Hi, This same error has resurfaced. Can someone please look into this for the groHMM package.
Regards, Tulip. ________________________________ From: Herv� Pag�s <hpages.on.git...@gmail.com> Sent: Saturday, October 28, 2023 1:51 PM To: Tulip Nandu <tulip.na...@utsouthwestern.edu>; Kern, Lori <lori.sheph...@roswellpark.org>; bioc-devel@r-project.org <bioc-devel@r-project.org> Subject: Re: [Bioc-devel] groHMM package error Package is all green today on the 3.18 report: https://bioconductor.org/checkResults/3.18/bioc-LATEST/groHMM/<https://urldefense.com/v3/__https://bioconductor.org/checkResults/3.18/bioc-LATEST/groHMM/__;!!MznTZTSvDXGV0Co!BPaBrGLFj6s1ULrvrPGL-g9u1P_xyFMmTDlj8JjuQ-UOQAVx6iJEdvKN8snzX83dFwTGJau1bFYs8EB_ull-gDtVQmUa3hlLalpPnA$> Cheers, H. On 10/25/23 16:11, Herv� Pag�s wrote: Addressed in S4Vectors 0.40.1. Today's builds have started already so the fix won't be reflected on tomorrow's report (Thursday), only on Friday. Sorry again for the inconvenience. Best, H. On 10/25/23 15:34, Herv� Pag�s wrote: Hi Tulip, I think this is caused by a late change in S4Vectors: https://github.com/Bioconductor/S4Vectors/commit/15349ef40f141b16df6daf3e38f3782ef54eb60c<https://urldefense.com/v3/__https://github.com/Bioconductor/S4Vectors/commit/15349ef40f141b16df6daf3e38f3782ef54eb60c__;!!MznTZTSvDXGV0Co!BPaBrGLFj6s1ULrvrPGL-g9u1P_xyFMmTDlj8JjuQ-UOQAVx6iJEdvKN8snzX83dFwTGJau1bFYs8EB_ull-gDtVQmUa3hltWFkgSA$> This was an attempt at implementing the following feature request: https://github.com/Bioconductor/DelayedArray/issues/108<https://urldefense.com/v3/__https://github.com/Bioconductor/DelayedArray/issues/108__;!!MznTZTSvDXGV0Co!BPaBrGLFj6s1ULrvrPGL-g9u1P_xyFMmTDlj8JjuQ-UOQAVx6iJEdvKN8snzX83dFwTGJau1bFYs8EB_ull-gDtVQmUa3hkh2QcYxQ$> Sorry that this change broken your subsetting operation kgChr7[de==1, ]. Honestly, it's hard (if not impossible) to anticipate that some code somewhere would use a Nx1 TestResults object (this is what 'de==1' is!) as a subscript to subset a Vector derivative like your GRanges object kgChr7. It was just luck that this was working so far. Anyways, I think we can make this work again. A patch is coming. Best, H. On 10/25/23 14:03, Tulip Nandu wrote: Hi Lori, Thank you for your prompt response. I haven't changed anything in the development package (on git on anywhere else) then why the error message has suddenly come up. As per the package what exactly they want me to change so it passes the R CMD Check goes on without errors. Regards, Tulip. ________________________________ From: Kern, Lori <lori.sheph...@roswellpark.org><mailto:lori.sheph...@roswellpark.org> Sent: Wednesday, October 25, 2023 6:06 AM To: Tulip Nandu <tulip.na...@utsouthwestern.edu><mailto:tulip.na...@utsouthwestern.edu>; bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> <bioc-devel@r-project.org><mailto:bioc-devel@r-project.org> Cc: Martin Grigorov <martin.grigo...@gmail.com><mailto:martin.grigo...@gmail.com> Subject: Re: groHMM package error You should make sure you are using the latest version of R and have updated Bioconductor/CRAN packages by running BiocManager::valid and/or BiocManager:install . I can reproduce this locally. Running your vignette it has to do with this line: upGenes <- kgChr7[de==1,] Error: invalid subscript Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 ________________________________ From: Tulip Nandu <tulip.na...@utsouthwestern.edu><mailto:tulip.na...@utsouthwestern.edu> Sent: Tuesday, October 24, 2023 3:33 PM To: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> <bioc-devel@r-project.org><mailto:bioc-devel@r-project.org> Cc: Kern, Lori <lori.sheph...@roswellpark.org><mailto:lori.sheph...@roswellpark.org>; Martin Grigorov <martin.grigo...@gmail.com><mailto:martin.grigo...@gmail.com> Subject: Re: groHMM package error Hi, Can someone explain as why has this error suddenly come up. I haven't changed anything from my end. Also, please if someone can help me tackle the error it would be great. Thanks. Regards, Tulip. ________________________________ From: Kern, Lori <lori.sheph...@roswellpark.org><mailto:lori.sheph...@roswellpark.org> Sent: Wednesday, October 18, 2023 3:45 PM To: Tulip Nandu <tulip.na...@utsouthwestern.edu><mailto:tulip.na...@utsouthwestern.edu> Subject: Re: groHMM package error As Martin also responded, The ERROR should not be neglected but you should push to the "devel" branch instead of "RELEASE_3_18". Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 ________________________________ From: Tulip Nandu <tulip.na...@utsouthwestern.edu><mailto:tulip.na...@utsouthwestern.edu> Sent: Wednesday, October 18, 2023 4:37 PM To: Kern, Lori <lori.sheph...@roswellpark.org><mailto:lori.sheph...@roswellpark.org>; bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> <bioc-devel@r-project.org><mailto:bioc-devel@r-project.org>; martin.grigo...@gmail.com<mailto:martin.grigo...@gmail.com> <martin.grigo...@gmail.com><mailto:martin.grigo...@gmail.com> Subject: Re: groHMM package error Is this error to be neglected then? Package: groHMM Version: 1.35.0 Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data groHMM StartedAt: 2023-10-17 17:05:26 -0400 (Tue, 17 Oct 2023) EndedAt: 2023-10-17 17:07:18 -0400 (Tue, 17 Oct 2023) EllapsedTime: 112.0 seconds RetCode: 1 Status: ERROR PackageFile: None PackageFileSize: NA According to the Multiple platform build/check report for BioC 3.18, the groHMM package has the following problem(s): o ERROR for 'R CMD build' on nebbiolo2. See the details here: 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Let me know. Thank you so much. Regards, Tulip. ________________________________ From: Kern, Lori <lori.sheph...@roswellpark.org><mailto:lori.sheph...@roswellpark.org> Sent: Wednesday, October 18, 2023 3:36 PM To: Tulip Nandu <tulip.na...@utsouthwestern.edu><mailto:tulip.na...@utsouthwestern.edu>; bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> <bioc-devel@r-project.org><mailto:bioc-devel@r-project.org> Subject: Re: groHMM package error EXTERNAL MAIL There is no RELEASE_3_18 branch until the release next week (created automatically by the core team on release day) . All updates should be pushed to the devel branch. 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-boun...@r-project.org><mailto:bioc-devel-boun...@r-project.org> on behalf of Tulip Nandu <tulip.na...@utsouthwestern.edu><mailto:tulip.na...@utsouthwestern.edu> Sent: Wednesday, October 18, 2023 4:30 PM To: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> <bioc-devel@r-project.org><mailto:bioc-devel@r-project.org> Subject: [Bioc-devel] groHMM package error Hi, I just got an email from the Bioconductor stating, According to the Multiple platform build/check report for BioC 3.18, the groHMM package has the following problem(s): o ERROR for 'R CMD build' on nebbiolo2. See the details here: 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I feel it's the version issue 3.17 to 3.18 and I need to release the package to 3.18 too. But moment I try to update it throws up a error message: git checkout RELEASE_3_18 error: pathspec 'RELEASE_3_18' did not match any file(s) known to git Can anyone help me with this update and error. Regards, Tulip. ________________________________ UT Southwestern Medical Center The future of medicine, today. [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list https://secure-web.cisco.com/1o-3kGonW8iymDY6hzo2pojCCdKoWNydSzBaeOshxpTMWcS-dfzElfuIu8M6bbKbMgi9xSSJNDZtNYzec3LEB3zPMDzCle8b1h-Fc9Goghdj-wU3b8HUAJvLrOTG1Gs6zfqGVytcKWBIRFjUd9kjTeKm1JvCR_QYqe21uwsn_e4-v_2AdgIHKp5qyT5CMLbvwOwyAHj9xeF8Qqi864p1xNwWxd8Rd49ErwRK84EOd3mBa90GB3kipbWY-Vp4HHnOXwYpiGjJybSbbjglSCDpbNiSmgphgVB7d1FhGX8Vfzs9-rdd3hN-A1rjRgggBFW5v/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel<https://urldefense.com/v3/__https://secure-web.cisco.com/1o-3kGonW8iymDY6hzo2pojCCdKoWNydSzBaeOshxpTMWcS-dfzElfuIu8M6bbKbMgi9xSSJNDZtNYzec3LEB3zPMDzCle8b1h-Fc9Goghdj-wU3b8HUAJvLrOTG1Gs6zfqGVytcKWBIRFjUd9kjTeKm1JvCR_QYqe21uwsn_e4-v_2AdgIHKp5qyT5CMLbvwOwyAHj9xeF8Qqi864p1xNwWxd8Rd49ErwRK84EOd3mBa90GB3kipbWY-Vp4HHnOXwYpiGjJybSbbjglSCDpbNiSmgphgVB7d1FhGX8Vfzs9-rdd3hN-A1rjRgggBFW5v/https*3A*2F*2Fstat.ethz.ch*2Fmailman*2Flistinfo*2Fbioc-devel__;JSUlJSUl!!MznTZTSvDXGV0Co!BPaBrGLFj6s1ULrvrPGL-g9u1P_xyFMmTDlj8JjuQ-UOQAVx6iJEdvKN8snzX83dFwTGJau1bFYs8EB_ull-gDtVQmUa3hlhX_mb6Q$><https://urldefense.com/v3/__https://secure-web.cisco.com/1td0EkI2g1ZyyIzNVYIaU-VUiHDiSr91F-inGjEawFZvB5JViUNifU0EALPtUw7ReHHjiMqy2HeqdlZB8zk0NxSDwWcQH2O_-Oh_P0cqwFek8ufqImlClbyeCwtqunO2lbB9apd3mRpL2Eb1geANGnQO8NgQXcnnd0EC1E_SJ2o_KbgtuMzZV2Q7wXfq5Im4QGsohIu9spjaJOHLLrPXx50W_vfkxSr8VSEAck07wZAFdxhLxGnVDQJXwirbDihP6Pq1PD7MkTh232Q7_1j3hzXuFmibt5X0lgCTpCURbfH9vI8_zSznz2px08tRx8DOI/https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2F*2Fsecure-web.cisco.com*2F1RMLblrjfbaF1NsYWdKMO_dcIU_pe5b5SdV9gZJjxY6kfyhczntKmvf74_0V1VnHrBTfrhv-7bIfnFSzsgKVQqdFeYKc1CTe1oBe3VRRBfHFDRvXTmvP8cz3BMuCdiH5fLof Kgi8b8vUYErmzGTCMLZrv-xKAXx8cBiVr_Pis_aznTgs8Cf5EOOD0ICYL2ogF9pj-yuCV96-3mQ3hDOE7DO7sU0max9WydlMdUzBt_RY5dh_-6VrqCFJA-Iymw9J6aDDJ-ZggxPWTV3IHbQ88j_eZTwg3QOCUZDoqorEC9WUtUQihiVmfXCv6WRynfwxu*2Fhttps*2A3A*2A2F*2A2Furldefense.com*2A2Fv3*2A2F__https*2A3A*2A2F*2A2Fsecure-web.cisco.com*2A2F1o-3kGonW8iymDY6hzo2pojCCdKoWNydSzBaeOshxpTMWcS-dfzElfuIu8M6bbKbMgi9xSSJNDZtNYzec3LEB3zPMDzCle8b1h-Fc9Goghdj-wU3b8HUAJvLrOTG1Gs6zfqGVytcKWBIRFjUd9kjTeKm1JvCR_QYqe21uwsn_e4-v_2AdgIHKp5qyT5CMLbvwOwyAHj9xeF8Qqi864p1xNwWxd8Rd49ErwRK84EOd3mBa90GB3kipbWY-Vp4HHnOXwYpiGjJybSbbjglSCDpbNiSmgphgVB7d1FhGX8Vfzs9-rdd3hN-A1rjRgggBFW5v*2A2Fhttps*2A2A3A*2A2A2F*2A2A2Fstat.ethz.ch*2A2A2Fmailman*2A2A2Flistinfo*2A2A2Fbioc-devel__*2A3BJSUlJSUl*2A21*2A21MznTZTSvDXGV0Co*2A21FHn7u-ed-EzEFNHx6AOJ5DifCmLXwOLVW22U69hqE2M9Ig6xlDM0yfg8aVv4ml6FAgs6ZEh0L7CNNYrvxd4kmb6tGSElzwkLI-p7bho*2A24__*3BJSUlJSUlJSUlJSUlJSUlJSUlJSUl*21*21MznTZTSvDXGV0Co*21CQdmhYdq0-C37GWMJwm0wPXgYZ1GnTG7CF0IRkSRTERUe6dO7rjL0BmYoLwlckm2Wv7nflkFw_L1HG3YfODPak8pDp4i Lo6VJZOUmB4*24__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUl!!MznTZTSvDXGV0Co!Amw3xom-SM3e3cfsWyoJb1tzyz6v_ttMAIJJAnoGProVnS0LgDu4QJfuSTSyUZHPs-in3lbx4Z6LeOXbhAEEj53cdAHd6Y_x_lLZC3Y$><https://urldefense.com/v3/__https://secure-web.cisco.com/1td0EkI2g1ZyyIzNVYIaU-VUiHDiSr91F-inGjEawFZvB5JViUNifU0EALPtUw7ReHHjiMqy2HeqdlZB8zk0NxSDwWcQH2O_-Oh_P0cqwFek8ufqImlClbyeCwtqunO2lbB9apd3mRpL2Eb1geANGnQO8NgQXcnnd0EC1E_SJ2o_KbgtuMzZV2Q7wXfq5Im4QGsohIu9spjaJOHLLrPXx50W_vfkxSr8VSEAck07wZAFdxhLxGnVDQJXwirbDihP6Pq1PD7MkTh232Q7_1j3hzXuFmibt5X0lgCTpCURbfH9vI8_zSznz2px08tRx8DOI/https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2F*2Fsecure-web.cisco.com*2F1RMLblrjfbaF1NsYWdKMO_dcIU_pe5b5SdV9gZJjxY6kfyhczntKmvf74_0V1VnHrBTfrhv-7bIfnFSzsgKVQqdFeYKc1CTe1oBe3VRRBfHFDRvXTmvP8cz3BMuCdiH5fLofKgi8b8vUYErmzGTCMLZrv-xKAXx8cBiVr_Pis_aznTgs8Cf5EOOD0ICYL2ogF9pj-yuCV96-3mQ3hDOE7DO7sU0max9WydlMdUzBt_RY5dh_-6VrqCFJA-Iymw9J6aDDJ-ZggxPWTV3IHbQ88j_eZTwg3QOCUZDoqorEC9WUtUQihiVmfXCv6WRynfwxu*2Fhttps*2A3A*2A2F*2A2Furldefense.com*2A2Fv3*2A2F__https*2A3A*2A2F*2A2Fsecure-web.cisco.com*2A2F1o-3kGonW8iymDY6hzo2pojCCdKoWNydSzBaeOshxpTMWcS-dfzElfuIu8M6bbKbMgi9xSSJNDZtNYzec3LEB3zPMDzCle8b1h-Fc9Goghdj-wU3b8HUAJvLrOTG1Gs6zfqGVytcKWBIRFjUd9kjTeKm1JvCR_QYqe21uwsn_e4-v_2AdgIHKp5qyT5CMLbvwOwyAHj9xeF8Qqi864p1xNwWxd8Rd49ErwRK84EOd3mBa90GB3kipbWY-Vp4HHnOXwYpiGjJybSbbjglSCDpbNiSmgphgVB7d1FhGX8Vfzs9-rdd3hN-A1rjRgggBFW5v*2A2Fhttps*2A2A3A*2A2A2F*2A2A2Fstat.ethz.ch*2A2A2Fmailman*2A2A2Flistinfo*2A2A2Fbioc-devel__*2A3BJSUlJSUl*2A21*2A21MznTZTSvDXGV0Co*2A21FHn7u-ed-EzEFNHx6AOJ5DifCmLXwOLVW22U69hqE2M9Ig6xlDM0yfg8aVv4ml6FAgs6ZEh0L7CNNYrvxd4kmb6tGSElzwkLI-p7bho*2A24__*3BJSUlJSUlJSUlJSUlJSUlJSUlJSUl*21*21MznTZTSvDXGV0Co*21CQdmhYdq0-C37GWMJwm0wPXgYZ1GnTG7CF0IRkSRTERUe6dO7rjL0BmYoLwlckm2Wv7nflkFw_L1HG3YfODPak8pDp4iLo6VJZOUmB4*24__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUl!!MznTZTSvDXGV0Co!Amw3xom-SM3e3cfsWyoJb1tzyz6v_ttMAIJJAnoGProVnS0LgDu4QJfuSTSyUZHPs-in3lbx4Z6LeOXbhAEEj53cdAHd6Y_x_lLZC3Y$> This email message may contain legally privileged and/or confidential information. 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