[Bioc-devel] New maintainer request for GAPGOM package
Dear Bioconductor, I wish to transfer the package maintainer for the GAPGOM Bioconductor package (https://doi.org/doi:10.18129/B9.bioc.GAPGOM). The new maintainer would be Rezvan Ehsani (rezvanehsan...@gmail.com). Thanks in advance. With kind regards, Casper van Mourik [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Passing BiocCheck with roxygen2 tags.
Hello,
Is there a way to add the value section in man pages using roxygen tags? I
am currently using "@section Value: ..." but this fails biocheck with
"WARNING: Add non-empty \value sections to the following...{{dropped:18}}
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Re: [Bioc-devel] Passing BiocCheck with roxygen2 tags.
I think it's looking for details on the return value for the functions. I
believe the correct syntax is @return to add a return value section in roxygen
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 Erik
Christensen
Sent: Thursday, June 25, 2020 11:24 AM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] Passing BiocCheck with roxygen2 tags.
Hello,
Is there a way to add the value section in man pages using roxygen tags? I
am currently using "@section Value: ..." but this fails biocheck with
"WARNING: Add non-empty \value sections to the following...{{dropped:23}}
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Re: [Bioc-devel] Passing BiocCheck with roxygen2 tags.
Hi Erik,
I think the #' @return tag will create the \value{} section in the Rd file.
Mike
On Thu, 25 Jun 2020 at 17:24, Erik Christensen wrote:
> Hello,
>
> Is there a way to add the value section in man pages using roxygen tags? I
> am currently using "@section Value: ..." but this fails biocheck with
>
> "WARNING: Add non-empty \value sections to the following...{{dropped:18}}
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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Re: [Bioc-devel] Passing BiocCheck with roxygen2 tags.
Thank you! @return was the correct tag.
-Original Message-From: Mike Smith To: Erik
Christensen Cc: bioc-devel Subject:
Re: [Bioc-devel] Passing BiocCheck with roxygen2 tags.Date: Thu, 25 Jun 2020
17:39:18 +0200
Hi Erik,
I think the #' @return tag will create the \value{} section in the Rd file.
Mike
On Thu, 25 Jun 2020 at 17:24, Erik Christensen wrote:
> Hello,
>
>
>
> Is there a way to add the value section in man pages using roxygen tags? I
>
> am currently using "@section Value: ..." but this fails biocheck with
>
>
>
> "WARNING: Add non-empty \value sections to the following...{{dropped:18}}
>
>
>
> ___
>
> Bioc-devel@r-project.org mailing list
>
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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Re: [Bioc-devel] lipidr: Unable to reproduce error (possibly from S4Vectors)
Hi Ahmed,
Just a heads up that Lori's workaround (reinstalling iheatmap from
source on all the builders) should be considered a temporary one and
that the fundamental problem remains. The fundamental problem being that
the iheatmap's Windows and Mac binaries that are on CRAN are broken. And
the reason they are broken is because they contain stale information in
their method cache.
As a consequence, the lipidr error you were seeing a few days ago on our
build report is back today on the devel report:
https://bioconductor.org/checkResults/3.12/bioc-LATEST/lipidr/
Note that this time it's only on Windows and Mac. This is because
yesterday we updated R to R 4.0.2 on the devel builders so the build
machines automatically reinstalled all the deps from scratch. iheatmap
is one of them and the build system picked up the Windows and Mac
binaries from CRAN, which are broken :-/
We'll see the same problem on the release builds when we update R to R
4.0.2 there too.
Bottom line: the only true fix is that the iheatmap authors/maintainers
upload a new version of their package to CRAN. The only change they need
to do is bump the version. Alternatively, they could reconsider
depending on S4Vectors. Bioconductor moves fast and CRAN packages that
depend on Bioconductor packages are inherently at the risk of seeing
their binaries become stale.
Hope this helps,
H.
On 6/22/20 04:50, Shepherd, Lori wrote:
I reinstalled iheatmap yesterday and it should be reflected in today's
(Mondays) report.
Cheers,
Lori Shepherd
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
*From:* Ahmed Mohamed
*Sent:* Monday, June 22, 2020 2:18 AM
*To:* Martin Morgan
*Cc:* Vincent Carey ; Hervé Pagès
; bioc-devel ; Shepherd,
Lori
*Subject:* Re: [Bioc-devel] lipidr: Unable to reproduce error (possibly
from S4Vectors)
Excellent catch Martin.
I was able to confirm the issue using the script below (on Bioc-Devel
Docker). The issue was also resolved by simply reinstalling iheatmapr.
It would be great if iheatmapr is reinstalled manually on the devel
build systems.
remove.packages(c("iheatmapr", "S4Vectors"))
devtools::install_github("Bioconductor/S4Vectors",
ref="e8dffc0157f2c4779fce3c85e5ef601bb0a35d33")
install.packages("iheatmapr")
packageVersion("S4Vectors")
# "0.27.0"
packageVersion("iheatmapr")
# "0.4.12"
library(lipidr)
library(iheatmapr)
example("iheatmap")
# Runs successfully
## Update S4Vector
rm(list = ls())
rstudioapi::restartSession()
devtools::install_github("Bioconductor/S4Vectors")
packageVersion("S4Vectors")
# "0.27.12"
library(iheatmapr)
example("iheatmap")
# Error in .wrap_in_length_one_list_like_object(value, name, x) :
# failed to coerce 'list(value)' to a IheatmapPlots object of length 1
## Reinstall iheatmapr
rm(list = ls())
rstudioapi::restartSession()
install.packages("iheatmapr")
library(iheatmapr)
example("iheatmap")
# Runs successfully
Cheers.
Ahmed.
On Thu, 18 Jun 2020 at 00:52, Martin Morgan > wrote:
You can see package versions on the build system from
https://bioconductor.org/checkResults/devel/bioc-LATEST/index.html
clicking on 'installed pkgs' link in the center top table. iheatmapr
is at version 0.4.12.
I think what is happening is like
https://support.bioconductor.org/p/131689/#131695
where S4Vector m
Re: [Bioc-devel] How to set dimnames inside constructor function?
Hi Muad,
I'm not able to reproduce this. With a naked 'count' matrix:
library(SummarizedExperiment)
count <- matrix(1:15, ncol=3)
row_data <- DataFrame(stuff=runif(5))
se1 <- SummarizedExperiment(list(count=count), rowData=row_data)
dimnames(se1) <- list(sprintf("Gene%04d", 1:5), sprintf("ID%03d", 1:3))
dimnames(se1)
# [[1]]
# [1] "Gene0001" "Gene0002" "Gene0003" "Gene0004" "Gene0005"
#
# [[2]]
# [1] "ID001" "ID002" "ID003"
With dimnames on the 'count' matrix:
dimnames(count) <- list(LETTERS[1:5], LETTERS[1:3])
se2 <- SummarizedExperiment(list(count=count), rowData=row_data)
dimnames(se2) <- list(sprintf("Gene%04d", 1:5), sprintf("ID%03d", 1:3))
dimnames(se2)
# [[1]]
# [1] "Gene0001" "Gene0002" "Gene0003" "Gene0004" "Gene0005"
#
# [[2]]
# [1] "ID001" "ID002" "ID003"
So I don't know how/when you get the error you reported. If the error
occurs in your .CalciumExperiment() internal function I would need to
have access to it in order to understand why it fails. Note that if the
function calls the assay() or assays() setter at some point then it
probably needs to use 'withDimnames=FALSE', as indicated by the error
message.
Thanks,
H.
> sessionInfo()
R version 4.0.0 Patched (2020-04-27 r78316)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.6 LTS
Matrix products: default
BLAS: /home/hpages/R/R-4.0.r78316/lib/libRblas.so
LAPACK: /home/hpages/R/R-4.0.r78316/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] SummarizedExperiment_1.19.5 DelayedArray_0.15.5
[3] matrixStats_0.56.0 Matrix_1.2-18
[5] Biobase_2.49.0 GenomicRanges_1.41.5
[7] GenomeInfoDb_1.25.4 IRanges_2.23.10
[9] S4Vectors_0.27.12 BiocGenerics_0.35.4
loaded via a namespace (and not attached):
[1] lattice_0.20-41bitops_1.0-6 grid_4.0.0
[4] zlibbioc_1.35.0XVector_0.29.3 tools_4.0.0
[7] RCurl_1.98-1.2 compiler_4.0.0 GenomeInfoDbData_1.2.3
On 6/18/20 02:17, Muad Abd El Hay wrote:
Hello everyone,
This is my first attempt at writing a package (wrote it in S3 and nowHi
porting it to S4). So it might be a trivial question.
I am trying to extend the SummarizedExperiment object for calcium
imaging data (no gene names as features). Features/rownames are the
number of the frames and colnames are the cells/ROIs.
Inside the constructor function, I wanted to set the rownames and
colnames as below:
```R
se <- SummarizedExperiment(list(raw=raw),
rowData = DataFrame(time = time),
...)
dimnames(se) <- list(paste("f", 1:nrow(se), sep=""),
paste("name", 1:ncol(se), sep="_"))
.CalciumExperiment(se)
```
But I keep getting the following error:
```R
Error in `assays<-`(`*tmp*`, withDimnames = withDimnames, ..., value =
`*vtmp*`) :
please use 'assay(x, withDimnames=FALSE)) <- value' or 'assays(x,
withDimnames=FALSE)) <- value' when the dimnames on the supplied
assay(s) are not identical to the dimnames on CalciumExperiment
object
'x'
```
I also tried using `rownames(se)`and `colnames(se)`with the same error.
Setting the `dimnames`, `colnames`, or `rownames` on the `raw` matrix
beforehand also did not work.
Am I missing something fundamental here?
Thank you in advance!
Best wishes,
Muad Abd El Hay
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Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax:(206) 667-1319
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