[Bioc-devel] groHMM package error

Thu Oct 26 01:11:58 CEST 2023

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, Hervé Pagès wrote:
>
> Hi Tulip,
>
> I think this is caused by a late change in S4Vectors: 
> https://github.com/Bioconductor/S4Vectors/commit/15349ef40f141b16df6daf3e38f3782ef54eb60c
>
> This was an attempt at implementing the following feature request: 
> https://github.com/Bioconductor/DelayedArray/issues/108
>
> 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.Shepherd using RoswellPark.org>
>> Sent: Wednesday, October 25, 2023 6:06 AM
>> To: Tulip Nandu<Tulip.Nandu using UTSouthwestern.edu>;bioc-devel using r-project.org  <bioc-devel using r-project.org>
>> Cc: Martin Grigorov<martin.grigorov using 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.Nandu using UTSouthwestern.edu>
>> Sent: Tuesday, October 24, 2023 3:33 PM
>> To:bioc-devel using r-project.org  <bioc-devel using r-project.org>
>> Cc: Kern, Lori<Lori.Shepherd using RoswellPark.org>; Martin Grigorov<martin.grigorov using 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.Shepherd using RoswellPark.org>
>> Sent: Wednesday, October 18, 2023 3:45 PM
>> To: Tulip Nandu<Tulip.Nandu using 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.Nandu using UTSouthwestern.edu>
>> Sent: Wednesday, October 18, 2023 4:37 PM
>> To: Kern, Lori<Lori.Shepherd using RoswellPark.org>;bioc-devel using r-project.org  <bioc-devel using r-project.org>;martin.grigorov using gmail.com  <martin.grigorov using 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:
>>       https://secure-web.cisco.com/1Gxx-FnOWCG92V7Tzo6WKfoWn5bSB3-JFD94GIphjmXdi4H2pB97FW0r5HHTt-hdeQj7zZhcmI6dFaU86awXiiWtmSvKjj9swVSo0aGgPMnXH3Z4vVOjbh4zpLrt5PzPE2mXDfaE3BRb3jfaDqsJCAvn19Xv6OnoDfdbzoSo0goZWmkpXfnPaq1s8LMbJi-bz6ToLic80fzSQUDNpW8RKr_Fp58b75XtS18m6wZ8OIc4mdPX4RUhJM2sQHnQzBSm__7z6vBdv4_U1kxAnlFpIs76-p-jNHR4piKZOR8UaySJSYNlzwkDfuBdQfpEXpU28/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fmaster.bioconductor.org%2FcheckResults%2F3.18%2Fbioc-LATEST%2FgroHMM%2Fnebbiolo2-buildsrc.html__;!!MznTZTSvDXGV0Co!EKNuDHTauIdmqCovMhm5TdBQxvFkgq7fpBEFI3kj-5n280k-q3LRrRl6Ob_W0vidU06EefTKfoj0ioHb1yG9hu35fXhzALBpFkA$<https://urldefense.com/v3/__https://secure-web.cisco.com/1gUrDMYAh-8fmjXWvwKvuTYLT1OWOtqrMJHRAccYOartRTyTWfM48qVa1VGmM9T32xk8Ev06tz3cPlPl8dhbVpA0gSoECMx0IWqDgYdqiVwUoxyxcHyTp9xTY278ELGk7n4Gd2ecxTYFUl14Ai_77fj5SpM_6Md1UsL0oZtABcTTCqYelO-Asx38NqsZVdJoRLaikZADKiDWPmSA41ghoujh8t0HCudzKSQ0zh4XZuVC6Jj0FEslvkGCns1PftCM9L9BUczFvsytbzLkKD7zsVDMbkdGlrKsYt3XMmdxBCcLDiAb9Go7EtTZqRSwI 
>> Pxdg/https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2F*2Fsecure-web.cisco.com*2F1krdleRu6rYX6knRc68ATtEj9N0jlIT2CFwqtkCoRkKdk1S9TJQrflUq-SqjwBR50ykjFHesLhPCllgM4ZWaR2oBzfwtLaw4dyPhxtk_xyGHn6Bkj6-o8kxAysmVIdiiFgnlLvok0W1_6vyPWWWWha7q8lYQvcupFRKoXiYSJ9AcelAcfw29j_ukt8hYLA5ntk1fihRrN6_f5GaQWmlSjC2BiDl4hbtErRHupbsU-GUwdvUm01qd_x1XDQNcyIvhpukhaHPCH_4LOdAa3LxHPkzC3fCqGB2jCF0HLmOYd3wSl91OV4UNbDho1eQ6L-qti*2Fhttps*2A3A*2A2F*2A2Furldefense.com*2A2Fv3*2A2F__https*2A3A*2A2F*2A2Fsecure-web.cisco.com*2A2F1Gxx-FnOWCG92V7Tzo6WKfoWn5bSB3-JFD94GIphjmXdi4H2pB97FW0r5HHTt-hdeQj7zZhcmI6dFaU86awXiiWtmSvKjj9swVSo0aGgPMnXH3Z4vVOjbh4zpLrt5PzPE2mXDfaE3BRb3jfaDqsJCAvn19Xv6OnoDfdbzoSo0goZWmkpXfnPaq1s8LMbJi-bz6ToLic80fzSQUDNpW8RKr_Fp58b75XtS18m6wZ8OIc4mdPX4RUhJM2sQHnQzBSm__7z6vBdv4_U1kxAnlFpIs76-p-jNHR4piKZOR8UaySJSYNlzwkDfuBdQfpEXpU28*2A2Fhttps*2A2A3A*2A2A2F*2A2A2Furldefense.com*2A2A2Fv3*2A2A2F__https*2A2A3A*2A2A2F*2A2A2Fmaster.bioconductor.org*2A2A2FcheckResults*2A2A2F3.18*2A2A2Fbioc-LATEST*2A2A2FgroHMM*2A2A2 
>> Fnebbiolo2-buildsrc.html__*2A3B*2A21*2A21MznTZTSvDXGV0Co*2A21EKNuDHTauIdmqCovMhm5TdBQxvFkgq7fpBEFI3kj-5n280k-q3LRrRl6Ob_W0vidU06EefTKfoj0ioHb1yG9hu35fXhzALBpFkA*2A24__*2A3BJSUlJSUlJSUlJSUlJQ*2A21*2A21MznTZTSvDXGV0Co*2A21FHn7u-ed-EzEFNHx6AOJ5DifCmLXwOLVW22U69hqE2M9Ig6xlDM0yfg8aVv4ml6FAgs6ZEh0L7CNNYrvxd4kmb6tGSElzwkL-19PXfs*2A24__*3BJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUl*21*21MznTZTSvDXGV0Co*21CQdmhYdq0-C37GWMJwm0wPXgYZ1GnTG7CF0IRkSRTERUe6dO7rjL0BmYoLwlckm2Wv7nflkFw_L1HG3YfODPak8pDp4iLo6V_zcxPRo*24__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUl!!MznTZTSvDXGV0Co!Amw3xom-SM3e3cfsWyoJb1tzyz6v_ttMAIJJAnoGProVnS0LgDu4QJfuSTSyUZHPs-in3lbx4Z6LeOXbhAEEj53cdAHd6Y_xqKS9fsU$>
>>
>> Let me know.
>>
>> Thank you so much.
>>
>> Regards,
>>
>> Tulip.
>>
>>
>> ________________________________
>> From: Kern, Lori<Lori.Shepherd using RoswellPark.org>
>> Sent: Wednesday, October 18, 2023 3:36 PM
>> To: Tulip Nandu<Tulip.Nandu using UTSouthwestern.edu>;bioc-devel using r-project.org  <bioc-devel using 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-bounces using r-project.org>  on behalf of Tulip Nandu<Tulip.Nandu using UTSouthwestern.edu>
>> Sent: Wednesday, October 18, 2023 4:30 PM
>> To:bioc-devel using r-project.org  <bioc-devel using 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:
>>       https://secure-web.cisco.com/1Gxx-FnOWCG92V7Tzo6WKfoWn5bSB3-JFD94GIphjmXdi4H2pB97FW0r5HHTt-hdeQj7zZhcmI6dFaU86awXiiWtmSvKjj9swVSo0aGgPMnXH3Z4vVOjbh4zpLrt5PzPE2mXDfaE3BRb3jfaDqsJCAvn19Xv6OnoDfdbzoSo0goZWmkpXfnPaq1s8LMbJi-bz6ToLic80fzSQUDNpW8RKr_Fp58b75XtS18m6wZ8OIc4mdPX4RUhJM2sQHnQzBSm__7z6vBdv4_U1kxAnlFpIs76-p-jNHR4piKZOR8UaySJSYNlzwkDfuBdQfpEXpU28/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fmaster.bioconductor.org%2FcheckResults%2F3.18%2Fbioc-LATEST%2FgroHMM%2Fnebbiolo2-buildsrc.html__;!!MznTZTSvDXGV0Co!EKNuDHTauIdmqCovMhm5TdBQxvFkgq7fpBEFI3kj-5n280k-q3LRrRl6Ob_W0vidU06EefTKfoj0ioHb1yG9hu35fXhzALBpFkA$<https://urldefense.com/v3/__https://secure-web.cisco.com/1gUrDMYAh-8fmjXWvwKvuTYLT1OWOtqrMJHRAccYOartRTyTWfM48qVa1VGmM9T32xk8Ev06tz3cPlPl8dhbVpA0gSoECMx0IWqDgYdqiVwUoxyxcHyTp9xTY278ELGk7n4Gd2ecxTYFUl14Ai_77fj5SpM_6Md1UsL0oZtABcTTCqYelO-Asx38NqsZVdJoRLaikZADKiDWPmSA41ghoujh8t0HCudzKSQ0zh4XZuVC6Jj0FEslvkGCns1PftCM9L9BUczFvsytbzLkKD7zsVDMbkdGlrKsYt3XMmdxBCcLDiAb9Go7EtTZqRSwI 
>> Pxdg/https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2F*2Fsecure-web.cisco.com*2F1krdleRu6rYX6knRc68ATtEj9N0jlIT2CFwqtkCoRkKdk1S9TJQrflUq-SqjwBR50ykjFHesLhPCllgM4ZWaR2oBzfwtLaw4dyPhxtk_xyGHn6Bkj6-o8kxAysmVIdiiFgnlLvok0W1_6vyPWWWWha7q8lYQvcupFRKoXiYSJ9AcelAcfw29j_ukt8hYLA5ntk1fihRrN6_f5GaQWmlSjC2BiDl4hbtErRHupbsU-GUwdvUm01qd_x1XDQNcyIvhpukhaHPCH_4LOdAa3LxHPkzC3fCqGB2jCF0HLmOYd3wSl91OV4UNbDho1eQ6L-qti*2Fhttps*2A3A*2A2F*2A2Furldefense.com*2A2Fv3*2A2F__https*2A3A*2A2F*2A2Fsecure-web.cisco.com*2A2F1Gxx-FnOWCG92V7Tzo6WKfoWn5bSB3-JFD94GIphjmXdi4H2pB97FW0r5HHTt-hdeQj7zZhcmI6dFaU86awXiiWtmSvKjj9swVSo0aGgPMnXH3Z4vVOjbh4zpLrt5PzPE2mXDfaE3BRb3jfaDqsJCAvn19Xv6OnoDfdbzoSo0goZWmkpXfnPaq1s8LMbJi-bz6ToLic80fzSQUDNpW8RKr_Fp58b75XtS18m6wZ8OIc4mdPX4RUhJM2sQHnQzBSm__7z6vBdv4_U1kxAnlFpIs76-p-jNHR4piKZOR8UaySJSYNlzwkDfuBdQfpEXpU28*2A2Fhttps*2A2A3A*2A2A2F*2A2A2Furldefense.com*2A2A2Fv3*2A2A2F__https*2A2A3A*2A2A2F*2A2A2Fmaster.bioconductor.org*2A2A2FcheckResults*2A2A2F3.18*2A2A2Fbioc-LATEST*2A2A2FgroHMM*2A2A2 
>> Fnebbiolo2-buildsrc.html__*2A3B*2A21*2A21MznTZTSvDXGV0Co*2A21EKNuDHTauIdmqCovMhm5TdBQxvFkgq7fpBEFI3kj-5n280k-q3LRrRl6Ob_W0vidU06EefTKfoj0ioHb1yG9hu35fXhzALBpFkA*2A24__*2A3BJSUlJSUlJSUlJSUlJQ*2A21*2A21MznTZTSvDXGV0Co*2A21FHn7u-ed-EzEFNHx6AOJ5DifCmLXwOLVW22U69hqE2M9Ig6xlDM0yfg8aVv4ml6FAgs6ZEh0L7CNNYrvxd4kmb6tGSElzwkL-19PXfs*2A24__*3BJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUl*21*21MznTZTSvDXGV0Co*21CQdmhYdq0-C37GWMJwm0wPXgYZ1GnTG7CF0IRkSRTERUe6dO7rjL0BmYoLwlckm2Wv7nflkFw_L1HG3YfODPak8pDp4iLo6V_zcxPRo*24__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUl!!MznTZTSvDXGV0Co!Amw3xom-SM3e3cfsWyoJb1tzyz6v_ttMAIJJAnoGProVnS0LgDu4QJfuSTSyUZHPs-in3lbx4Z6LeOXbhAEEj53cdAHd6Y_xqKS9fsU$>
>>
>>
>> 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 using 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/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$>
>>
>>
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> -- 
> Hervé Pagès
>
> Bioconductor Core Team
> hpages.on.github using gmail.com

-- 
Hervé Pagès

Bioconductor Core Team
hpages.on.github using gmail.com

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