Re: [R-pkg-devel] Issue with Biostrings-- can't find the base rgb function on r-devel
That was a bug in Biostrings that has been fixed in the meantime.
Best,
Uwe Ligges
On 05.12.2019 05:19, Hugh Parsonage wrote:
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
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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]]
>
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>
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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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