n `rownames<-`(`*tmp*`, value = .get_colnames_from_first_assay(assays))
:
invalid rownames length
What is the subtle difference? It also seems like there could be a clearer
error message emitted if this is caught in the right place.
------
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that the package has never built
successfully in Bioconductor 3.17.
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Good day,
So, is the ultimate solution to manually change everything to the format of
\item{\code{show(x)}:}{
...
} ?
The warnings persist, so it does not seem as though R will revert to allowing
the currently-popular syntax past its check.
--
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seven years ago.
What should the new convention be? Or could R developers be convinced to get
rid of this check before this prototype is released?
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ong but works:
allFeatures <- unique(unlist(lapply(DFL, colnames)))
DFL <- lapply(DFL, function(DF)
{
missingFeatures <- setdiff(allFeatures, colnames(DF))
DF[missingFeatures] <- NA
DF
})
DFLflattened <- do.call(rbind, DFL)
Is there a one-line function for it?
----
measuring the largely the
same set of features and patient outcome, but on completely different sets of
patients in each organisation.
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Hello,
Might it instead made possible to set an RNGseed value by specifying one to
bpparam but still get the automated back-end selection, so that it could easily
be set to a particular value in an R package?
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Camperdown
() which sets no RNGseed. I am
wondering about the desirability of changing the RNGseed default in
BiocParallel to a particular uncontroversial number, such as 12345, so that
beginners get deterministic behaviour.
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Camperdown
ge, according
to top.
> system.time(CrossValParams("Leave-k-Out", leave = 2))
user system elapsed
760.018 15.093 775.090
Strangely, if I rerun this code again, it works quickly the second time.
> system.time(CrossValParams("Leave-k-Out", leave = 2))
user
It doesn't seem to apply to S4 slots
based on my understanding of it.
> r <- ResubstituteParams()
> delayedAssign("r@nFeatures", nrow(measurements))
> measurements <- matrix(1:100, ncol = 10)
> r@nFeatures # Still the value from empty constructor.
[1] 10 20 30 40
.
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in my code to help it pass? The error doesn't
appear on the two other Bioconductor servers.
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Hello,
The problem stemed from an .Rprofile file which was setting .libPaths with the
directory path to a library of packages for the previous version of R and
starting R with the --vanilla option avoided the problem.
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e harmless. I will reinstall R. The extracted directory and prefix
directory were the same, which might be problematic.
------
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Good day,
No, the temporary directory has space remaining. I wonder what file it is
referring to by "No such file or directory". I had an idea to reinstall
Biostrings using force = TRUE, but it didn't help.
------
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University of Sydney
ACK: /dskh/biostat/software/R-4.1.0/lib/libRlapack.so
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It looks like you are creating a MultiAssayExperiment in your vignette.
Numerous Bioconductor packages relying on MultiAssayExperiment infrastructure
started failing a few days ago with the release of version 1.17.3, but I don't
see the breaking change explained in the News file.
This also happens to ClassifyR.
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Good day,
Step 1: Follow the steps at
http://bioconductor.org/developers/how-to/git/push-to-github-bioc/
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triggers the
error shown in Bioconductor's daily build.
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collected in the ellipsis, so
the functional approach might still be the best in that case.
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not happen on the Linux or MacOS operating systems. It happens
using both R 3.6 and the upcoming version 4. The error can be reproduced
running the examples of runTests function in ClassifyR.
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Bioconductor package S4Vectors.
It's better than a data.frame and won't flood your console with output.
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Good day,
Could the forum have automatic saving of drafted text like some other forums?
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Good day,
In the development branch, all packages are only built on Linux.
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Good day,
No; anything older than the release branch at present is not modifiable.
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Good day,
Should setting workers to 1 and RNGseed to a number result in a warning to the
user that the seed will effectively be ignored?
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ructor didn't run off the edge of the PDF page in the reference manual
by using \preformatted. Also, I wonder why seqnames is automatically converted
into a factor Rle, but strand isn't. Couldn't strand also use .asFactorRle?
------
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ments be made
explicit?
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uot;)
qQCReport(testFile) # Fails because figure margins too large
plot(1:10) # Also fails because figure margins too large
The value of par("mar") is different before and after using qQCReport. Can
QuasR be changed so that it does not clobber the R session's graphics
parameters?
-
Good day,
You need to provide more information to get useful guidance. What version of R
did you use? From the error message, it seems that it's less than 3.5.0 but it
should be R Under Development.
--
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Good day,
I don't, but your software package imports agricolae which imports spdep. spdep
is available from CRAN, so it's strange that the Bioconductor build server
running Linux has not been able to install it.
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: package needs dependence on R (>= 2.10)
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observed
on the build servers was not clear about what the problem was.
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Good day,
There is an error for ClassifyR on malbec1 and merida1 caused by a
documentation example. However, it doesn't occur on tokay1. Can I get more
information about which example is emitting the error on malbec1 server?
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Good day,
You could also copy the private key from the old computer to the new computer,
if you still can use the old computer.
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.
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Good day,
The import of BigWig files does not work on Windows and is documented. Execute
?BigWigFile-class and notice in the Description section: "These functions do
not work on Windows.".
------
Dario Strbenac
University of Sydney
Camperdown NSW 2050
Good day,
Similar to you, I am awaiting the restoration of sparsediscrim which was
removed on the same day as PREDA.
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asthma.RData715Kb484Kbbzip2
Should I ignore it or save it again with compression? The 231 Kb reduction in
file size seems insignificant.
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m Files/R/R-3.5.0/library/BiocParallel"
$master
[1] "127.0.0.1"
$port
[1] 2559
> do.call(parallel::makeCluster, cargs) # Freezes.
Should I ask the question on R-devel because it doesn't appear to be specific
to Bioconductor ?
---
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocParallel_1.14.1
loaded via a namespace (and not attached):
[1] compiler_3.5.0 snow_0.4-2 parallel_3.5.0
--
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Camperdown
Good day,
Thanks. I'll use the [limma] specifier to avoid the Warning from the build
system.
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Good day,
I created a minimalist package that demonstrates the issue and it is attached
to this letter. After using R CMD build, the subsequent R CMD check process
emits one warning.
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Good day,
limma was installed using biocLite, so it would be built before R CMD check was
run. I could summarise all of the relevant information and send to
R-package-devel mailing list to check if it is a bug.
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Good day,
Indeed, it is in the Suggests component of the dependency specification. I
didn't find any extra requirements for this case in the Cross-references
section of Writing R Extensions, so I'm unsure of where to read about the rule.
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Alignments")
to install the GenomicAlignments package in a subsequent R session, for
instance. This avoids repetitive sourcing of the biocLite script from the
Bioconductor server.
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-linux-gnu (64-bit)
* using session charset: UTF-8
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. Is there a way to make ClassifyR guard
against this problem in Windows? I don't know how to begin solving this issue.
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Good day,
You could make use of the package named BSgenome.Celegans.UCSC.ce11. It
contains the DNA sequences of all of the chromosomes of the roundworm and
doesn't add any size to your package.
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3
dataTableS4 <- DataFrame(aFeature = 1:5, anotherFeature = 5:1)
colMeans(dataTableS4)
Error in colMeans(dataTableS4) :
'x' must be an array of at least two dimensions
--
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University of Sydney
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Aus
Good day,
Although the maintainer is unreachable, the original developer, Gábor Csárdi,
is an active member of the R programming community. You should write to him.
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earlier this week.
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encode
No documentation for ‘encode’ in specified packages and libraries
Anyway, the transcript ID is also missing from txt.
Browse[7]> grep("ENST0485971", txt)
integer(0)
It's hard to know what the obfuscated code of RCurl is doing.
--
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Un
simply wish to avoid that situation with
genomic plotting. Indeed, I wouldn't be as cautious if I was considering csaw,
for example, and noticed build system warnings close to the deadline.
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?
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Good day,
It might be useful to readers to have a comparison table (ticks and crosses) in
the MultiAssayExperiment vignette that compares the features available in it to
those available in SummarizedExperiment, to allow quicker decision making.
--
Dario
.34.2 of ShortRead which is the newest one.
------
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.
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Good day,
Thanks for your help. In the end, export GIT_SSH_COMMAND='ssh -i
~/SSHkeys/digiOcean' did the trick. The write access is showing.
R Wpackages/ClassifyR
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io/SSHkeys/digiOcean
Copying the private key to ~/.ssh/ does not help. How can I do it?
------
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classes)
measurementsSet[1, 1, ]
other attached packages:
[1] S4Vectors_0.15.7BiocGenerics_0.23.1
MultiAssayExperiment_1.3.34
--
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Good day,
Whatever the problem is, it's gone with R Under Development and all packages
installed from the development branch of Bioconductor.
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;3.2.3" "0.9-8"
Repository
rJava "https://cran.rstudio.com/src/contrib;
update with biocLite()
Error: 1 package(s) out of date
The same example works on another computer using Windows operating system.
What's the issue with this Linux e
Good day,
I like the idea of a commits log on the Bioconductor website. It was useful
being able to see at a glance which packages have recently been changing.
--
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, object creation using new is discouraged. Perhaps
SnpSet could have a proper constructor, like ExpressionSet does?
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Good day,
Is the private key in a location other than the default SSH key folders? If so,
use the ssh-add command to have the SSH agent know about it.
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Good day,
I filled out the form on Thursday, but can't fetch the repository.
$ git fetch upstream
Permission denied (publickey).
fatal: Could not read from remote repository.
--
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verage(foo, bar, ..., NA.value=-1)?"
- Tim Triche, Jr., January 2013.
Might this plan be restored (with a default value of 0 for backwards
compatibility)?
------
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University of Sydney
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Hello,
It would be convenient if the colour or the width of the edges could be
customised to represent whether an edge is equally present in two experimental
conditions or the degree to which it is enriched in one of them of an RNA-seq
dataset.
--
Dario
ocumented in
Numeric Summary Methods? Unlike nchar and score, they are not numerical
summaries of the data.
It'd be nice to see this part of Biostrings thoroughly refactored with more
focus on UX.
--
Dario Strbenac
ved in binary format, the size on disk is 2.0 GB. Is a lot of unnecessary
detail saved when the object is serialised?
--
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.
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counts + 0.5)/(lib.size + 1)
Basically, the values added to the counts and the library size ignore the
library size of each sample in the voom function.
--
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Good day,
The cpm function in edgeR uses a default offset of 0.25 and voom in limma uses
0.5 (and provides no user modification) to calculate the base 2 logarithm of
the counts per million. Might these be made consistent?
--
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University
Good day,
In a future release, could the user be allowed to specify an alternative
hypothesis such as the coefficient being positive? DESeq2 provides an
altHypothesis parameter for such a purpose.
--
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University of Sydney
Camperdown NSW 2050
Good day,
Now I know about invertStrand, I agree that it's best to keep the strandMode
only for paired-end data. Indeed, it's an example at the end of the lengthy
documentation of GAlignments.
--
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Camperdown NSW 2050
cs_0.20.0
loaded via a namespace (and not attached):
[1] lattice_0.20-34bitops_1.0-6 grid_3.3.2 zlibbioc_1.20.0
Matrix_1.2-7.1 BiocParallel_1.8.1
[7] tools_3.3.2
------
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for readGAlignments and
other similar functions in GenomicAlignments.
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cores = 2 and it also resulted in an error. Each of the files
has 30 to 40 million mappings, so I wouldn't expect them to be too big. I'll
stick to bplapply.
------
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University of Sydney
Camperdown NSW 2050
IRanges_2.8.1 S4Vectors_0.12.0 BiocGenerics_0.20.0
loaded via a namespace (and not attached):
[1] zlibbioc_1.20.0BiocParallel_1.8.1 lattice_0.20-34tools_3.3.2
grid_3.3.2 DBI_0.5-1 Matrix_1.2-7.1
[8] rtracklayer_1.34.1 bitops_1.0-
of CRISPR genomic screens
without leaving the R analysis environment, which is a new use case not
existing before.
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attern() does not support indels yet
This is utilising Biostrings 2.42.0 in R 3.3.1.
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to their corresponding
sequence
in 'x'
It's rare, but still a problem, nonetheless.
> table(unlist(endIndex(primerLocations)) > 75)
FALSE TRUE
366225 2
This happens with Biostrings 2.42.0.
------
Dario Strbenac
University of Sydney
C
d since it duplicates the functionality of substr?
> substr(words, start(matches), end(matches))
[1] "GOAT" "MOAT" NA
Also, the expected subsetting fails for MIndex objects.
> class(matches)
[1] "ByPos_MIndex"
> length(matches)
[1] 3
> length(matches[1])
[1] 3
Good day,
The log at http://bioconductor.org/developers/svnlog/ stopped updating two
weeks ago.
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for the file's existence at the
beginning of the function. For example,
if(file.exists(filename))
# Do fusion file import.
else
stop("Could not find the specified fusion file.")
------
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University of Sydney
Camperdown NSW 2050
.
-
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: Warning message:
In file(file, "rt") :
cannot open file 'Thu_Nov_3_13-46-27_2016': No such file or directory
The section of code where the error occurs seems to be in the .starImport
function.
------
Dario Strbenac
Univ
provide GTF and GFF3 files, which can
easily be imported into R with functions provided by rtracklayer.
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to be consistent?
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Good day,
I see it, too. There's no problem.
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s gigantic.
------
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hat
is 4 GB in size when compressed. I can't imagine how long that would take.
Can the code of readVcf be optimised ?
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d user.
R version 3.3.1 (2016-06-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 15.10
VariantAnnotation 1.18.7
------
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nction documentation with runnable examples and
a vignette. Sleuth isn't currently at the R package quality level necessary for
Bioconductor.
------
Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia
calling DNAString
(it's odd that vmatchPattern - for searching BSgenome objects - requires a
DNAString for the pattern, rather than a DNAStringSet) or DNAStringSet ?
--
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Hello,
Actually, I thought that substr unintentionally worked and perhaps they should
both produce an error message. Thanks for adding the functionality for
strsplit, though!
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University of Sydney
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split(IDs, " ") : non-character argument
I think that both of these functions shouldn't work or both should work, to be
consistent.
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Recently, the overview webpage of the development version of Repitools has
vanished. It is still listed in the build report, though. There are also some
strange build errors on Linux.
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University of Sydney
Camperdown NSW 2050
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