Dear R-devel,
I did a systematic comparison of write.csv with similar functions, and
observed two asymptotic inefficiencies that could be improved.
1. write.csv is quadratic time (N^2) in the number of columns N.
Can write.csv be improved to use a linear time algorithm, so it can handle
CSV files
Dear R-devel,
A number of people have observed anecdotally that read.csv is slow for
large number of columns, for example:
https://stackoverflow.com/questions/7327851/read-csv-is-extremely-slow-in-reading-csv-files-with-large-numbers-of-columns
I did a systematic comparison of read.csv with
Some more not-necessarily helpful observations. You can get verbose output with
curl::curl_fetch_disk(url, tempfile(), handle = new_handle(verbose = TRUE))
and on the command line with curl -v -L �
Also, it seems that other BAM files can be downloaded, e.g., from
eh[["EH3502"]] (also
good catch, but really enigmatic, BAI files work, but BAM don't:
dat <-
read.csv("https://raw.githubusercontent.com/functionalgenomics/gDNAinRNAseqData/devel/inst/extdata/metadata_LiYu22subsetBAMfiles.csv;)
rdatapath <- strsplit(dat$RDataPath, ":")
bamfiles <- unlist(rdatapath)[seq(1, 18, 2)]
Not really helpful but this could be simplified a bit by removing the redirect
from experiment hub, and the layer from httr to curl, so
url =
"https://functionalgenomics.upf.edu/experimenthub/gdnainrnaseqdata/LiYu22subsetBAMfiles/s32gDNA0.bam;
curl::curl_fetch_disk(url, tempfile())
Error in
Hi developers,
A couple of days ago I moved the rowSums, colSums, rowMeans, colMeans generics
from *BiocGenerics* to *MatrixGenerics*, and this seems to break a lot of
packages on today's build report for devel, sorry for that. I didn't have
time to look closely at the damage caused by this
hi,
we recently added a few new ExperimentHub resources, consisting of BAM
files and their corresponding BAI files and hosted in my own server.
while it seems that they are accessible, they cannot be downloaded
through the ExperimentHub API. the minimum example reproducing the
problem is this
Please remember, The Bioconductor 3.16 branch will be frozen Monday April
10th. After that date, no changes will be permitted ever on that branch.
The deadline for devel Bioconductor 3.17 for packages to pass R CMD build and R
CMD check is April 21th. While you will still be able to make
> Alexey Sergushichev writes:
Thanks. This is now fixed for the upcoming 4.3.0 release.
Best
-k
> HI,
> I've noticed what I think is an incorrect behavior of stats::psmirnov
> function and consequently of ks.test when run in an exact mode.
> For example:
> psmirnov(1, sizes=c(50, 50),
