Re: [Rd] Producing different text formats in R
Lluís, You sent a 8+ mb file to a (I presume) 1000+ subscribers of this list. That is not generally a good idea, and I am surprised this got past the mailman software which (usually) filters at 100k (and for a reason). In the future, please consider uploading the file somewhere (GitHub gists are easy) and send a link. We also often talk about "minimally complete verifiable examples" (mcve) and the minimal is there for a reason. Thanks for your consideration, Dirk -- http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Underscores in package names
On 08/08/2019 10:31 a.m., Jim Hester wrote: Are there technical reasons that package names cannot be snake case? This seems to be enforced by `.standard_regexps()$valid_package_name` which currently returns "[[:alpha:]][[:alnum:].]*[[:alnum:]]" Is there any technical reason this couldn't be altered to accept `_` as well, e.g. "[[:alpha:]][[:alnum:]._]*[[:alnum:]]" I realize that historically `_` has not always been valid in variable names, but this has now been acceptable for 15+ years (since R 1.9.0 I believe). Might we also allow underscores for package names? The tarball names separate the package name from the version number using an underscore. There is code that is written to assume there is at most one underscore, e.g. .check_package_CRAN_incoming in src/library/tools/R/QC.r. That code could be changed, but so could the proposed package name... Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Underscores in package names
Are there technical reasons that package names cannot be snake case? This seems to be enforced by `.standard_regexps()$valid_package_name` which currently returns "[[:alpha:]][[:alnum:].]*[[:alnum:]]" Is there any technical reason this couldn't be altered to accept `_` as well, e.g. "[[:alpha:]][[:alnum:]._]*[[:alnum:]]" I realize that historically `_` has not always been valid in variable names, but this has now been acceptable for 15+ years (since R 1.9.0 I believe). Might we also allow underscores for package names? Jim __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Bioc-devel] Changing the Bioconductor package maintainer
Hi, You should be able activate your BiocCredentials account with the email address chuklina.jel...@gmail.com. Once you activate, you need to add your SSH keys. You should be able to then sync your package with the Github changes. Best, Nitesh > On Aug 8, 2019, at 8:16 AM, Jelena Chuklina wrote: > > Dear Bioconductor team, > > I’ve stepped in as a “proBatch” package maintainer. Could you please allow me > to get BiocCredentials, so that I can sync our GitHub changes with > BioConductor? > > Best regards, > Jelena Čuklina > > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Canceled event: Biocondutor Developers Forum @ Thu Aug 15, 2019 12pm - 1pm (EDT) (bioc-devel@r-project.org)
This event has been canceled. Title: [Bioc-devel] Biocondutor Developers Forum Dear all, I am excited to announce a new initiative within the Bioconductor project - the Bioconductor Developers' Forum. This monthly teleconference is intended as a platform for Bioconductor developers to describe existing software infrastructure to other members of the BioC community, to present plans for future developments, and discuss changes that may impact other developers or software tools within the Bioconductor. The intended audience is anyone interested in software development and infrastructure, whether you're a member of the BioC core team with responsibility for multiple packages, or you're just getting started with creating a Bioconductor package. Our first meeting will take place on Thursday 15th August at 09:00 PDT/ 12:00 EDT / 18:00 CEST using BlueJeans and can be joined via: https://bluejeans.com/136043474?src=join_info (Meeting ID: 136 043 474) More details on the... When: Thu Aug 15, 2019 12pm – 1pm Eastern Time - New York Calendar: bioc-devel@r-project.org Who: * seand...@gmail.com - organizer * peter.hic...@gmail.com * grimbo...@gmail.com * bioc-devel@r-project.org Invitation from Google Calendar: https://www.google.com/calendar/ You are receiving this courtesy email at the account bioc-devel@r-project.org because you are an attendee of this event. To stop receiving future updates for this event, decline this event. Alternatively you can sign up for a Google account at https://www.google.com/calendar/ and control your notification settings for your entire calendar. Forwarding this invitation could allow any recipient to send a response to the organizer and be added to the guest list, or invite others regardless of their own invitation status, or to modify your RSVP. Learn more at https://support.google.com/calendar/answer/37135#forwarding ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Invitation: Biocondutor Developers Forum @ Thu Aug 15, 2019 12pm - 1pm (EDT) (bioc-devel@r-project.org)
You have been invited to the following event. Title: [Bioc-devel] Biocondutor Developers Forum Dear all, I am excited to announce a new initiative within the Bioconductor project - the Bioconductor Developers' Forum. This monthly teleconference is intended as a platform for Bioconductor developers to describe existing software infrastructure to other members of the BioC community, to present plans for future developments, and discuss changes that may impact other developers or software tools within the Bioconductor. The intended audience is anyone interested in software development and infrastructure, whether you're a member of the BioC core team with responsibility for multiple packages, or you're just getting started with creating a Bioconductor package. Our first meeting will take place on Thursday 15th August at 09:00 PDT/ 12:00 EDT / 18:00 CEST using BlueJeans and can be joined via: https://bluejeans.com/136043474?src=join_info (Meeting ID: 136 043 474) More details on the... When: Thu Aug 15, 2019 12pm – 1pm Eastern Time - New York Calendar: bioc-devel@r-project.org Who: * seand...@gmail.com - organizer * peter.hic...@gmail.com * grimbo...@gmail.com * bioc-devel@r-project.org Event details: https://www.google.com/calendar/event?action=VIEW=NWtjYWFjN2IxZXRrYms0Mm04YTFoOTlqajkgYmlvYy1kZXZlbEByLXByb2plY3Qub3Jn=MTgjc2VhbmRhdmlAZ21haWwuY29tMjFhMjA5YjUzNzczZTVlZDAxNzhkZGJjYjA2Y2VkODBjODg4MTk5NA=America%2FNew_York=en=0 Invitation from Google Calendar: https://www.google.com/calendar/ You are receiving this courtesy email at the account bioc-devel@r-project.org because you are an attendee of this event. To stop receiving future updates for this event, decline this event. Alternatively you can sign up for a Google account at https://www.google.com/calendar/ and control your notification settings for your entire calendar. Forwarding this invitation could allow any recipient to send a response to the organizer and be added to the guest list, or invite others regardless of their own invitation status, or to modify your RSVP. Learn more at https://support.google.com/calendar/answer/37135#forwarding ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Rd] Producing different text formats in R
> "Lluís" ==writes:
Lluís> Dear all,
Lluís> I am facing a strange problem with text files formats.
Lluís> I am currently using a C++ code named voro++
(http://math.lbl.gov/voro++/). This code accepts text files with four columns:
Lluís>
Lluís> where id is an identification number and x,y,z are the coordinates
of a point in a 3D space.
Lluís> The input file, name it myfile_cpp.txt, is generated by another C++
code written by myself (named quadscheme.cpp). So far, these calculations
involve no R code and it works just fine.
Lluís> However, now I am trying to replace my C++ code quadscheme.cpp by a
R function. The four columns (id,x,y,z) are produced in a matrix or Data Frame
and then saved in a file myfile_r.txt using write.table(). For example using
the following function:
Lluís> quadscheme <- function(window, ntile) {
Lluís> # Creates a grid of points in a 3D orthohedron.
Lluís> # First point lies at the (mix,miny,miz) corner of the volume and
the last one at (maxx,maxy,maxz)
Lluís> # window: vector. Contains the minimum and maximum values of a 3D
orthohedron
Lluís> # window <- c(minx, maxx, miny, maxy, minz, maxz)
Lluís> # ntile: vector. Number of points per dimension minus one. We
manually add a extra row of points per dimension
Lluís> # ntile <- c(nstepx, nstepy, nstepz)
Lluís> M <- prod(ntile+1)
Lluís> mat <- matrix(NA,M,4)
Lluís> mat[,1] <- 1:M # id column
Lluís> # step length per dimension
Lluís> hi <- (window[2] - window[1])/ntile[1]
Lluís> hj <- (window[4] - window[3])/ntile[2]
Lluís> hk <- (window[6] - window[5])/ntile[3]
Lluís> c <- 1
Lluís> for(i in 0:ntile[1]) {
Lluís> x <- i*hi + window[1]
Lluís> for(j in 0:ntile[2]) {
Lluís> y <- hj*j + window[3]
Lluís> for(k in 0:ntile[3]) {
Lluís> z <- k*hk + window[5]
Lluís> mat[c,2:4] <- c(x,y,z) # Add a new point to the grid
Lluís> c <- c + 1
Lluís> }
Lluís> }
Lluís> }
Lluís> write.table(mat, file="myfile_r.txt", row.names=FALSE,
col.names=FALSE)
Lluís> }
Lluís> And then calling:
>> window <- c(18, 43, 171, 196, 95, 102)
>> ntile <- c(100,100,28)
>> quadscheme(window, ntile)
Lluís> I see no difference between both myfile_*.txt files,
Lluís> one is created with C++ and the other one with
Lluís> R. However, function voro++ do not accept the later one
Lluís> (created with R and saved with write.table). I've also
Lluís> noted that voro++ usually accepts R generated files
Lluís> when they are small enough, but it accepts all C++
Lluís> generated files, regardless the size.
Lluís> I know this is more a C++ than a R question, but may be
Lluís> you can help me as well. I suspect that even if both
Lluís> files are *.txt they have some differences that I
Lluís> cannot see. Is there any way in R to produce different
Lluís> kinds of txt files? Like binary instead of text files?
Lluís> Could this be the problem?
Lluís> I attach two identical files, one produced by C++
Lluís> (myfile_cpp.txt) and another one by the previous R
Lluís> function (myfile_r.txt). I attach as well the C++ code
Lluís> used to generate myfile_cpp.txt.
Lluís> Thank you in advance,
Lluís> Lluís Hurtado-Gil
In your R file, scientific notation is used:
R:
9 26.5 174.5 96.5
1e+05 26.5 174.5 96.75
11 26.5 174.5 97
cpp:
9 26.5 174.5 96.5
10 26.5 174.5 96.75
11 26.5 174.5 97
Try setting options(scipen = 20) before you write the
file in R.
--
Enrico Schumann
Lucerne, Switzerland
http://enricoschumann.net
__
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[Bioc-devel] Changing the Bioconductor package maintainer
Dear Bioconductor team, I’ve stepped in as a “proBatch” package maintainer. Could you please allow me to get BiocCredentials, so that I can sync our GitHub changes with BioConductor? Best regards, Jelena Čuklina [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Biocondutor Developers Forum
Great initiative, Mike! Could these meetings please be recorded? These will be in the middle of the night in my time zone and I'm sure others would appreciate being able to view them if they can't make the call. rOpenSci do something similar with their community calls ( https://ropensci.org/commcalls/). Cheers, Pete On Thu., 8 Aug. 2019, 6:31 pm Mike Smith, wrote: > Dear all, > > I am excited to announce a new initiative within the Bioconductor project - > the Bioconductor Developers' Forum. This monthly teleconference is > intended as a platform for Bioconductor developers to describe existing > software infrastructure to other members of the BioC community, to present > plans for future developments, and discuss changes that may impact other > developers or software tools within the Bioconductor. > > The intended audience is anyone interested in software development and > infrastructure, whether you're a member of the BioC core team with > responsibility for multiple packages, or you're just getting started with > creating a Bioconductor package. > > Our first meeting will take place on Thursday 15th August at 09:00 PDT/ > 12:00 EDT / 18:00 CEST using BlueJeans and can be joined via: > > https://bluejeans.com/136043474?src=join_info (Meeting ID: 136 043 474) > > More details on the intentions for this initiative, including a list of > proposed topics, can found at: > > > https://www.huber.embl.de/users/msmith/Bioconductor-Developers-Forum-Proposal.pdf > > > The agenda for the first meeting is still open, so if you have a proposal > or a particular topic you wish to prioritise please reach out to me. > > Best wishes, > > Mike > > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Biocondutor Developers Forum
Dear all, I am excited to announce a new initiative within the Bioconductor project - the Bioconductor Developers' Forum. This monthly teleconference is intended as a platform for Bioconductor developers to describe existing software infrastructure to other members of the BioC community, to present plans for future developments, and discuss changes that may impact other developers or software tools within the Bioconductor. The intended audience is anyone interested in software development and infrastructure, whether you're a member of the BioC core team with responsibility for multiple packages, or you're just getting started with creating a Bioconductor package. Our first meeting will take place on Thursday 15th August at 09:00 PDT/ 12:00 EDT / 18:00 CEST using BlueJeans and can be joined via: https://bluejeans.com/136043474?src=join_info (Meeting ID: 136 043 474) More details on the intentions for this initiative, including a list of proposed topics, can found at: https://www.huber.embl.de/users/msmith/Bioconductor-Developers-Forum-Proposal.pdf The agenda for the first meeting is still open, so if you have a proposal or a particular topic you wish to prioritise please reach out to me. Best wishes, Mike [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
