name to yours.
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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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in strsplit(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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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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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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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
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___
nings to the end 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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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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e R logo is gigantic.
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Good day,
I see it, too. There's no problem.
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to be consistent?
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provide GTF and GFF3 files, which can
easily be imported into R with functions provided by rtracklayer.
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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.
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ent
issue.
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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.")
------
Dario Strbenac
University of Sydney
Camp
Good day,
The log at http://bioconductor.org/developers/svnlog/ stopped updating two
weeks ago.
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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
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.
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Dario Strben
, :
vmatchPattern() does not support indels yet
This is utilising Biostrings 2.42.0 in R 3.3.1.
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of CRISPR genomic screens
without leaving the R analysis environment, which is a new use case not
existing before.
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[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
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.
------
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University of Sydney
Campe
n for readGAlignments and
other similar functions in GenomicAlignments.
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x "bam" instead of "sam"?
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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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University of Sydney
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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
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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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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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.
------
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ne else has
encountered this bug before.
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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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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.
--
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
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
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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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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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Dario Strbenac
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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,
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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"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,
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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classes)
measurementsSet[1, 1, ]
other attached packages:
[1] S4Vectors_0.15.7BiocGenerics_0.23.1
MultiAssayExperiment_1.3.34
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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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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.
--
Dario Strbenac
Universi
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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class.
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a.
I used version 1.34.2 of ShortRead which is the newest one.
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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.
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year?
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t have any effect or also be ignored?
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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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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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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.
earlier this week.
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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.
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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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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
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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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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University of Sydney
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___
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form: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
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)
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.
------
Dario Strbenac
University of Sydney
Camperdow
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
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,
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,
Thanks. I'll use the [limma] specifier to avoid the Warning from the build
system.
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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
;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 ?
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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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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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
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stems.
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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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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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observed
on the build servers was not clear about what the problem was.
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rning: package needs dependence on R (>= 2.10)
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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
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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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
ments be made
explicit?
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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?
---
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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Good day,
No; anything older than the release branch at present is not modifiable.
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Good day,
In the development branch, all packages are only built on Linux.
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Good day,
Could the forum have automatic saving of drafted text like some other forums?
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from Bioconductor package S4Vectors.
It's better than a data.frame and won't flood your console with output.
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___
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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.
------
Dario Strbenac
University of Sydney
Camperdown NSW 2050
collected in the ellipsis, so
the functional approach might still be the best in that case.
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triggers the
error shown in Bioconductor's daily build.
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stallation guide simply advises
"Visit the Workflows page and software package list to discover available
packages."
------
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PhD Student
University of Sydney
Camperdown NSW 2050
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___
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Thanks for this code. I was interested in all of the BSgenome packages, so the
results are sufficient for what we want on our group's server.
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We could simply remove the GDL2GRL function once the GenomeData and
GenomeDataList are defunct.
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th can
also contain time to last follow-up, but then why isn't it the same as
days_to_tumor_recurrence, for the first sample ?
--
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___
difying the edgeR description file to have limma in the Imports field ?
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7;LargeDataObject', 'vector')"
This is because of LargeDataObject from limma is not imported into edgeR. Can
you add that one, too ?
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PhD Student
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s:
Name: .Data
Class: list
Extends:
Class "list", from data part
Class "LargeDataObject", directly
Class "vector", by class "list", distance 2
That's why edgeR needs to know about that class.
--
ir dependencies, and consequently will not find their
dependencies unless hacked.
>From my introductory reading, it seems to be that Imports is preferred over
>Depends.
------
Dario Strbenac
PhD Student
University of Sydney
Cam
tly.
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ames differ between assayData
and phenoData
invalid class “ExpressionSet” object: 2: sampleNames differ between phenoData
and protocolData
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PhD Student
University of Sydney
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___
I am using the latest release version. I understand your recommendation about
colData and will use it.
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und a previous question that remains unanswered.
https://stat.ethz.ch/pipermail/bioc-devel/2007-March/001001.html
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needs to be changed ?
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