[Rd] Part of fastpass in 'sort.list' can make sorting unstable

In the code of functions 'order' and 'sort.list' in R 3.5.0 alpha (in https://svn.r-project.org/R/branches/R-3-5-branch/src/library/base/R/sort.R), in "fastpass, take advantage of ALTREP metadata", there is "try the reverse since that's easy too...". If it succeeds, ties are reordered,

Re: [Rd] Part of fastpass in 'sort.list' can make sorting unstable

Thanks for catching this. This is easy to take out without touching the rest of the machinery. It also wouldn't be too hard to write a still-faster-but-not-quite-as-much-path which correctly reverses the sortedness of a sorted vector that includes ties. My suspicion, without being the one who will

Re: [Rd] potential file.copy() or documentation bug when copy.date = TRUE

Thanks for the report, fixed in R-devel. Best, Tomas On 04/05/2018 05:01 PM, Gábor Csárdi wrote: This is a recent R-devel. file.copy() is not vectorized if multiple destinations succeed: cat("foo1\n", file = "foo1") cat("foo2\n", file = "foo2") unlink(c("copy1", "copy2"), recursive = TRUE)

[Rd] survival updates and testing

I've run the latest version of survival through the test suites of 486 of the 565 packages that depend on it (Depends, Imports, LinkingTo, Suggests), and have a couple small issues that I'm taking to other authors about. The exercise turned up a half dozen real errors in my package.  I plan to

[R-pkg-devel] GPL + other licence

Dear all, I'd appreciate help with a licence conundrum I have with the geometry package (https://davidcsterratt.github.io/geometry/) that I maintain. The geometry package contains some functions (e.g. convhulln(), delaunayn()) that wrap the Qhull library (http://www.qhull.org), which has its

Re: [R-pkg-devel] Cannot submit package due to misspell note

FWIW, the first (many) times I read the warning "The Title field should be in title case, current version then in title case:" I couldn't parse it at all. Brevity is wonderful, but I might submit a patch/wish for this warning to be changed to (something like): "The Title field should be in

Re: [R-pkg-devel] Cannot submit package due to misspell note

Thanks a lot !!! I've been blind, I've read this message about twenty times and haven't noticed that letter v after - sign is not capitalized so my thoughts went to spelling issues. In fact after capitalizing this letter package has passed pre-tests. (Even without Bervin's solution which I

Re: [R-pkg-devel] Cannot submit package due to misspell note

On 06/04/2018 3:14 PM, Ben Bolker wrote: FWIW, the first (many) times I read the warning "The Title field should be in title case, current version then in title case:" I couldn't parse it at all. Brevity is wonderful, but I might submit a patch/wish for this warning to be changed to

Re: [R-pkg-devel] Cannot submit package due to misspell note

Since this message appears also in R CMD check locally, maybe change in Duncan's text 'submission' to something like The Title field should be in title case! Your title is blah blah blah This is not in title case, which would be Blah, Blah, Blah" - Georgi Boshnakov

Re: [R-pkg-devel] Cannot submit package due to misspell note

On 06/04/2018 7:29 PM, Georgi Boshnakov wrote: Since this message appears also in R CMD check locally, maybe change in Duncan's text 'submission' to something like The Title field should be in title case! Your title is blah blah blah This is not in title case, which would be

Re: [R-pkg-devel] Cannot submit package due to misspell note

In fact, the reason for rejection is just after the 'misspelled' words: >The Title field should be in title case, current version then in title case: '>Searching for Optimal MDS Procedure for Metric and Interval-valued Symbolic Data' >'Searching for Optimal MDS Procedure for Metric and

Re: [R-pkg-devel] Cannot submit package due to misspell note

Ok, my fault sorry: This is the original message for current submission from prof. Ligges --- Dear maintainer, package mdsOpt_0.3-1.tar.gz does not pass the

Re: [Bioc-devel] Update of miRBaseVersions.db annotation package

I'd be happy to update your annotation package. The package, however, appears to have multiple warnings and errors occurring on check and BiocCheck. There appear to be some documentation issues and a test failure in check. For BiocCheck, just be sure the BiocViews you are using are from one

[Bioc-devel] Permission denied to Bioconductor repository

Hi, I'm the TarSeqQC package maintainer. I'have recently sent my new public key through the google form, I have received an e-mail confirming that my new key was added but I can't access the Bioconductor repository. git clone g...@git.bioconductor.org:packages/TarSeqQC Cloning into

[Bioc-devel] BioC 3.7 Windows check warning "file link zz in package yy does not exist "

Dear All, Two packages I maintain are showing, in Windows, a warning during check with messages like Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp21WlQD/R.INSTALL23343f935731/OncoSimulR/man/oncoSimulIndiv.Rd:570: file link 'mclapply' in package 'parallel' does not exist and so has

Re: [Bioc-devel] BioC 3.7 Windows check warning "file link zz in package yy does not exist "

I have recently faced a similar warning. This is when a link to a help page of another package is broken (there is not such help page). Although those could be false positives: mclapply help page does exists in parallel package. as.MAList does exists in devel limma HTH On 6 April 2018 at 16:35,

Re: [Bioc-devel] BioC 3.7 Windows check warning "file link zz in package yy does not exist "

Dear Lluis and Vincent, Thanks for confirming this in other packages. In the two examples shown, these must be false positives, as the links exist. But also the fact that the warnings only appear in Windows suggests a false positive: I do not understand how this warning would not be triggered in

Re: [Bioc-devel] BioC 3.7 Windows check warning "file link zz in package yy does not exist "

ive seen this too apropos bigrquery on windows On Fri, Apr 6, 2018 at 10:22 AM Ramon Diaz-Uriarte wrote: > > Dear All, > > Two packages I maintain are showing, in Windows, a warning during check > with messages like > > Rd warning: >

[Bioc-devel] Bioc 3.7 build failed for GenvisR package

Hi All, I've noticed GenVisR is failing to build the vignette on windows for bioc-devel. the error seems to be: "Invalid Parameter - /figure-html" This seems like it may be related to the use of BiocStyle given this post on stackoverflow:

Re: [Bioc-devel] BioC 3.7 Windows check warning "file link zz in package yy does not exist "

On 04/06/2018 10:44 AM, Lluís Revilla wrote: I have recently faced a similar warning. This is when a link to a help page of another package is broken (there is not such help page). Although those could be false positives: mclapply help page does exists in parallel package. as.MAList does