[Bioc-devel] Request for undeprecation of motifbreakR
Dear bioc-devel,
I am sorry for not being responsive to the error messages related to the
building of motifbreakR.
As you can likely see, I was responsive to errors earlier in the year, entering
many changes to keep up to date with the changing conditions of the Bioc
universe, and bugs that I discovered (with the help of users on my github
issues).
Earlier in the year, perhaps as a result of altering my email notifications and
organization as a result of going on paternity leave, I somehow lost track of a
recurrent error introduced as a response to my most recent change to
motifbreakR, despite your repeated emails to that effect. On Tuesday June 27, I
got an email from my PI indicating that the package has been depreciated.
It appears as though the errors were from the most recent change altering the
examples to a couple of my functions, and I have fixed them on upstream/devel.
Additionally, I have made sure that any email filters and organizational
changes have been reverted to their previously functional states.
As a result of these remedies, I hope that, once again, motifbreakR can be
reinstated to good standing in Bioconductor. Is there anything else that I can
do to prove my continued enthusiasm and commitment to the package and community?
Thank you,
Simon Coetzee
IMPORTANT WARNING: This message is intended for the use ...{{dropped:11}}
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Re: [Rd] Correct use of tools::R_user_dir() in packages?
On 27 June 2023 at 15:36, Carl Boettiger wrote:
| tools::R_user_dir() provides configurable directories for R packages
| to write persistent information consistent with standard best
| practices relative to each supported operating systems for
| applications to store data, config, and cache information
| respectively. These standard best practices include writing to
| directories in the users home filespace, which is also specifically
| against CRAN policy.
|
| These defaults can be overridden by setting the environmental
| variables R_USER_DATA_DIR , R_USER_CONFIG_DIR, R_USER_CACHE_DIR,
| respectively.
|
| If R developers should be using the locations provided by
| tools::R_user_dir() in packages, why does CRAN's check procedure not
| set these three environmental variables to CRAN compliant location by
| default (e.g. tempdir())?
|
| In order to comply with CRAN policy, a package developer can obviously
| set these environmental variables themselves within the call for every
| example, every unit test, and every vignette. Is this the recommended
| approach or is there a better technique?
My use evolved to something like this (from in this case r2u, but similar in
a few other packages)
.defaultConfigFile <- function() {
pkgdir <- tools::R_user_dir(packageName()) # ~/.local/share/R/ +
package
if (dir.exists(pkgdir)) {
fname <- file.path(pkgdir, "config.dcf")
if (file.exists(fname)) {
return(fname)
}
}
return("")
}
You can then create config reader and writers functions that have a file
argument (set to the above) whicg you can override in tests with tempfile()
allowing you to write and then read.
Given the 'thou shalt not write to $HOME' rule, I often have parameter
getters with default values which, if a config file is found (with the name
per the helper above), also read it and use it to override the defaults.
Works for me, and is lightweight via a 'using batteries included'
zero-depends approach.
Dirk
--
dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
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[Rd] Correct use of tools::R_user_dir() in packages?
tools::R_user_dir() provides configurable directories for R packages to write persistent information consistent with standard best practices relative to each supported operating systems for applications to store data, config, and cache information respectively. These standard best practices include writing to directories in the users home filespace, which is also specifically against CRAN policy. These defaults can be overridden by setting the environmental variables R_USER_DATA_DIR , R_USER_CONFIG_DIR, R_USER_CACHE_DIR, respectively. If R developers should be using the locations provided by tools::R_user_dir() in packages, why does CRAN's check procedure not set these three environmental variables to CRAN compliant location by default (e.g. tempdir())? In order to comply with CRAN policy, a package developer can obviously set these environmental variables themselves within the call for every example, every unit test, and every vignette. Is this the recommended approach or is there a better technique? Thanks for any clarification! Regards, Carl --- Carl Boettiger http://carlboettiger.info/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Bioc-devel] psygenet2r bioconductor question
To get rid of the BiocStyle you need to add BiocStyle to your DESCRIPTION in the suggests field. To have the changes be on the release branch, you need to alter and push changes on RELEASE_3_17 branch of git.bioconductor.org instead of to devel on git.bioconductor.org. See: http://contributions.bioconductor.org/git-version-control.html#bug-fix-in-release-and-devel 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 on behalf of alba gutierrez Sent: Tuesday, June 27, 2023 10:10 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] psygenet2r bioconductor question Dear Bioconductor Team, I have been trying to fix my package that was failing in Bioconductor due to a warning (not an error) on the code. I updated my github and try to push the changes to Bioconductor, and for some reason, I cannot update the main one. As you can see, my last push to the dev environment was on May 22nd, and the package is building fine, http://secure-web.cisco.com/1BLsNasLT7jE0dM8Qu4VbJF2l4zp2AwcK2Yje6tPlpzPO_8WjF0lau6pZgC7DRuSytIPUUUMGZGVHgH4aPiCkjgAYap4CYvXil1ddwO8l0O7WLwnQPAKStIb2Rv3O7C7d71L3CYf3ZJ0963jLyLVPjFv94nVnlrBuHXCe9edHon3hxEdiy7QncCb03Z43bcBt18Tk8vvolJLTCnxtghJzETb7yME_gkMd3GSi4NZAf5Dc_gPxpnZevqVTusB_FvToENt7dvS8P9TMAy0ggN4BoSAKzyLMFtmkVvoSUlD24OkovK0kdUjv0wNXmyAuezfG/http%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2Fpsygenet2r%2F (even if I see now an error on Linux due to BiocStyle package on the CHECK step) BUT I could not push the same changes to the main one, my last successful push was on May 15th. http://secure-web.cisco.com/1GrH89YAgTat9RKKgsO-F-LKhAIoVNMaX4cdUxHDH_qB2q01LUl42LyG_qUGxuZF24t_Sdmu7s8zSTdJDxpLbHgg5w2k7lKa2IyGxqNh1tJlhdk9O8QWDZ6wfkws1dx_XE3GKemSsOltuUntVr61u7FqqGXxxeyz1B1aVkwKWTzUi5_EYg5dq9cvg7VcVbTJNoiEQCo2lP0Fjpq30ablC-ClH2OlES88mnvvvAJgns-ctvXbOWAmMRf8Guuwg-1P0TjyLDqGH7fJ3Pd2irJijP1io6wcUFpVNeKNDYWZESst88bZOa9D66QiSJQFFvRSI/http%3A%2F%2Fbioconductor.org%2FcheckResults%2Frelease%2Fbioc-LATEST%2Fpsygenet2r%2Fnebbiolo1-buildsrc.html instead of May 22nd. https://secure-web.cisco.com/16IYMq-X5pv9dp6RlqGxG8CVMv5GOU9kIh0zpMhK2Y_9Ud0P3BOEG1_Wjvj0AsOhnKDPv2M8YpaV6pSz0gCyM1lIEyukmUAi4nTvzHd8_n8AtlVtINzyTO1OghS4oT_mmbrIgp2qS2M5fxwpGghHyzelPz6SuYgu9vfpWygV1Aaes4ON-Bcvx-VSOKe5yjBwy68rsCWkFVFIMhspt5WrY802WezSU3J76nO_QzbsT5j9e4IzSca-a__QkHN-6cCr49j9fSbwjXOgEkI5GgiTbIR1SkbvvfRDacxO6-hx63lUe-S1OA_awIcRdhsJrtpAe/https%3A%2F%2Fgithub.com%2FaGutierrezSacristan%2Fpsygenet2r Could you help me with this? I am not sure why I cannot push changes anymore to the main one. Thanks in advance, Alba [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://secure-web.cisco.com/1RPMe8Z551EucdL_xAulDmZfI62ExpuJ1v476tQANSBGezvZ6fMbWdI-3-3Hn1PQt2EUmkZpknt2W6Gvb5IxS-AuAjv9gWEn2oyXCzDxqKZuOrg9WaUdjCC0hJADBKpbLcc_A0Nap6rPZ-y8whcrHI8R4xKF7UMLmXa2tNnOUOKXV4vLFjBODuLCnz7L91ed73Q0jkXqvZdjR_BNli2Qxm47nUWZZtoFKyVRWYwUhG5SBSYtczIUDnVa0X6eAPwB8JGJAc58tiPnIDTscnSFqpmoGpWMcIZpdLG2uPz_7YbxMGVPAZbo3xYsw9M4UqZlC/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] psygenet2r bioconductor question
Dear Bioconductor Team, I have been trying to fix my package that was failing in Bioconductor due to a warning (not an error) on the code. I updated my github and try to push the changes to Bioconductor, and for some reason, I cannot update the main one. As you can see, my last push to the dev environment was on May 22nd, and the package is building fine, http://bioconductor.org/checkResults/devel/bioc-LATEST/psygenet2r/ (even if I see now an error on Linux due to BiocStyle package on the CHECK step) BUT I could not push the same changes to the main one, my last successful push was on May 15th. http://bioconductor.org/checkResults/release/bioc-LATEST/psygenet2r/nebbiolo1-buildsrc.html instead of May 22nd. https://github.com/aGutierrezSacristan/psygenet2r Could you help me with this? I am not sure why I cannot push changes anymore to the main one. Thanks in advance, Alba [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [R-pkg-devel] Package broke with R 4.3.0
On Tue, 27 Jun 2023 at 18:45, Jeff Newmiller wrote:
>
> if (any(c( "alaska", "hawaii") %in% zoom)){}
Note that this changes behavior. If e.g. zoom is c("something",
"alaska"), the code above returns TRUE. Previous behavior was FALSE
(with a warning).
Iñaki
> On June 27, 2023 9:11:09 AM PDT, "Göran Broström" wrote:
> >
> >
> >Den 2023-06-27 kl. 17:17, skrev Göran Broström:
> >> If(zoom %in% c(“alaska”, “hawaii”)…
> >
> >Wrong, maybe
> >
> >if (("alaska" %in% zoom) || ("hawaii" %in% zoom)){}
> >
> >
> >>
> >> Göran
> >>
> >>> 27 juni 2023 kl. 16:32 skrev arilamst...@gmail.com:
> >>>
> >>> It appears that my R package choroplethr broke due to this change in R
> >>> 4.3.0:
> >>>
> >>> CHANGES IN R 4.3.0:
> >>>
> >>> SIGNIFICANT USER-VISIBLE CHANGES:
> >>>
> >>> Calling && or || with LHS or (if evaluated) RHS of length greater than one
> >>> is now always an error, with a report of the form
> >>>
> >>> 'length = 4' in coercion to 'logical(1)'
> >>> Environment variable R_CHECK_LENGTH_1_LOGIC2 no longer has any effect.
> >>>
> >>> The specific line which broke is this:
> >>> https://github.com/arilamstein/choroplethr/blob/master/R/usa.R#L24
> >>>
> >>> The bug can be reproduced like this:
> >>>
> >>> zoom = c("arizona", "arkansas", "louisiana", "minnesota", "mississippi",
> >>> "montana", "new mexico", "north dakota", "oklahoma", "pennsylvania",
> >>> "tennessee", "virginia", "california", "delaware", "west virginia",
> >>> "wisconsin", "wyoming", "alabama", "alaska", "florida", "idaho",
> >>> "kansas", "maryland", "colorado", "new jersey", "north carolina",
> >>> "south carolina", "washington", "vermont", "utah", "iowa",
> >>> "kentucky",
> >>> "maine", "massachusetts", "connecticut", "michigan", "missouri",
> >>> "nebraska", "nevada", "new hampshire", "new york", "ohio", "oregon",
> >>> "rhode island", "south dakota", "district of columbia", "texas",
> >>> "georgia", "hawaii", "illinois", "indiana")
> >>>
> >>> if (zoom == "alaska" || zoom == "hawaii") {}
> >>> Error in zoom == "alaska" || zoom == "hawaii" :
> >>> 'length = 51' in coercion to 'logical(1)'
> >>>
> >>> I have two questions:
> >>>
> >>> 1. Can someone explain why this change was introduced to the language?
> >>> 2. Can someone tell me if there is a preferred, idiomatic way to rewrite
> >>> my
> >>> code?
> >>>
> >>> I came up with two solutions that work. The first checks whether zoom is
> >>> of
> >>> length 1:
> >>>
> >>> if ((length(zoom) == 1) && (zoom %in% c("alaska", "hawaii"))) { }
> >>>
> >>> The second keeps the vector recycling, but then uses all to coerce the
> >>> vector to be a single value. In retrospect, I think I likely assumed that
> >>> this is what R < 4.3.0 was doing when the code worked. (But I wrote this
> >>> code many years ago, so I can't be sure!):
> >>>
> >>> if (all(zoom == "alaska") || all(zoom == "hawaii")) {}
> >>>
> >>> Thanks in advance.
> >>>
> >>> Ari
> >>>
> >>> [[alternative HTML version deleted]]
> >>>
> >>> __
> >>> R-package-devel@r-project.org mailing list
> >>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
> >>
> >> __
> >> R-package-devel@r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/r-package-devel
> >
> >__
> >R-package-devel@r-project.org mailing list
> >https://stat.ethz.ch/mailman/listinfo/r-package-devel
>
> --
> Sent from my phone. Please excuse my brevity.
>
> __
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Re: [R-pkg-devel] Package broke with R 4.3.0
if (any(c( "alaska", "hawaii") %in% zoom)){}
On June 27, 2023 9:11:09 AM PDT, "Göran Broström" wrote:
>
>
>Den 2023-06-27 kl. 17:17, skrev Göran Broström:
>> If(zoom %in% c(“alaska”, “hawaii”)…
>
>Wrong, maybe
>
>if (("alaska" %in% zoom) || ("hawaii" %in% zoom)){}
>
>
>>
>> Göran
>>
>>> 27 juni 2023 kl. 16:32 skrev arilamst...@gmail.com:
>>>
>>> It appears that my R package choroplethr broke due to this change in R
>>> 4.3.0:
>>>
>>> CHANGES IN R 4.3.0:
>>>
>>> SIGNIFICANT USER-VISIBLE CHANGES:
>>>
>>> Calling && or || with LHS or (if evaluated) RHS of length greater than one
>>> is now always an error, with a report of the form
>>>
>>> 'length = 4' in coercion to 'logical(1)'
>>> Environment variable R_CHECK_LENGTH_1_LOGIC2 no longer has any effect.
>>>
>>> The specific line which broke is this:
>>> https://github.com/arilamstein/choroplethr/blob/master/R/usa.R#L24
>>>
>>> The bug can be reproduced like this:
>>>
>>> zoom = c("arizona", "arkansas", "louisiana", "minnesota", "mississippi",
>>> "montana", "new mexico", "north dakota", "oklahoma", "pennsylvania",
>>> "tennessee", "virginia", "california", "delaware", "west virginia",
>>> "wisconsin", "wyoming", "alabama", "alaska", "florida", "idaho",
>>> "kansas", "maryland", "colorado", "new jersey", "north carolina",
>>> "south carolina", "washington", "vermont", "utah", "iowa",
>>> "kentucky",
>>> "maine", "massachusetts", "connecticut", "michigan", "missouri",
>>> "nebraska", "nevada", "new hampshire", "new york", "ohio", "oregon",
>>> "rhode island", "south dakota", "district of columbia", "texas",
>>> "georgia", "hawaii", "illinois", "indiana")
>>>
>>> if (zoom == "alaska" || zoom == "hawaii") {}
>>> Error in zoom == "alaska" || zoom == "hawaii" :
>>> 'length = 51' in coercion to 'logical(1)'
>>>
>>> I have two questions:
>>>
>>> 1. Can someone explain why this change was introduced to the language?
>>> 2. Can someone tell me if there is a preferred, idiomatic way to rewrite my
>>> code?
>>>
>>> I came up with two solutions that work. The first checks whether zoom is of
>>> length 1:
>>>
>>> if ((length(zoom) == 1) && (zoom %in% c("alaska", "hawaii"))) { }
>>>
>>> The second keeps the vector recycling, but then uses all to coerce the
>>> vector to be a single value. In retrospect, I think I likely assumed that
>>> this is what R < 4.3.0 was doing when the code worked. (But I wrote this
>>> code many years ago, so I can't be sure!):
>>>
>>> if (all(zoom == "alaska") || all(zoom == "hawaii")) {}
>>>
>>> Thanks in advance.
>>>
>>> Ari
>>>
>>> [[alternative HTML version deleted]]
>>>
>>> __
>>> R-package-devel@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>
>> __
>> R-package-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>
>__
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Sent from my phone. Please excuse my brevity.
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Re: [R-pkg-devel] Package broke with R 4.3.0
Den 2023-06-27 kl. 17:17, skrev Göran Broström:
If(zoom %in% c(“alaska”, “hawaii”)…
Wrong, maybe
if (("alaska" %in% zoom) || ("hawaii" %in% zoom)){}
Göran
27 juni 2023 kl. 16:32 skrev arilamst...@gmail.com:
It appears that my R package choroplethr broke due to this change in R
4.3.0:
CHANGES IN R 4.3.0:
SIGNIFICANT USER-VISIBLE CHANGES:
Calling && or || with LHS or (if evaluated) RHS of length greater than one
is now always an error, with a report of the form
'length = 4' in coercion to 'logical(1)'
Environment variable R_CHECK_LENGTH_1_LOGIC2 no longer has any effect.
The specific line which broke is this:
https://github.com/arilamstein/choroplethr/blob/master/R/usa.R#L24
The bug can be reproduced like this:
zoom = c("arizona", "arkansas", "louisiana", "minnesota", "mississippi",
"montana", "new mexico", "north dakota", "oklahoma", "pennsylvania",
"tennessee", "virginia", "california", "delaware", "west virginia",
"wisconsin", "wyoming", "alabama", "alaska", "florida", "idaho",
"kansas", "maryland", "colorado", "new jersey", "north carolina",
"south carolina", "washington", "vermont", "utah", "iowa",
"kentucky",
"maine", "massachusetts", "connecticut", "michigan", "missouri",
"nebraska", "nevada", "new hampshire", "new york", "ohio", "oregon",
"rhode island", "south dakota", "district of columbia", "texas",
"georgia", "hawaii", "illinois", "indiana")
if (zoom == "alaska" || zoom == "hawaii") {}
Error in zoom == "alaska" || zoom == "hawaii" :
'length = 51' in coercion to 'logical(1)'
I have two questions:
1. Can someone explain why this change was introduced to the language?
2. Can someone tell me if there is a preferred, idiomatic way to rewrite my
code?
I came up with two solutions that work. The first checks whether zoom is of
length 1:
if ((length(zoom) == 1) && (zoom %in% c("alaska", "hawaii"))) { }
The second keeps the vector recycling, but then uses all to coerce the
vector to be a single value. In retrospect, I think I likely assumed that
this is what R < 4.3.0 was doing when the code worked. (But I wrote this
code many years ago, so I can't be sure!):
if (all(zoom == "alaska") || all(zoom == "hawaii")) {}
Thanks in advance.
Ari
[[alternative HTML version deleted]]
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Re: [R-pkg-devel] Package broke with R 4.3.0
If(zoom %in% c(“alaska”, “hawaii”)…
Göran
> 27 juni 2023 kl. 16:32 skrev arilamst...@gmail.com:
>
> It appears that my R package choroplethr broke due to this change in R
> 4.3.0:
>
> CHANGES IN R 4.3.0:
>
> SIGNIFICANT USER-VISIBLE CHANGES:
>
> Calling && or || with LHS or (if evaluated) RHS of length greater than one
> is now always an error, with a report of the form
>
> 'length = 4' in coercion to 'logical(1)'
> Environment variable R_CHECK_LENGTH_1_LOGIC2 no longer has any effect.
>
> The specific line which broke is this:
> https://github.com/arilamstein/choroplethr/blob/master/R/usa.R#L24
>
> The bug can be reproduced like this:
>
> zoom = c("arizona", "arkansas", "louisiana", "minnesota", "mississippi",
> "montana", "new mexico", "north dakota", "oklahoma", "pennsylvania",
> "tennessee", "virginia", "california", "delaware", "west virginia",
> "wisconsin", "wyoming", "alabama", "alaska", "florida", "idaho",
> "kansas", "maryland", "colorado", "new jersey", "north carolina",
> "south carolina", "washington", "vermont", "utah", "iowa",
> "kentucky",
> "maine", "massachusetts", "connecticut", "michigan", "missouri",
> "nebraska", "nevada", "new hampshire", "new york", "ohio", "oregon",
> "rhode island", "south dakota", "district of columbia", "texas",
> "georgia", "hawaii", "illinois", "indiana")
>
> if (zoom == "alaska" || zoom == "hawaii") {}
> Error in zoom == "alaska" || zoom == "hawaii" :
> 'length = 51' in coercion to 'logical(1)'
>
> I have two questions:
>
> 1. Can someone explain why this change was introduced to the language?
> 2. Can someone tell me if there is a preferred, idiomatic way to rewrite my
> code?
>
> I came up with two solutions that work. The first checks whether zoom is of
> length 1:
>
> if ((length(zoom) == 1) && (zoom %in% c("alaska", "hawaii"))) { }
>
> The second keeps the vector recycling, but then uses all to coerce the
> vector to be a single value. In retrospect, I think I likely assumed that
> this is what R < 4.3.0 was doing when the code worked. (But I wrote this
> code many years ago, so I can't be sure!):
>
> if (all(zoom == "alaska") || all(zoom == "hawaii")) {}
>
> Thanks in advance.
>
> Ari
>
>[[alternative HTML version deleted]]
>
> __
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Re: [R-pkg-devel] Package broke with R 4.3.0
On Tue, 27 Jun 2023 at 16:31, wrote:
>
> It appears that my R package choroplethr broke due to this change in R
> 4.3.0:
>
> CHANGES IN R 4.3.0:
>
> SIGNIFICANT USER-VISIBLE CHANGES:
>
> Calling && or || with LHS or (if evaluated) RHS of length greater than one
> is now always an error, with a report of the form
>
> 'length = 4' in coercion to 'logical(1)'
> Environment variable R_CHECK_LENGTH_1_LOGIC2 no longer has any effect.
>
> The specific line which broke is this:
> https://github.com/arilamstein/choroplethr/blob/master/R/usa.R#L24
>
> The bug can be reproduced like this:
>
> zoom = c("arizona", "arkansas", "louisiana", "minnesota", "mississippi",
> "montana", "new mexico", "north dakota", "oklahoma", "pennsylvania",
> "tennessee", "virginia", "california", "delaware", "west virginia",
> "wisconsin", "wyoming", "alabama", "alaska", "florida", "idaho",
> "kansas", "maryland", "colorado", "new jersey", "north carolina",
> "south carolina", "washington", "vermont", "utah", "iowa",
> "kentucky",
> "maine", "massachusetts", "connecticut", "michigan", "missouri",
> "nebraska", "nevada", "new hampshire", "new york", "ohio", "oregon",
> "rhode island", "south dakota", "district of columbia", "texas",
> "georgia", "hawaii", "illinois", "indiana")
>
> if (zoom == "alaska" || zoom == "hawaii") {}
> Error in zoom == "alaska" || zoom == "hawaii" :
> 'length = 51' in coercion to 'logical(1)'
>
> I have two questions:
>
> 1. Can someone explain why this change was introduced to the language?
This was incorrect code before, and should be fixed; this didn't
change. The change is that now it always triggers an error.
> 2. Can someone tell me if there is a preferred, idiomatic way to rewrite my
> code?
Option 1:
if (identical(zoom, "alaska") || identical(zoom, "hawaii")) {}
Option 2:
if (isTRUE(zoom == "alaska") || isTRUE(zoom == "hawaii")) {}
> I came up with two solutions that work. The first checks whether zoom is of
> length 1:
>
> if ((length(zoom) == 1) && (zoom %in% c("alaska", "hawaii"))) { }
This works too.
> The second keeps the vector recycling, but then uses all to coerce the
> vector to be a single value. In retrospect, I think I likely assumed that
> this is what R < 4.3.0 was doing when the code worked. (But I wrote this
> code many years ago, so I can't be sure!):
Before R 4.3.0, there was a warning, and the string was compared with
the first value only.
Iñaki
> if (all(zoom == "alaska") || all(zoom == "hawaii")) {}
>
> Thanks in advance.
>
> Ari
>
> [[alternative HTML version deleted]]
>
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--
Iñaki Úcar
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[R-pkg-devel] Package broke with R 4.3.0
It appears that my R package choroplethr broke due to this change in R
4.3.0:
CHANGES IN R 4.3.0:
SIGNIFICANT USER-VISIBLE CHANGES:
Calling && or || with LHS or (if evaluated) RHS of length greater than one
is now always an error, with a report of the form
'length = 4' in coercion to 'logical(1)'
Environment variable R_CHECK_LENGTH_1_LOGIC2 no longer has any effect.
The specific line which broke is this:
https://github.com/arilamstein/choroplethr/blob/master/R/usa.R#L24
The bug can be reproduced like this:
zoom = c("arizona", "arkansas", "louisiana", "minnesota", "mississippi",
"montana", "new mexico", "north dakota", "oklahoma", "pennsylvania",
"tennessee", "virginia", "california", "delaware", "west virginia",
"wisconsin", "wyoming", "alabama", "alaska", "florida", "idaho",
"kansas", "maryland", "colorado", "new jersey", "north carolina",
"south carolina", "washington", "vermont", "utah", "iowa",
"kentucky",
"maine", "massachusetts", "connecticut", "michigan", "missouri",
"nebraska", "nevada", "new hampshire", "new york", "ohio", "oregon",
"rhode island", "south dakota", "district of columbia", "texas",
"georgia", "hawaii", "illinois", "indiana")
if (zoom == "alaska" || zoom == "hawaii") {}
Error in zoom == "alaska" || zoom == "hawaii" :
'length = 51' in coercion to 'logical(1)'
I have two questions:
1. Can someone explain why this change was introduced to the language?
2. Can someone tell me if there is a preferred, idiomatic way to rewrite my
code?
I came up with two solutions that work. The first checks whether zoom is of
length 1:
if ((length(zoom) == 1) && (zoom %in% c("alaska", "hawaii"))) { }
The second keeps the vector recycling, but then uses all to coerce the
vector to be a single value. In retrospect, I think I likely assumed that
this is what R < 4.3.0 was doing when the code worked. (But I wrote this
code many years ago, so I can't be sure!):
if (all(zoom == "alaska") || all(zoom == "hawaii")) {}
Thanks in advance.
Ari
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[Bioc-devel] List of Deprecated Packages for Bioc3.18
The Bioconductor Team is continuing to identify packages that will be deprecated in the next release to allow for the Bioconductor community to respond accordingly. This is the current list of deprecated packages for Bioc 3.17: Software: Unresponsive: * baySeq * BGmix * BioMM * biomvRCNS * deco * genbankr * HPAStainR * hypeR * imageHTS * motifbreakR * netbiov * plethy * qrqc * RNAdecay * SOMNiBUS * TCseq * Travel * tweeDEseq It should be noted, we did try to reach out to these package maintainers multiple times and they were either unresponsive or had emails bounce. We encourage anyone that is familiar with a package maintainer on this list to reach out to them and notify them directly. Packages can be un-deprecated if a maintainer fixes the package to build/check cleanly before the next release and requests un-deprecation on the bioc-devel@r-project.org mailing list Please do not undeprecate a package yourself. You must request undeprecation from the Bioconductor core team at bioc-devel@r-project.org. Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 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] SVMDO Bioc 3.18 Kunpeng2 error
Hi, Last week we updated R from 4.3.0 to 4.3.1 with empty site-library/ folder. All packages are being re-installed and some of them timed out. I just checked and both klaR and org.Hs.eg.db are installed. Please re-check the results later today! Regards, Martin On Tue, Jun 27, 2023 at 11:25 AM erhanozer19 via Bioc-devel < bioc-devel@r-project.org> wrote: > Dear Bioconductor Community, > > In BioC 3.18 build/check, kunpeng2 linux ARM64 reports this error: > > ERROR: dependencies ‘klaR’, ‘org.Hs.eg.db’ are not available for package > ‘SVMDO’ > > Is this a kunpeng2 related problem? > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] SVMDO Bioc 3.18 Kunpeng2 error
Dear Bioconductor Community, In BioC 3.18 build/check, kunpeng2 linux ARM64 reports this error: ERROR: dependencies ‘klaR’, ‘org.Hs.eg.db’ are not available for package ‘SVMDO’ Is this a kunpeng2 related problem? ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
