[Bioc-devel] Unsure about why package is not updating
Dear Bioconductor, Thank you for all the help so far. Unfortunately, I have a few more issues. I updated the version of my package to 0.99.5, found here http://www.bioconductor.org/checkResults/3.12/bioc-LATEST/TimiRGeN/, but the new version is not being built, regardless of check successes or errors. When I did git clone g...@git.bioconductor.org:packages/TimiRGeN, version 0.99.5 was downloaded so I think the update was successful. However, I am getting a message "NO, built version is lower than internal version". The previous version was 0.99.4158, so I think the version bump should have worked. What is the issue here, and how can the version update be completed properly? Best, Krutik [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Issue with connecting to 'git.bioconductor.org' during git fetch --all
Hi Bioconductor, Wanted to clarify a small issue before continuing with a package update. I just added a new SSH key to biocredentials and my github account. It seems to have worked fine, but I got a warning when I tried to fetch. I have copied the output from git remove -v and git fetch --all below. Is there something else I need to do before continuing with merging the upstream and master braches? Best, Krutik $ git remote -v origin g...@github.com:Krutik6/TimiRGeN.git (fetch) origin g...@github.com:Krutik6/TimiRGeN.git (push) upsteam g...@git.bioconductor.org:packages/TimiRGeN.git (fetch) upsteam g...@git.bioconductor.org:packages/TimiRGeN.git (push) $ git fetch --all Fetching origin Warning: Permanently added the RSA host key for IP address '140.82.121.4' to the list of known hosts. Enter passphrase for key '/home/krutik/.ssh/id_rsa': Fetching upsteam The authenticity of host 'git.bioconductor.org (34.192.48.227)' can't be established. ECDSA key fingerprint is SHA256:nXILc5fVCnDfOID8HgPi+mSufGtr2JMYgnRa1JAQj/Q. Are you sure you want to continue connecting (yes/no)? yes Warning: Permanently added 'git.bioconductor.org,34.192.48.227' (ECDSA) to the list of known hosts. Enter passphrase for key '/home/krutik/.ssh/id_rsa': Connection to git.bioconductor.org closed by remote host. fatal: Could not read from remote repository. Please make sure you have the correct access rights and the repository exists. error: Could not fetch upsteam [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Few questions of maintaining a new bioconductor package
Hi Nitesh, Sorry for the late response. I have attempted what you suggested and several variations of the email address, and the same message returns. k.pat...@newcastle.ac.uk is not associated with a maintainer of a Bioconductor package. Please check the spelling or contact bioc-devel@r-project.org for help. Would it have been better if I had the email all lower case on submission? The package is still in the devel stage, could this be the issue? Best, Krutik From: Nitesh Turaga Sent: 24 September 2020 13:37 To: Krutik Patel (PGR) Cc: bioc-devel@r-project.org Subject: Re: [Bioc-devel] Few questions of maintaining a new bioconductor package Everything on our end seems to be fine. You have to first activate your account, and it might be case sensitive "k.pat...@newcastle.ac.uk<mailto:k.pat...@newcastle.ac.uk>” Try that. Nitesh On Sep 19, 2020, at 4:46 AM, Krutik Patel (PGR) mailto:k.pat...@newcastle.ac.uk>> wrote: Thank you for your advice Nitesh and Lori, To expand on my issue with the Bioconductor Git Credentials site, when I try to activate my account, I get this message. "k.pat...@newcastle.ac.uk<mailto:k.pat...@newcastle.ac.uk> is not associated with a maintainer of a Bioconductor package. Please check the spelling or contact bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> for help." The email used here is the one which is attached to the package. Best, Krutik From: Shepherd, Lori mailto:lori.sheph...@roswellpark.org>> Sent: 18 September 2020 15:29 To: Krutik Patel (PGR) mailto:k.pat...@newcastle.ac.uk>>; bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> mailto:bioc-devel@r-project.org>> Subject: Re: Few questions of maintaining a new bioconductor package ⚠ External sender. Take care when opening links or attachments. Do not provide your login details. In Addition to Nitesh's comments: Please do not push the version to 1.0.0 yourself. This will be done at the time of release by the core team. Continue to increment z of verion x.y.z. For example 0.99.5. For now, you have to wait for a nightly build to view the results of the build/check. http://bioconductor.org/checkResults/devel/bioc-LATEST/TimiRGeN/ Information on timing of build report and how long from push to viewing is summarized at the top of this page: http://bioconductor.org/developers/how-to/troubleshoot-build-report/ Remember new builds will only register with a valid version bump. You could always create a temporary directory and try checking the code out from git.bioconductor.org to see if the changes got successfully pushed to the server. Or check out the RSS feed Cheers, Lori Shepherd 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 Krutik Patel (PGR) Sent: Friday, September 18, 2020 5:01 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] Few questions of maintaining a new bioconductor package Dear Bioconductor team, I've recently had my package, TimiRGeN, accepted into bioconductor and have a few questions on the maintenance side of things. 1) I am ready to push a newer version of the package. Will I have to set the version to 1.0.0 now? Currently it is version 0.99.4158. 2) Once pushed, how can I check if the build has been successful? Will I have to wait and see if it has passed the nightly builds on build/checkResults? Or is there a faster method. 3) I would like to set up a new SSH key and use this to maintain my package. To do this I will need to activate my account on Bioconductor Git Credentials, but I do not remember setting up a password for this. Any help in these matters would be great. Best, Krutik [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://secure-web.cisco.com/1N9JTq9dmE62aCcK0jY2e9hma_u-zPCjcGL_mljxPLb0eDq7zD_2o_qjLUe1liO0r-RSxQlkQ8svE9VrU1TW03csGPOz06yAtgFBRBu2xsXKZJC1ZQxlVK5MLbzEp6BJ_QC6fzzuoPS_jr6Pd03IroGsRwAHWIBZjmkPR3HwAFETaIyKyjJ-s2WlDot3-nqLqYVDE6UMzKg8CiaSgovdQsVaeWsPisTtRpa21w1oMdz_51AVw4nMjnRB0z8LH_SfJxP9HBKccpDVLBSVc2A8h4HzwwwvEMY94vtuzw-sAnlP_XL8_wiEoXAaZGevK0VKb/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 mess
Re: [Bioc-devel] Few questions of maintaining a new bioconductor package
Thank you for your advice Nitesh and Lori, To expand on my issue with the Bioconductor Git Credentials site, when I try to activate my account, I get this message. "k.pat...@newcastle.ac.uk is not associated with a maintainer of a Bioconductor package. Please check the spelling or contact bioc-devel@r-project.org for help." The email used here is the one which is attached to the package. Best, Krutik From: Shepherd, Lori Sent: 18 September 2020 15:29 To: Krutik Patel (PGR) ; bioc-devel@r-project.org Subject: Re: Few questions of maintaining a new bioconductor package ⚠ External sender. Take care when opening links or attachments. Do not provide your login details. In Addition to Nitesh's comments: Please do not push the version to 1.0.0 yourself. This will be done at the time of release by the core team. Continue to increment z of verion x.y.z. For example 0.99.5. For now, you have to wait for a nightly build to view the results of the build/check. http://bioconductor.org/checkResults/devel/bioc-LATEST/TimiRGeN/ Information on timing of build report and how long from push to viewing is summarized at the top of this page: http://bioconductor.org/developers/how-to/troubleshoot-build-report/ Remember new builds will only register with a valid version bump. You could always create a temporary directory and try checking the code out from git.bioconductor.org to see if the changes got successfully pushed to the server. Or check out the RSS feed Cheers, Lori Shepherd 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 Krutik Patel (PGR) Sent: Friday, September 18, 2020 5:01 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] Few questions of maintaining a new bioconductor package Dear Bioconductor team, I've recently had my package, TimiRGeN, accepted into bioconductor and have a few questions on the maintenance side of things. 1) I am ready to push a newer version of the package. Will I have to set the version to 1.0.0 now? Currently it is version 0.99.4158. 2) Once pushed, how can I check if the build has been successful? Will I have to wait and see if it has passed the nightly builds on build/checkResults? Or is there a faster method. 3) I would like to set up a new SSH key and use this to maintain my package. To do this I will need to activate my account on Bioconductor Git Credentials, but I do not remember setting up a password for this. Any help in these matters would be great. Best, Krutik [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://secure-web.cisco.com/1N9JTq9dmE62aCcK0jY2e9hma_u-zPCjcGL_mljxPLb0eDq7zD_2o_qjLUe1liO0r-RSxQlkQ8svE9VrU1TW03csGPOz06yAtgFBRBu2xsXKZJC1ZQxlVK5MLbzEp6BJ_QC6fzzuoPS_jr6Pd03IroGsRwAHWIBZjmkPR3HwAFETaIyKyjJ-s2WlDot3-nqLqYVDE6UMzKg8CiaSgovdQsVaeWsPisTtRpa21w1oMdz_51AVw4nMjnRB0z8LH_SfJxP9HBKccpDVLBSVc2A8h4HzwwwvEMY94vtuzw-sAnlP_XL8_wiEoXAaZGevK0VKb/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. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Build report has not been received yet
Dear Bioconductor team, I made a valid push of my package (TimiRGeN, #1337) on Tuesday and have not yet received a build report, how should I proceed? Best Krutik [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Changing the name of your package while it has been submitted
Thank you for the instructions, will do so soon. Best Wishes, Krutik From: Shepherd, Lori Sent: 18 February 2020 14:28 To: Krutik Patel (PGR) ; bioc-devel@r-project.org Subject: Re: Changing the name of your package while it has been submitted Excellent - much easier process than trying to change the name of a package already in Bioconductor - Change the name of the issue Change the link for the repository in the first comment https://github.com/Bioconductor/Contributions/issues/1337#issue-549669447 Change the name in the DESCRIPTION of the package We will also have to change the github link in our database for the version bump to trigger a new build - so once you have done the above please comment in the issue you are ready for us to change the database and tag @lshep (also I would double check that the webhooks stayed initialized) Cheers, Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 ____ From: Krutik Patel (PGR) Sent: Tuesday, February 18, 2020 9:22 AM To: Shepherd, Lori ; bioc-devel@r-project.org Subject: Re: Changing the name of your package while it has been submitted Hi Lori, The name of my package is smiRk, issue #1337. The package is still in the review process. Best Krutik From: Shepherd, Lori Sent: 18 February 2020 13:00 To: Krutik Patel (PGR) ; bioc-devel@r-project.org Subject: Re: Changing the name of your package while it has been submitted A few clarification points: What is the name of your package? Has your package already been accepted into Bioconductor or is it still in the review process? Lori Shepherd 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 Krutik Patel (PGR) Sent: Monday, February 17, 2020 4:34 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] Changing the name of your package while it has been submitted Hello, I am planning to push some updates on my package, including a name change. My question is what is the cleanest way of changing the name of an already submitted package which is the process of review? Is it OK to just manually edit the name of the package on the issue page? Best, Krutik [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-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. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Changing the name of your package while it has been submitted
Hi Lori, The name of my package is smiRk, issue #1337. The package is still in the review process. Best Krutik From: Shepherd, Lori Sent: 18 February 2020 13:00 To: Krutik Patel (PGR) ; bioc-devel@r-project.org Subject: Re: Changing the name of your package while it has been submitted A few clarification points: What is the name of your package? Has your package already been accepted into Bioconductor or is it still in the review process? Lori Shepherd 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 Krutik Patel (PGR) Sent: Monday, February 17, 2020 4:34 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] Changing the name of your package while it has been submitted Hello, I am planning to push some updates on my package, including a name change. My question is what is the cleanest way of changing the name of an already submitted package which is the process of review? Is it OK to just manually edit the name of the package on the issue page? Best, Krutik [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-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. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Changing the name of your package while it has been submitted
Hello, I am planning to push some updates on my package, including a name change. My question is what is the cleanest way of changing the name of an already submitted package which is the process of review? Is it OK to just manually edit the name of the package on the issue page? Best, Krutik [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Use of SummerisedExperiments or MultiAssayExperiments of many many Dataframes/ nested List objects
Hello Bioc-Devel, This will be a long winded question and I apologise for that, I just want to be thorough. I recently submitted a package onto bioconductor for review, and received a response to have SummerisedExperiments or MultiAssayExperiments as the standard format for my package. I looked into the usage of SE/ MAE and do think they are very useful. I just find it difficult to envision the usage of these objects in my package. Namely, because I do not use sequencing data and so I do not have any phenoData. The input to my package is deferentially expressed data from microRNA and mRNA data, and I feel like that should stay as data frames to make it easier for users to use. From these data frames, many other data frames and nested lists are created. I will give a short demonstration of how my package functions below and I would appreciate it if any user could demonstrate to me how to incorporate SE's or MAE's. # This will load test data > miR <- mm_miR > mRNA <- mm_mRNA # Visualise the data > head(miR [1:5, 1:5]) D1.Log2FC D1.adjPValD2.Log2FC D2.adjPVal D3.Log2FC mmu-let-7b-3p -0.008006934 0.97706031 -0.008296431 0.9503666129 -0.1153951 mmu-let-7c-5p 0.299802302 0.30094186 0.511083040 0.0489321072 0.4663393 mmu-let-7d-3p 0.430125310 0.06476131 0.483677350 0.0228474958 0.4301441 mmu-let-7e-3p 0.417901606 0.06543412 0.448677130 0.0301945611 0.3051121 mmu-let-7e-5p 0.637167321 0.01010895 0.984529549 0.0001462246 0.8917273 > head(mRNA [1:5, 1:5]) D1.Log2FC D1.adjPVal D2.Log2FC D2.adjPVal D3.Log2FC A2m 1.336002 0.4627700063 4.0470385 0.0114355180 3.688919 AA986860 -1.886142 0.0239685308 -0.8686382 0.2892313624 -1.115943 Aadac-2.493883 0.0022213531 -2.1678098 0.0051038251 -1.338884 Aadat-3.647727 0.0006583596 -3.3660043 0.0011145806 -2.616356 Aass -1.283668 0.0101430103 -1.9567394 0.0004421697 -1.315752 # As you can see creating this type of data for a user would be quite simple if it is kept as data frames # We use the following functions to retrieve annotation IDs # They will produce several data frames each > getIDs_miR_mouse(miR) > head(miR_ensembl) GENENAME ID 1 mmu-let-7b-3p 2 mmu-let-7c-5p 3 mmu-let-7d-3p 4 mmu-let-7e-3p 5 mmu-let-7e-5p 6 mmu-let-7f-1-3p > head(miR_entrez) GENENAME ID 1 mmu-let-7b-3p 2 mmu-let-7c-5p 3 mmu-let-7d-3p 4 mmu-let-7e-3p 5 mmu-let-7e-5p 6 mmu-let-7f-1-3p > getIDs_miR_mouse(mRNA) GENENAME ID 1 A2m ENSMUSG0030111 2 AA986860 ENSMUSG0042510 3Aadac ENSMUSG0027761 4Aadat ENSMUSG0057228 5 Aass ENSMUSG0029695 6 Abat ENSMUSG0057880 GENENAME ID 1 A2m 232345 2 AA986860 212439 3Aadac 67758 4Aadat 23923 5 Aass 30956 6 Abat 268860 # The following function will combine the two data frames into a new one genetic_data <- CombineGenes(miR_data = miR, mRNA_data = mRNA) # This function will alter the new data frame into a nested list separated by a common string genelist <- GenesList(method = "c", genetic_data = genetic_data, timeString = "D") > as.data.frame(lapply(genelist, function(x) dim(x))) D1 D2 D3 D7 D14 1 2278 2278 2278 2278 2278 222222 # Then we can filter out "non-significant" values > as.data.frame(lapply(filtered_genelist, function(x) dim(x))) D1 D2 D3 D7 D14 1 1108 1389 1037 1196 380 22222 2 I could go on but I think the point is clear. This package is full of data frames and nested lists and it would be nice to use SE or MAE to tidy up the global environment. Is there a way of turning many many data frames/ nested lists into an SE or MEA object? If there is please do let me know, I am not sure how to do this, and I feel as though it would be a necessary process to (at least) explore if I want my package on bioconductor. Many Thanks, Krutik. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Question about github repo
Hi Bioconductor dev team, I am ready to submit my first package to bioconductor. It is currently on a private github and I wish to start the process of submission. Do I need to make my github repo public prior to sending it to the bioconductor contributions github repo. I understand that the code and concept of my project needs to be made public, but I have just had some worries about individuals potentially scooping my work while it is made public. This package is part of my PhD so I am perhaps a bit paranoid about this. Apologies if this was a bit of a silly question. Hope to hear back soon. Kind Regards, Krutik Patel [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
