocCheck but our current resources do not allow for that. We will look into some other options for trying to run BiocCheck on the current Bioconductor packages for at least status checks. Hopefully we can find a way to identify these types of packages without increasing the build resource load. > > 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 <bioc-devel-bounces at r-project.org> on behalf of Llu?s Revilla <lluis.revilla at gmail.com> > Sent: Monday, August 1, 2022 5:36 PM > To: bioc-devel <bioc-devel at r-project.org> > Subject: [Bioc-devel] Packages removing documentation > > Dear Bioconductor community, > > One of the oldest requirements of Bioconductor is a vignette with some > executed code. > > Recently I found some packages that do not have examples for some > functions and vignettes with executed code in the current release > while they did some versions ago. The vignette was replaced with a > link to resources outside the Bioconductor repository. > These resources might not be in sync with the released code of the > package or might not work. Users, as I did, might get confused if code > linked from the vignette does not work or is not found in the package. > > This is possible because submitted packages need to pass all checks > specified by R CMD check and by BioCheck() in the BiocCheck package. > However, once accepted, checks are no longer done with BiocCheck() and > just with R CMD check. > > I think it would be desirable to keep the initial high quality of the > packages after the peer review and with the BiocCheck. If authors need > to move their code to a book they can use the book infrastructure set > up by Bioconductor too. > Perhaps Bioconductor checks on existing packages could use the same > version of BiocCheck that was initially used or some specific tests to > ensure that documentation is not dismissed. > > I would appreciate your thoughts on this. > > Best, > > Llu?s > > _______________________________________________ > Bioc-devel at r-project.org mailing list > https://secure-web.cisco.com/1Bp9IWsmviNqtOXHZ8gQHEN2itJq-bl9sZVS3MlFqyqvm1ZUu_ETpQJ8E-kMwnkpHMw1wQ1jvRfZtcX47aEKiC-NeK9LKh_EqowOHdf6xg9D6BusJI6T19FILEzgFk43YumLMXkNcCK_pr5WLn1gnw9SjAysgQccaW2L1r8wBp7DLdxH1vsMzx_-bpYzxze13pD8CC4BiH379f56RX07mkreVsMmm9HJZmUXllPZioNdw3vzkVRsGSk_bsYhq9VLMJUMbFJLI62oalZJlnTVibPl5_vqRx85wdrx1kxQNsUcXZHnteaBD4mzTjmrEMw0C/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. 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.