Did you 'git commit' the changes to the branch? Get Outlook for iOS<https://aka.ms/o0ukef> ________________________________ From: Xiaowen Chen <xiaowen.c...@jax.org> Sent: Wednesday, December 23, 2020 2:56:01 PM To: Kern, Lori <lori.sheph...@roswellpark.org> Cc: bioc-devel@r-project.org <bioc-devel@r-project.org> Subject: Re: [EXTERNAL]epihet problems reported in the Multiple platform build/check report for BioC 3.12
Hi Kern, I am sorry. I ran the following command, I also show the output of the corresponding commands. However the release branch still is not updated. Could you help me? Thank you. Best, Xiaowen 1.go to https://github.com/TheJacksonLaboratory/epihet/blob/master/DESCRIPTION update version 1.7.1 of DESCRIPTION FILE to 1.6.1 2.(base) [chenx@helix ~]$ git clone https://github.com/TheJacksonLaboratory/epihet.git<https://secure-web.cisco.com/10MdtT2vtU5z5f6CdVlC7mUvYXYpLKtzYPugTqMgU9x_pQJeHAMy6b5aKZ0bJko-d--Tqm5c-uyiepw4-o6NxQ8d6Opn7MWIl4QHE2iiZuyHZ1kKGNqh3uMyS0ekkQHf19hOm87R7C077XBSjlBGr05qkqKY99p4IXQyCn1Hz0D3bNr1eG97oTB1qDwVJOW-e3vQuC5lW7fHQ5krFVSeyE3PNA_tHhMJmIfY-kvBq56_2ukpEx3vYWe4O_UrAyLtrl9fakMFvyP8bqj3_10vEL-JnCaMP4GxMNfSxZWoCeFeK_IdqHfIiqtt1QbsQ-hJU/https%3A%2F%2Fgithub.com%2FTheJacksonLaboratory%2Fepihet.git> Initialized empty Git repository in /home/c-chenx/epihet/.git/ remote: Enumerating objects: 35, done. remote: Counting objects: 100% (35/35), done. remote: Compressing objects: 100% (32/32), done. remote: Total 874 (delta 16), reused 5 (delta 2), pack-reused 839 Receiving objects: 100% (874/874), 4.61 MiB, done. Resolving deltas: 100% (465/465), done. 3. (base) [chenx@helix ~]$ cd epihet 4. (base) [chenx@helix epihet]$ git remote add upstream g...@git.bioconductor.org:packages/epihet.git (base) [chenx@helix epihet]$ git remote -v origin https://github.com/TheJacksonLaboratory/epihet.git (fetch) origin https://github.com/TheJacksonLaboratory/epihet.git (push) upstream g...@git.bioconductor.org:packages/epihet.git (fetch) upstream g...@git.bioconductor.org:packages/epihet.git (push) 5.(base) [chenx@helix epihet]$ git fetch --all Fetching origin Fetching upstream Enter passphrase for key '/home/c-chenx/.ssh/id_rsa': From git.bioconductor.org:packages/epihet * [new branch] RELEASE_3_10 -> upstream/RELEASE_3_10 * [new branch] RELEASE_3_11 -> upstream/RELEASE_3_11 * [new branch] RELEASE_3_12 -> upstream/RELEASE_3_12 * [new branch] RELEASE_3_9 -> upstream/RELEASE_3_9 * [new branch] master -> upstream/master 6.(base) [chenx@helix epihet]$ git checkout RELEASE_3_12 error: pathspec 'RELEASE_3_12' did not match any file(s) known to git. 7. (base) [chenx@helix epihet]$ git checkout -b RELEASE_3_12 upstream/RELEASE_3_12 Branch RELEASE_3_12 set up to track remote branch RELEASE_3_12 from upstream. Switched to a new branch 'RELEASE_3_12' 8. (base) [chenx@helix epihet]$ git checkout RELEASE_3_12 Already on 'RELEASE_3_12' 9.(base) [chenx@helix epihet]$ git merge upstream/RELEASE_3_12 Already up-to-date. (base) [chenx@helix epihet]$ git merge origin/RELEASE_3_12 Already up-to-date. (base) [chenx@helix epihet]$ git push upstream RELEASE_3_12 Enter passphrase for key '/home/c-chenx/.ssh/id_rsa': Everything up-to-date (base) [chenx@helix epihet]$ git push origin RELEASE_3_12 Everything up-to-date From: "Kern, Lori" <lori.sheph...@roswellpark.org> Date: Friday, December 18, 2020 at 3:24 PM To: Xiaowen Chen <xiaowen.c...@jax.org> Subject: Re: [EXTERNAL]epihet problems reported in the Multiple platform build/check report for BioC 3.12 If you are on the RELEASE_3_12 branch and made changes, you will need to update the version number regardless. The numbering schema in release and devel are different. of version x.y.z the y is even in release and odd in devel... you could try while you are on the release branch to bump the version to 1.6.1 and push that up. but again, I do not see any code changes on the RELEASE_3_12 branch so you would need to make sure those changes are also there before pushing up. Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 ________________________________ From: Xiaowen Chen <xiaowen.c...@jax.org> Sent: Friday, December 18, 2020 3:19 PM To: Kern, Lori <lori.sheph...@roswellpark.org> Subject: Re: [EXTERNAL]epihet problems reported in the Multiple platform build/check report for BioC 3.12 I totally understand what you are talking about. I need to push the latest code to release branch3_12. but I ran the following command line several days. git clone https://github.com/TheJacksonLaboratory/epihet.git cd epihet git remote add upstream g...@git.bioconductor.org:packages/epihet.git git remote -v git fetch �all git checkout master git merge origin/master git merge upstream/master git push upstream master git push origin master git checkout RELEASE_3_12 git merge upstream/RELEASE_3_12 git merge origin/RELEASE_3_12 git push upstream RELEASE_3_12 git push origin RELEASE_3_12 And everything looked fine. No error. But RELEASE_3_12 branch still is not updated. From: "Kern, Lori" <lori.sheph...@roswellpark.org> Date: Friday, December 18, 2020 at 3:15 PM To: Xiaowen Chen <xiaowen.c...@jax.org>, "bioc-devel@r-project.org" <bioc-devel@r-project.org> Subject: Re: [EXTERNAL]epihet problems reported in the Multiple platform build/check report for BioC 3.12 That is the code on the devel branch. You need to make the same code changes you did on devel to fix the ERROR on the RELEASE_3_12 branch. It does not get carried over across branches. Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 ________________________________ From: Xiaowen Chen <xiaowen.c...@jax.org> Sent: Friday, December 18, 2020 3:13 PM To: Kern, Lori <lori.sheph...@roswellpark.org> Subject: Re: [EXTERNAL]epihet problems reported in the Multiple platform build/check report for BioC 3.12 Yes, I pretty sure I changed it. See http://bioconductor.org/checkResults/devel/bioc-LATEST/epihet/<http://secure-web.cisco.com/1ss2p3h9ANyNT9W8y-gVvJ1KbvbgAU6VoEbg03GV6jHmEl4erXbnsDaG-ROfqsyQGMzad9KFhNgmVA_ivTR1W03ngAunrGPvRx24iE6IlZUvaTJCabDEqPOjoejdyK7lYLqmU27lqVi60M4TeOZK4kTLkq_wrawtGkv35wwbEGtpqPi1PQomhuSdJ9sYfJqiZ6E-iE05qOZu7VPtMKOhzwZvPeNaABthKkMYfR_7TIwj_C9n3Of2u_3LmP_o0xWSWjcHAdq2c8tvCUzLZ3AbfpG5Vavxl7t4U3I8kcSYYZJDk_28xQLE1HOoSnU-wkMx9/http%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2Fepihet%2F> Everything is ok. No error. Should I change version from 1.7.1 to 1.7.2 before pushing RELEASE_3_12? From: "Kern, Lori" <lori.sheph...@roswellpark.org> Date: Friday, December 18, 2020 at 3:10 PM To: Xiaowen Chen <xiaowen.c...@jax.org> Subject: Re: [EXTERNAL]epihet problems reported in the Multiple platform build/check report for BioC 3.12 I don't see any changes pushed to the release 12 branch. You did remember to make the code changes and commit before pushing? git checkout RELEASE_3_12 git merge upstream/RELEASE_3_12 git merge origin/RELEASE_3_12 # # Make code changes # Make version bump in DESCRIPTION # git commit # git push upstream RELEASE_3_12 git push origin RELEASE_3_12 Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 ________________________________ From: Xiaowen Chen <xiaowen.c...@jax.org> Sent: Friday, December 18, 2020 3:07 PM To: Kern, Lori <lori.sheph...@roswellpark.org> Subject: Re: [EXTERNAL]epihet problems reported in the Multiple platform build/check report for BioC 3.12 Yes, I changed to RELEASE_3_12. From: "Kern, Lori" <lori.sheph...@roswellpark.org> Date: Friday, December 18, 2020 at 3:05 PM To: Xiaowen Chen <xiaowen.c...@jax.org>, "bioc-devel@r-project.org" <bioc-devel@r-project.org> Subject: Re: [EXTERNAL]epihet problems reported in the Multiple platform build/check report for BioC 3.12 The current Bioconductor release is 3.12 so you changed the commands below to reflect 3_12? (i.e git checkout RELEASE_3_12 ) 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-boun...@r-project.org> on behalf of Xiaowen Chen <xiaowen.c...@jax.org> Sent: Friday, December 18, 2020 1:30 PM To: bioc-devel@r-project.org <bioc-devel@r-project.org> Subject: [Bioc-devel] FW: [EXTERNAL]epihet problems reported in the Multiple platform build/check report for BioC 3.12 Hi , I have follow the website http://secure-web.cisco.com/1ki-xUKhxTFvXD89R9PKgLZ7QzTWrJmmqO4-C2dcwSY6S49z9pnD4Uwb-IwLQbPQwqTXgzORisNeH2wSNY2LGbVsu6Axv1BGH6AFGEgbF0RjwLdoVd8_1EWbXbGSoFT8nzhz8y9QLN3NmeV8g1C37v3rXOnIn0PaxcvwSRWlw_I6lrx6I1qNqBsuxUqrEbv2wpn0P1b5zwzLFvKglQ0-Ay0F-L2Iv-pjGVy94y0VFe2YY862AIjuNwQqALODdPILpFNstWCEVWe32N2i8DbTGyzHZEUwimKkmMI18LIIZy8NKviBBdNJ7NPr5Xm9H37-Sd28eqzkh0_BNFquKNP1M9Q/http%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2Fsync-existing-repositories%2F To push the latest epihet version to release branch. Why I still to receive the email to complain there are error, seem I did not push successfully. What should I do, I did not see some error when I run the following commands git checkout RELEASE_3_6 git merge upstream/RELEASE_3_6 git merge origin/RELEASE_3_6 git push upstream RELEASE_3_6 git push origin RELEASE_3_6 Best, Xiaowen On 12/18/20, 1:00 PM, "bbs-nore...@bioconductor.org" <bbs-nore...@bioconductor.org> wrote: [This is an automatically generated email. Please don't reply.] Hi epihet maintainer, According to the Multiple platform build/check report for BioC 3.12, the epihet package has the following problem(s): o ERROR for 'R CMD build' on malbec1. See the details here: https://secure-web.cisco.com/1N16ddKrue9rDFh3tuFZy4oYqtH_lPGE1wFJSNmYq9CGAPOvjzxWr2oNJaeWVDpF1cXtgBetx3wy-j7xKSfCPiZ5s7aBmpsg3HnS5ZBVNbUFEmX1N_NOw41wLgrar1BDgzhYbz3aUjR-iQfBsr3o44hHi3aFi2TqrnSD7QvBX9oU9X71vskBLNE0qLn4zb7F2m0QRZNn3FfzwrDFx2HPgmEFmCn20nhjLeNHNqVQpcDEZFWE7ksGBgwz01pay9miJogls3v_CQGMK3uxJcocmNUdAGHsGpnHk_2At5DutG5Gk4_-zdU96cwayYzY_XETE4uWmv7diTM5fPpKZds1qjQ/https%3A%2F%2Fmaster.bioconductor.org%2FcheckResults%2F3.12%2Fbioc-LATEST%2Fepihet%2Fmalbec1-buildsrc.html Please take the time to address this by committing and pushing changes to your package at git.bioconductor.org Notes: * This was the status of your package at the time this email was sent to you. Given that the online report is updated daily (in normal conditions) you could see something different when you visit the URL(s) above, especially if you do so several days after you received this email. * It is possible that the problems reported in this report are false positives, either because another package (from CRAN or Bioconductor) breaks your package (if yours depends on it) or because of a Build System problem. If this is the case, then you can ignore this email. * Please check the report again 24h after you've committed your changes to the package and make sure that all the problems have gone. * If you have questions about this report or need help with the maintenance of your package, please use the Bioc-devel mailing list: https://secure-web.cisco.com/1ITLuhkhrpzci7u6plVZo9TFrWiJ1MzVOUBx9WqUhPA6zBFCNM8wR1nufug4eu7ECact05ykq9LbqEpwGsHwO6i6JbM8EYGJmNsf6LrU3fNXjpTqDo6LGmKEKr3CghS33pM4UhYs3DtKYFBti9uDh_HGFiXpTSMKmryQICoTNOfo0XbcflYm__s9fN5az2G0OMRhn_Ls2sfm4Kh7mbrWzeYIfzJD4RW_ex11NcNlkHVP1qaN3p1Sovr_nUG6omdf8BM2ecKDssPDgBd4iegjICmKOUm9cjR3a50KDaq387W8uL3abQ8GfuvytrbK9IE7BjSnTfu-G0rmZyH1uqie6eQ/https%3A%2F%2Fbioconductor.org%2Fhelp%2Fmailing-list%2F (all package maintainers are requested to subscribe to this list) For immediate notification of package build status, please subscribe to your package's RSS feed. Information is at: https://secure-web.cisco.com/19Itd5tGpkn-yobGMTU4mGRnADAyZ-PWgfh5rTjihtFeUwU-nLbCRiS7JwKbz2aMTulz5mEjGzSEKgRKW0v9XYXjtuJoUNk4o_njhw8qiJJ9eRSbEXdgqcQowrlWiO9hHSDspdEUYhcLexQsM7WsvLgBQ-qB_6lfUEoQFHwsUpM7cjDOeON9Fb_uhUYe8Plwtr4WiOkvJ1-BFQC5FkwlDlLeqQMOlXxU8dHYkO02fMaLFR05gweEAQuJf876do0NJf-phYFUgw_E23xoq3hDxRGthtNpCMLE9bpdQPApIp3LwMBdPMHQcM05cGu5W4RTrgbzLHBbPk4GBQJOsivD6Fg/https%3A%2F%2Fbioconductor.org%2Fdevelopers%2Frss-feeds%2F Thanks for contributing to the Bioconductor project! --- The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible. _______________________________________________ Bioc-devel@r-project.org mailing list https://secure-web.cisco.com/1xTRQNRNDqgmcgJeydPO78TXe2ONAA3Dgu7eRgMsb_k1x8OPAuoNR_UE3k2PeDxujYa2B6Hs-AOyuOgaL5wZrslJ0yjvzkT3zgckaJht9c5En4Qcv-7mnF1aXdwrx6LaAFTqeqOcRB5pEEQ1uM9jGiYORN8IzHQuT9iEO-x18-YcMzeq30ooI2onLQ2zEg41hkRf74VYUasdv2a5yKLGnUXmBmFBzAMAJ0hHPpMpUlUDcaKIwDGxRb8yKbZPlLuebdU8YvdGzTUp1dyDd0J7MHWaY2NYIdiSq7dgcjCuLxdm-eQ5f-wMbmtS-A9kxAlUT473F7AWu4wo3sLN9I3U-oA/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. --- The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible. 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. --- The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible. 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. --- The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible. 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. --- The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible. 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. [[alternative HTML version deleted]]
_______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
