))
Error in `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.
------
Dario Strbena
y indicates 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.
--
Dario
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?
----
tions 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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University of Sydney
Camperdown NSW 2050
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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?
--
Dario Strbenac
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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
"characterOrMissing", "integerOrMissing",
"integerOrMissing", "integerOrMissing"),
function(A = c('L', 'M', 'N'), B = 500, C = 100, D, E, F, G, H)
{
if(missing(A)) A <- 'L' # Mimick match.arg.
i
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
.
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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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University of Sydney
t were harmless. I will reinstall R. The extracted directory and prefix
directory were the same, which might be problematic.
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University of Sydney
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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 Sy
bian GNU/Linux 10 (buster)
BLAS: /dskh/biostat/software/R-4.1.0/lib/libRblas.so
LAPACK: /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.
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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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r does 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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University of Sydney
Camperdown NSW 2050
from 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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would increase readability if
the constructor 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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explicit?
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samtools")
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
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.
------
Dario Strbenac
University
rning: 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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stems.
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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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;C:/Program 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 ?
ages:
[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
------
Dario Strbenac
University of Sydney
Camper
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.
------
Dari
)
biocLite("GenomicAlignments")
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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University of Sydney
Camperdow
form: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
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ere 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
------
Dario Strbenac
University of Sydney
Camperdown NS
e, I
don't think this preprocessing stage should happen in R which is a statistical
programming language. Modularity is good.
--
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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.
--
Dario Strbenac
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earlier this week.
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se[7]> ?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.
s.html
Perhaps making the line corresponding to the strand the gene is encoded on
thicker than the other line might also be useful?
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nd. I 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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University of Sydney
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t have any effect or also be ignored?
------
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University of Sydney
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year?
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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
a.
I used version 1.34.2 of ShortRead which is the newest one.
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class.
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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
------
Dario Strbenac
University of Sydney
Camperdown NSW 2050
Good day,
Yes, that's the end of the key digiOcean.pub. I also copied the private key to
/tmp and re-generated the public key. The newly made public key is exactly the
same as the one in ~/SSHkeys/ so the key pair matches.
--
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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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Aust
"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 wi
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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ust pseudocode. Also, 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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University of Sydney
Camperdown NSW 2050
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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.
--
Dario Strbenac
University of Sydney
Camperdown NSW 2050
Aust
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)?
------
Dario Strbenac
University of Sydney
Camperdown NSW 2050
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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
ndel documented 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.
--
ved in binary format, the size on disk is 2.0 GB. Is a lot of unnecessary
detail saved when the object is serialised?
--
Dario Strbenac
University of Sydney
Camperdown NSW 2050
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___
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ne else has
encountered this bug before.
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voom:
t(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.
------
Dario Strbenac
University of Sydney
Camperdown NS
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?
--
Dario Strbenac
University of
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.
--
Dario Strbenac
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.
------
Dario Strbenac
University of Sydney
Camperdow
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
------
Dario Strbenac
University of Sydney
Camperdown NSW 2050
x "bam" instead of "sam"?
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n for readGAlignments and
other similar functions in GenomicAlignments.
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d mc.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.
------
Dario Strbenac
University of Sydney
Campe
[11] 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
of CRISPR genomic screens
without leaving the R analysis environment, which is a new use case not
existing before.
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University of Sydney
Camperdown NSW 2050
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, :
vmatchPattern() does not support indels yet
This is utilising Biostrings 2.42.0 in R 3.3.1.
------
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University of Sydney
Camperdown NSW 2050
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h respect 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 Strben
deprecated 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
Good day,
The log at http://bioconductor.org/developers/svnlog/ stopped updating two
weeks ago.
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University of Sydney
Camperdown NSW 2050
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ng 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
Camp
ent
issue.
-----
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ition: 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.
--
Dari
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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e R logo is gigantic.
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ile that
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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