Re: [R-pkg-devel] Issue with Biostrings-- can't find the base rgb function on r-devel
rgb is from package grDevices not package base.
On Thu, 5 Dec 2019 at 2:48 pm, Dalgleish, James (NIH/NCI) [V] via
R-package-devel wrote:
> Question:
>
> NIPTeR is experiencing new warnings when loading Biostrings. I have the
> exact same warnings with my package, CNVScope.
>
> It seems a little odd that the base function rgb cannot be found. What can
> cause a base package to not be found? I can't replicate this issue on
> either of my linux or windows machines or on winbuilder.
>
> I have already asked the Bioconductor community, but didn't get a response
> (https://support.bioconductor.org/p/126878/).
>
> Thanks,
> James Dalgleish
> Maintainer, CNVScope
> NIH/NCI
> Source: https://cran.r-project.org/web/checks/check_results_NIPTeR.html
> Check Details
> Version: 1.0.2
> Check: whether the package can be unloaded cleanly
> Result: WARN
> Error: package or namespace load failed for 'NIPTeR':
> .onLoad failed in loadNamespace() for 'Biostrings', details:
> call: rgb(1, 1, 1)
> error: could not find function "rgb"
> Execution halted
> Flavor: r-devel-linux-x86_64-debian-clang
>
> Version: 1.0.2
> Check: whether the namespace can be loaded with stated dependencies
> Result: WARN
> Error: .onLoad failed in loadNamespace() for 'Biostrings', details:
> call: rgb(1, 1, 1)
> error: could not find function "rgb"
> Execution halted
>
> A namespace must be able to be loaded with just the base namespace
> loaded: otherwise if the namespace gets loaded by a saved object, the
> session will be unable to start.
>
> Probably some imports need to be declared in the NAMESPACE file.
> Flavor: r-devel-linux-x86_64-debian-clang
>
> Version: 1.0.2
> Check: dependencies in R code
> Result: NOTE
> Error: package or namespace load failed for 'NIPTeR':
> .onLoad failed in loadNamespace() for 'Biostrings', details:
> call: rgb(1, 1, 1)
> error: could not find function "rgb"
> Call sequence:
> 6: stop(msg, call. = FALSE, domain = NA)
> 5: value[[3L]](cond)
> 4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
> 3: tryCatchList(expr, classes, parentenv, handlers)
> 2: tryCatch({
> attr(package, "LibPath") <- which.lib.loc
> ns <- loadNamespace(package, lib.loc)
> env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)
> }, error = function(e) {
> P <- if (!is.null(cc <- conditionCall(e)))
> paste(" in", deparse(cc)[1L])
> else ""
> msg <- gettextf("package or namespace load failed for %s%s:\n %s",
> sQuote(package), P, conditionMessage(e))
> if (logical.return)
> message(paste("Error:", msg), domain = NA)
> else stop(msg, call. = FALSE, domain = NA)
> })
> 1: library(package, lib.loc = lib.loc, character.only = T
> Execution halted
> Flavor: r-devel-linux-x86_64-debian-clang
>
> Version: 1.0.2
> Check: R code for possible problems
> Result: NOTE
> Error: .onLoad failed in loadNamespace() for 'Biostrings', details:
> call: rgb(1, 1, 1)
> error: could not find function "rgb"
> Execution halted
> Flavor: r-devel-linux-x86_64-debian-clang
>
>
> [[alternative HTML version deleted]]
>
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>
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[R-pkg-devel] Issue with Biostrings-- can't find the base rgb function on r-devel
Question:
NIPTeR is experiencing new warnings when loading Biostrings. I have the exact
same warnings with my package, CNVScope.
It seems a little odd that the base function rgb cannot be found. What can
cause a base package to not be found? I can't replicate this issue on either of
my linux or windows machines or on winbuilder.
I have already asked the Bioconductor community, but didn't get a response
(https://support.bioconductor.org/p/126878/).
Thanks,
James Dalgleish
Maintainer, CNVScope
NIH/NCI
Source: https://cran.r-project.org/web/checks/check_results_NIPTeR.html
Check Details
Version: 1.0.2
Check: whether the package can be unloaded cleanly
Result: WARN
Error: package or namespace load failed for 'NIPTeR':
.onLoad failed in loadNamespace() for 'Biostrings', details:
call: rgb(1, 1, 1)
error: could not find function "rgb"
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.0.2
Check: whether the namespace can be loaded with stated dependencies
Result: WARN
Error: .onLoad failed in loadNamespace() for 'Biostrings', details:
call: rgb(1, 1, 1)
error: could not find function "rgb"
Execution halted
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.0.2
Check: dependencies in R code
Result: NOTE
Error: package or namespace load failed for 'NIPTeR':
.onLoad failed in loadNamespace() for 'Biostrings', details:
call: rgb(1, 1, 1)
error: could not find function "rgb"
Call sequence:
6: stop(msg, call. = FALSE, domain = NA)
5: value[[3L]](cond)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
3: tryCatchList(expr, classes, parentenv, handlers)
2: tryCatch({
attr(package, "LibPath") <- which.lib.loc
ns <- loadNamespace(package, lib.loc)
env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)
}, error = function(e) {
P <- if (!is.null(cc <- conditionCall(e)))
paste(" in", deparse(cc)[1L])
else ""
msg <- gettextf("package or namespace load failed for %s%s:\n %s",
sQuote(package), P, conditionMessage(e))
if (logical.return)
message(paste("Error:", msg), domain = NA)
else stop(msg, call. = FALSE, domain = NA)
})
1: library(package, lib.loc = lib.loc, character.only = T
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.0.2
Check: R code for possible problems
Result: NOTE
Error: .onLoad failed in loadNamespace() for 'Biostrings', details:
call: rgb(1, 1, 1)
error: could not find function "rgb"
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
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Re: [R-pkg-devel] Static PDF Vignette
On Wed, 4 Dec 2019 at 22:54, Charith Karunarathna wrote: > > Hi, > > I followed these instructions, > (https://www.markvanderloo.eu/yaRb/2019/01/11/add-a-static-pdf-vignette-to-an-r-package/), > to add a pdf (perfectphyloR.pdf) as the vignette of my package > (perfectphyloR). However, I am getting the following Warning message and > NOTE from the win-builder: > > Warning messge: > > * checking files in 'vignettes' ... WARNING > Files in the 'vignettes' directory but no files in 'inst/doc': > 'perfectphyloR.pdf' > > NOTE: > > * checking for hidden files and directories ... NOTE > Found the following hidden files and directories: > vignettes/.Rnw > These were most likely included in error. See section 'Package > structure' in the 'Writing R Extensions' manual. > > CRAN-pack does not know about > vignettes/.Rnw > > I am having a hardship to fix those two. Could someone direct me to fix those > issue? The post doesn't mean ".Rnw" literally. Give it a filename instead of just .Rnw: perfectphyloR.Rnw seems appropriate. Iñaki __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] New Package olr 4 NOTES
Hi,
Thank you. I am wondering why the log would output .Rproj.user when it was
already in the .Rignorefile. Hope the .Rignore file is correct anyways as I
have mentioned below.
Thanks,
Mathew
Sent from Yahoo Mail for iPhone
On Wednesday, December 4, 2019, 2:11 PM, Duncan Murdoch
wrote:
On 04/12/2019 1:02 p.m., Mat Fok via R-package-devel wrote:
> Hi All,
> This is the first time I am trying to upload a package. It is fun learning
> this stuff.
> Thank you all for kindly looking at the NOTES.
> This is the log I recevied from CRAN volunteers:
> https://win-builder.r-project.org/incoming_pretest/olr_1.0.0.2000_20191129_024844/Windows/00check.log
> (I was wondering how to reproduce that log. I have run other things like
> devtools::check())
>
> The package is here: https://github.com/MatHatter/olr_r/tree/master/Rstuff
>
> I will address every problem below:
> 1. OK. Not misspelled:
> Possibly mis-spelled words in DESCRIPTION:
> olr (8:18, 9:20)
> 2. FIXED thisThe Description field should not start with the package name,
> 'This package' or similar.
> 3. FIXED thisThe Description field contains
> https://pypi.org/project/olr/.
> Please enclose URLs in angle brackets (<...>).
> 4. Don't know how to fix this, unless it is not anything.
> The build time stamp is missing.
That's a sign that you didn't build the package using "R CMD build" at
the command line (or one of the R functions that calls it). Don't use
tar directly to create it, let R do it (because adding a timestamp is
not the only thing it does).
If you used a devtools function to build the tarball, then you probably
did something wrong, but it's hard to say what without seeing the
command you used. Or maybe devtools has a bug, but it's pretty widely
used, so I doubt that.
> 5. First I took these files out of the folder completely, but then I thought
> that it might be needed for something and .Rhistory probably will be there no
> matter what so I used the function
>> usethis::use_build_ignore(c(".Rproj.user", ".gitignore", ".Rhistory"))✔
>> Setting active project to 'C:/Rstuff/olr'✔ Adding '^\\.gitignore$',
>> '^\\.Rhistory$' to '.Rbuildignore'
> but as you see .Rproj.user was already in my .Rbuildignore so I don't know if
> this is going to work.* checking for hidden files and directories ... NOTE
> Found the following hidden files and directories:
> .Rhistory
> .gitignore
> .Rproj.user
> These were most likely included in error. See section 'Package
> structure' in the 'Writing R Extensions' manual.
If you had .Rbuildignore set to ignore them, then R would not put them
in the tarball.
Duncan Murdoch
>
> 6. Lastly, I do not know how to fix this. I used the use_gpl3_license() I
> believe.
> * checking top-level files ... NOTE
> Non-standard files/directories found at top level:
> 'LICENSE.md' 'olr.Rproj'
> FYI,This is what my .Rbuildignore file looks
> like^olr\.Rproj$^\.Rproj\.user$^LICENSE\.md$^\.gitignore$^\.Rhistory$
> Thank you all so much.
> From,
> Mathew Fok
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[R-pkg-devel] Static PDF Vignette
Hi, I followed these instructions, (https://www.markvanderloo.eu/yaRb/2019/01/11/add-a-static-pdf-vignette-to-an-r-package/), to add a pdf (perfectphyloR.pdf) as the vignette of my package (perfectphyloR). However, I am getting the following Warning message and NOTE from the win-builder: Warning messge: * checking files in 'vignettes' ... WARNING Files in the 'vignettes' directory but no files in 'inst/doc': 'perfectphyloR.pdf' NOTE: * checking for hidden files and directories ... NOTE Found the following hidden files and directories: vignettes/.Rnw These were most likely included in error. See section 'Package structure' in the 'Writing R Extensions' manual. CRAN-pack does not know about vignettes/.Rnw I am having a hardship to fix those two. Could someone direct me to fix those issue? Thank you! Charith. [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] New Package olr 4 NOTES
On 04/12/2019 1:02 p.m., Mat Fok via R-package-devel wrote:
Hi All,
This is the first time I am trying to upload a package. It is fun learning this
stuff.
Thank you all for kindly looking at the NOTES.
This is the log I recevied from CRAN volunteers:
https://win-builder.r-project.org/incoming_pretest/olr_1.0.0.2000_20191129_024844/Windows/00check.log
(I was wondering how to reproduce that log. I have run other things like
devtools::check())
The package is here: https://github.com/MatHatter/olr_r/tree/master/Rstuff
I will address every problem below:
1. OK. Not misspelled:
Possibly mis-spelled words in DESCRIPTION:
olr (8:18, 9:20)
2. FIXED thisThe Description field should not start with the package name,
'This package' or similar.
3. FIXED thisThe Description field contains
https://pypi.org/project/olr/.
Please enclose URLs in angle brackets (<...>).
4. Don't know how to fix this, unless it is not anything.
The build time stamp is missing.
That's a sign that you didn't build the package using "R CMD build" at
the command line (or one of the R functions that calls it). Don't use
tar directly to create it, let R do it (because adding a timestamp is
not the only thing it does).
If you used a devtools function to build the tarball, then you probably
did something wrong, but it's hard to say what without seeing the
command you used. Or maybe devtools has a bug, but it's pretty widely
used, so I doubt that.
5. First I took these files out of the folder completely, but then I thought
that it might be needed for something and .Rhistory probably will be there no
matter what so I used the function
usethis::use_build_ignore(c(".Rproj.user", ".gitignore", ".Rhistory"))✔ Setting
active project to 'C:/Rstuff/olr'✔ Adding '^\\.gitignore$', '^\\.Rhistory$' to '.Rbuildignore'
but as you see .Rproj.user was already in my .Rbuildignore so I don't know if
this is going to work.* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.Rhistory
.gitignore
.Rproj.user
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
If you had .Rbuildignore set to ignore them, then R would not put them
in the tarball.
Duncan Murdoch
6. Lastly, I do not know how to fix this. I used the use_gpl3_license() I
believe.
* checking top-level files ... NOTE
Non-standard files/directories found at top level:
'LICENSE.md' 'olr.Rproj'
FYI,This is what my .Rbuildignore file looks
like^olr\.Rproj$^\.Rproj\.user$^LICENSE\.md$^\.gitignore$^\.Rhistory$
Thank you all so much.
From,
Mathew Fok
__
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[R-pkg-devel] New Package olr 4 NOTES
Hi All,
This is the first time I am trying to upload a package. It is fun learning this
stuff.
Thank you all for kindly looking at the NOTES.
This is the log I recevied from CRAN volunteers:
https://win-builder.r-project.org/incoming_pretest/olr_1.0.0.2000_20191129_024844/Windows/00check.log
(I was wondering how to reproduce that log. I have run other things like
devtools::check())
The package is here: https://github.com/MatHatter/olr_r/tree/master/Rstuff
I will address every problem below:
1. OK. Not misspelled:
Possibly mis-spelled words in DESCRIPTION:
olr (8:18, 9:20)
2. FIXED thisThe Description field should not start with the package name,
'This package' or similar.
3. FIXED thisThe Description field contains
https://pypi.org/project/olr/.
Please enclose URLs in angle brackets (<...>).
4. Don't know how to fix this, unless it is not anything.
The build time stamp is missing.
5. First I took these files out of the folder completely, but then I thought
that it might be needed for something and .Rhistory probably will be there no
matter what so I used the function
> usethis::use_build_ignore(c(".Rproj.user", ".gitignore", ".Rhistory"))✔
> Setting active project to 'C:/Rstuff/olr'✔ Adding '^\\.gitignore$',
> '^\\.Rhistory$' to '.Rbuildignore'
but as you see .Rproj.user was already in my .Rbuildignore so I don't know if
this is going to work.* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.Rhistory
.gitignore
.Rproj.user
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
6. Lastly, I do not know how to fix this. I used the use_gpl3_license() I
believe.
* checking top-level files ... NOTE
Non-standard files/directories found at top level:
'LICENSE.md' 'olr.Rproj'
FYI,This is what my .Rbuildignore file looks
like^olr\.Rproj$^\.Rproj\.user$^LICENSE\.md$^\.gitignore$^\.Rhistory$
Thank you all so much.
From,
Mathew Fok
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