[Bioc-devel] How to change the name of a package on Bioconductor

Wed Feb 24 15:18:58 CET 2021

This should be taken care of. The page now displays :
bioconductor.org/packages/devel/bioc/html/VaSP.html

The badges at the top of the page should fill in, in the next day or so.

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 <bioc-devel-bounces using r-project.org> on behalf of Yu Huihui <yuhuihui2011 using foxmail.com>
Sent: Monday, February 22, 2021 10:05 AM
To: Martin Morgan <mtmorgan.bioc using gmail.com>
Cc: bioc-devel <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] How to change the name of a package on Bioconductor

Hello,

The build is still failed and the url https://secure-web.cisco.com/1S4bmGsPw12M8thFYS-sMO512HXmteKbsvB2c6_z7pcyoXiy972BnmQn4dstgWWf3znvfbJ63k0NIjQr1AB4w1x1qytt6nwNiJMuwjGfKerc-VOwX4FJOZDxg4bwsdezctF6NPe90tPjCoKdU7ipCAadGNi4Qf57AwFCKM0hI6sAZVA8B0zrfnUe0A1kWCgvbtBd1xAhlkiVAQJFtpad0hwXnHucbsAfq2gwdRHgKH0X1J8R5Qvr19TWQGcxR-WMlWpegKsE6lYb1RK7Du3BqYzYHVzH75MQPgJgHQUTwgkAKT_AY3c6cexPDGHOZ1KRs/https%3A%2F%2Fbioconductor.org%2Fpackages%2FVaSP still points to "removed packages". I could successfully build it on my own computer. Would you please check what's the problem?

Thanks,
Huihui

------------------ Original ------------------
From:                                                                                                                        "Yu Huihui"                                                                                    <yuhuihui2011 using foxmail.com>;
Date: Thu, Feb 18, 2021 07:02 AM
To: "Martin Morgan"<mtmorgan.bioc using gmail.com>;"nturaga.bioc"<nturaga.bioc using gmail.com>;
Cc: "bioc-devel"<bioc-devel using r-project.org>;"Chi&nbsp;Zhang"<zhang.chi97 using gmail.com>;
Subject: Re: [Bioc-devel] How to change the name of a package on Bioconductor

Thank you, Martin,

I have renamed 'vasp' to "VaSP" in release and devel branches. I will wait for the build result. If it success, I will keep the name "VaSP" and just maintain "VaSP".

Huihui

------------------ Original ------------------
From:                                                                                                                        "Martin Morgan"                                                                                    <mtmorgan.bioc using gmail.com>;
Date: Thu, Feb 18, 2021 06:40 AM
To: "Yu Huihui"<yuhuihui2011 using foxmail.com>;"nturaga.bioc"<nturaga.bioc using gmail.com>;
Cc: "bioc-devel"<bioc-devel using r-project.org>;
Subject: Re: [Bioc-devel] How to change the name of a package on Bioconductor

Your package will build under the new name. When it builds successfully, the url https://secure-web.cisco.com/1S4bmGsPw12M8thFYS-sMO512HXmteKbsvB2c6_z7pcyoXiy972BnmQn4dstgWWf3znvfbJ63k0NIjQr1AB4w1x1qytt6nwNiJMuwjGfKerc-VOwX4FJOZDxg4bwsdezctF6NPe90tPjCoKdU7ipCAadGNi4Qf57AwFCKM0hI6sAZVA8B0zrfnUe0A1kWCgvbtBd1xAhlkiVAQJFtpad0hwXnHucbsAfq2gwdRHgKH0X1J8R5Qvr19TWQGcxR-WMlWpegKsE6lYb1RK7Du3BqYzYHVzH75MQPgJgHQUTwgkAKT_AY3c6cexPDGHOZ1KRs/https%3A%2F%2Fbioconductor.org%2Fpackages%2FVaSP will point to the new landing page. The user will install it with `BiocManager::install("VaSP")`. The user will use the package with `library("VaSP")`.

The old version of your package, with the original name, will remain available at https://secure-web.cisco.com/10ofYP_VeIS5JlZxufUf0ym00MQ6dXdY63R4iMmsITwTWujSpqAbT_fue5sq8WwBrSPYSsGuZf9FdketEps8mGk9ab9zbL1wWMvCJ-Y50UJsqtElgU5swTiigWDBXmyn3YX2VMWoKUkow6g-6D5zwsG_VqBL61V-RxpomfR0o-WNBCJf8yT_7JfwqZUwP_YoXLdPZzP-6mvCniXQcmDco_70umCQLha7nZ0A6CEKeEZUtjIMgYNRDfOx51f93bLLmqCSAnHjJCvlSHOqq4T2rJO2RdZ3qOB18WVFFCRi-8ZGH8MpzO0aw2dlXsrSmOy0e/https%3A%2F%2Fbioconductor.org%2Fpackages%2F3.11%2Fvasp.

Note that your users who have already installed your package may experience problems, e.g., on some operating systems that respect differences in directory case, library(vasp) and library(VaSP) will return different versions of the package. On operating systems with file systems that do not differentiate between case their previous installation of vasp will be replaced by VaSP, and library(vasp) will no longer work. This problem will only persist for existing users of Bioconductor version 3.12.

Issues like this make renaming packages very tedious. A more formal approach would have deprecated 'vasp' over two release cycles (introduce deprecation in devel, wait for next release, remove from devel, leading to final removal two releases from now) and at the same time introduce a new package into devel. But the new package could not have been named 'VaSP', for the file naming reasons mentioned. So you would have had to rename your package something else, SuperVaSP, but then you would not have addressed your concern, that you had published your package under the name VaSP rather than vasp.

I chose to simply replace 'vasp' with 'VaSP', in both the release and devel branches, rather than force you though these hoops.

We will not create and maintain a special redirect for your package.

Martin

From: Yu Huihui <yuhuihui2011 using foxmail.com>
Date: Wednesday, February 17, 2021 at 4:59 PM
To: "mtmorgan.bioc" <mtmorgan.bioc using gmail.com>, "nturaga.bioc" <nturaga.bioc using gmail.com>
Cc: bioc-devel <bioc-devel using r-project.org>
Subject: Re:[Bioc-devel] How to change the name of a package on Bioconductor

Hello,

I am just following my last email. I find it is a bad way to change package name. An alternative way is to let the link jump to the package webpage, that is both http://secure-web.cisco.com/1Rv22BJg79QrNIb2Rw_Lk8Oxacx5KWAgiJtWR0nGpxwH-u2NTOhnQtLJd8pE-FpAQDssjuUBOH9MFxB7BXKjE5UkKjCcV4Pob1QCd8KNtPCG76XetYC_J2gsGNTHzj8f1fFJxCOZlUVPVQ1SJ08IcygDdNOonzQqoeKlqYAUFyr7tokbalX7Qfy4r3FMR15Zfs3hdp5VMlP6LqgdvuhY3yWwx-f2XrzRMnBfkgRv2c5DDEEtQZmLwhqfdD9qCsCnPBIMQ2atr84iNJZXyZ3K3u3j548keGUgb_BmQBy2BmFc3Z7b4k1hewLmdignSvr_p/http%3A%2F%2Fbioconductor.org%2Fpackages%2Fvasp and http://secure-web.cisco.com/1UykM7No5ekwsHM_YsFG9C9PpmlhRpqjvLFFLX9UXJhrgigjW568TgjzbmAvAqj9uN4Tdng4J_uLJ4NgPPvA5hXfvuXjUAQn8h_M0MFHHifRaF4iF5qrpjxwBSTvPjWur4maxSn-Nhs5qtd1Hh2NuXHhXcP3Jf0PZke4HKOKSJ3X28ARtaXAkNZAdDmfC3q6Euc-LH-QdaQ5jpagRtbptMqe7540aiOzpUV0uhm1kNh_wPZdiRHKZpTHe6ixsRwPXu8J0ENdFoZkQG_wUYqQOaQ73Bq-lfgCas3_kfg5BKBTtNaPEgjtAHipge3c_byJZ/http%3A%2F%2Fbioconductor.org%2Fpackages%2FVaSP can jump to http://secure-web.cisco.com/1w8V-mWUnTdcvfygc4qSymzVCvubGT6_8kWraNr37En8NFrAgQwVTOvxaaSAUtO6Pbrp-O6n6xLtOf_9e-smtsCoRPhvZYzt7dTK27kFDZ4s4NByAvMPi2PEZrqcYawEZri7_g_nHtiz_V4LfL5lldtQxeZJpQl9UgHQKB7MIiOWPSeNg_KXslWvSHm97YzcQ3BtN2xmlSUp2s2JxYRpMRR4CsctV_44jYB0XsHrCqQrAjprUbkstwxrRdvS1SsH1KHiZPeeRPTE3042lILZxdGOAQagswZmN4p5qaTo5poWxSzsYHycG5Jx0HmQRZDM6/http%3A%2F%2Fbioconductor.org%2Fpackages%2Frelease%2Fbioc%2Fhtml%2Fvasp.html. Is that possible? Currently the link http://secure-web.cisco.com/1UykM7No5ekwsHM_YsFG9C9PpmlhRpqjvLFFLX9UXJhrgigjW568TgjzbmAvAqj9uN4Tdng4J_uLJ4NgPPvA5hXfvuXjUAQn8h_M0MFHHifRaF4iF5qrpjxwBSTvPjWur4maxSn-Nhs5qtd1Hh2NuXHhXcP3Jf0PZke4HKOKSJ3X28ARtaXAkNZAdDmfC3q6Euc-LH-QdaQ5jpagRtbptMqe7540aiOzpUV0uhm1kNh_wPZdiRHKZpTHe6ixsRwPXu8J0ENdFoZkQG_wUYqQOaQ73Bq-lfgCas3_kfg5BKBTtNaPEgjtAHipge3c_byJZ/http%3A%2F%2Fbioconductor.org%2Fpackages%2FVaSP will jump to http://secure-web.cisco.com/1KJ_ArH7QFzVmMZG0LF7XS0767uEZTBNfiEX7WdTCNWImqkpnlqDNnxMqBYOZLk8M1LJcdHNG9UO0xaENk6bmu6deRrY-Gq0tFrxBqBGX67ElWcPiqLJhEqO_wpFTjN9GkQlvqqVh2BhFdLJt9xrpSOH4uf_G7ZqHHXilbNso4Q3XokbvNk4AaJw_WeVimQvF71amw7sMcCaYKLto2wrJtSrODu9pImu1qsS6WaAXAy6UIn3j_e_0cFrMVp8UHFN_s49UPiAgRv_yBY2_KldmWqqxbzmGf8WoKrGfZBHjX7c8T-n0tPCI0fB1I7qDIcgr/http%3A%2F%2Fbioconductor.org%2Fabout%2Fremoved-packages%2F.%26nbsp; Please give me your suggestions.

Thanks,
Huihui

------------------ Original ------------------
From: "Yu Huihui" <yuhuihui2011 using foxmail.com>;
Date: Wed, Feb 17, 2021 11:55 AM
To: "mtmorgan.bioc"<mtmorgan.bioc using gmail.com>;
Cc: "bioc-devel"<bioc-devel using r-project.org>;
Subject: [Bioc-devel] How to change the name of a package on Bioconductor

Hello,

I have released a package vasp to&nbsp;Bioconductor (http://secure-web.cisco.com/1Rv22BJg79QrNIb2Rw_Lk8Oxacx5KWAgiJtWR0nGpxwH-u2NTOhnQtLJd8pE-FpAQDssjuUBOH9MFxB7BXKjE5UkKjCcV4Pob1QCd8KNtPCG76XetYC_J2gsGNTHzj8f1fFJxCOZlUVPVQ1SJ08IcygDdNOonzQqoeKlqYAUFyr7tokbalX7Qfy4r3FMR15Zfs3hdp5VMlP6LqgdvuhY3yWwx-f2XrzRMnBfkgRv2c5DDEEtQZmLwhqfdD9qCsCnPBIMQ2atr84iNJZXyZ3K3u3j548keGUgb_BmQBy2BmFc3Z7b4k1hewLmdignSvr_p/http%3A%2F%2Fbioconductor.org%2Fpackages%2Fvasp). Recently I had a manuscript about this package published&nbsp;on New Physiologist (https://secure-web.cisco.com/16CQtWuweknWDAtIfu9BdZzRJYn9i_C9IBlSJYCM5oSQ2VGbMKiux8cfnBKJDnad-wV0rOG6lpGo_njjwzUc0b8a73ykwCAL0IHR6K0TB2TamX7sbN_kLD7K__8nL0MruOjeBr2X_gnBBshCRvHBAJqNzwJ5busgaK86_OVzYM8S8wiZI60AaqvvIDGVbi_KnyuCYqWxOCiYfPUkH0cnaucAiTfqhFlYhrIBwzzyKR2CpGuhjI47RWq5_A9U7V5T3Fwemt3G9ZeywdxljIHaNiH0_-Kvo6M0imU302O8oyAA-7KmerWPj4MAWCGl7Hc7h/https%3A%2F%2Fnph.onlinelibrary.wiley.com%2Fdoi%2F10.1111%2Fnph.17189). However, on the manuscript, the link to the package is http://secure-web.cisco.com/1UykM7No5ekwsHM_YsFG9C9PpmlhRpqjvLFFLX9UXJhrgigjW568TgjzbmAvAqj9uN4Tdng4J_uLJ4NgPPvA5hXfvuXjUAQn8h_M0MFHHifRaF4iF5qrpjxwBSTvPjWur4maxSn-Nhs5qtd1Hh2NuXHhXcP3Jf0PZke4HKOKSJ3X28ARtaXAkNZAdDmfC3q6Euc-LH-QdaQ5jpagRtbptMqe7540aiOzpUV0uhm1kNh_wPZdiRHKZpTHe6ixsRwPXu8J0ENdFoZkQG_wUYqQOaQ73Bq-lfgCas3_kfg5BKBTtNaPEgjtAHipge3c_byJZ/http%3A%2F%2Fbioconductor.org%2Fpackages%2FVaSP. I want to change the name of the package to VaSP from vasp.&nbsp; I changed the package name and updated it in&nbsp;git.bioconductor.org, but the build failed and it said "ERROR&nbsp; (Bad DESCRIPTION file)".&nbsp;

Can I change the name of a package existing on Bioconductor? How can I do that?

Thanks,
Huihui
[[alternative HTML version deleted]]

_______________________________________________
Bioc-devel using r-project.org mailing list
https://secure-web.cisco.com/1LQHbDBxKggfgUq3rTjQeKWIAralkCW2l1AGnf-wRxbH8WAjOnqIGpMH-Al1tw0n1o9Y8zY_GlK43XTmeIQpDL3wV2RMabjjjWw7O6xb6RbYvoDJXzx_KrdicN4XZLppdTllCGpf1LfhM3Rj1XeJ1zc-4dyiAAVk956D-iQaxBt6V8rPhGEQ2y7v20bOcmvZgtUuFKfvXbQ0iKV_TOWcf3O5R_Mi7QcD68fe7zhWmtAErUp-w-mvmhQ_ctgBdHbrahepQ66XJbO4GlGtc2B-7KtKiZk7tBDytA6SY-6l0S0ETTgpakLEZm8K1Vyoxnall/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel
        [[alternative HTML version deleted]]

_______________________________________________
Bioc-devel using r-project.org mailing list
https://secure-web.cisco.com/1LQHbDBxKggfgUq3rTjQeKWIAralkCW2l1AGnf-wRxbH8WAjOnqIGpMH-Al1tw0n1o9Y8zY_GlK43XTmeIQpDL3wV2RMabjjjWw7O6xb6RbYvoDJXzx_KrdicN4XZLppdTllCGpf1LfhM3Rj1XeJ1zc-4dyiAAVk956D-iQaxBt6V8rPhGEQ2y7v20bOcmvZgtUuFKfvXbQ0iKV_TOWcf3O5R_Mi7QcD68fe7zhWmtAErUp-w-mvmhQ_ctgBdHbrahepQ66XJbO4GlGtc2B-7KtKiZk7tBDytA6SY-6l0S0ETTgpakLEZm8K1Vyoxnall/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]]