[Bioc-devel] skipped, ERROR

2020-10-29 Thread ????
Dear Devel team�� My package encountered an error "ERROR: this R is version 4.0.3, package 'RLassoCox' requires R = 4.1". I don't know if it is because I added Depends: R (= 4.1) in the DESCRIPTION file as suggested by BiocCheck. How to fix this error? === R CMD

Re: [Rd] [External] Something is wrong with the unserialize function

2020-10-29 Thread Jiefei Wang
Thanks for the fix! I will wait for the update and try it again. Best, Jiefei On Fri, Oct 30, 2020 at 1:42 AM wrote: > I found that also; fixed in r79386 in the trunk. Will port to R-patched > shortly. > > Best, > > luke > > On Thu, 29 Oct 2020, Martin Morgan wrote: > > > This > > > > Index:

Re: [Bioc-devel] Possible DNS issue?

2020-10-29 Thread Damian Szklarczyk
Dear Herve, Thank you for the feedback. The IP is indeed correct. I’ll write if it again starts being recurring issue on one platform. Thanks and all the best, Damian. -- Damian Szklarczyk, PhD Bioinformatics / Systems Biology Group SIB | Swiss Institute of Bioinformatics UZH, Institute of

Re: [Bioc-devel] Possible DNS issue?

2020-10-29 Thread Pages, Herve
Hi Damian, Looks like today the problem went away and that STRINGdb 2.2.0 is now available on all platforms. We should still keep an eye on this for a few more days though so we get an idea of whether this is intermittent or gone for good. Cheers, H. On 10/28/20 23:45, Pages, Herve wrote: >

Re: [R-pkg-devel] checking PDF version of manual without hyperrefs or index ... ERROR

2020-10-29 Thread Georgi Boshnakov
This seems to be the code for "small latin capital fl". Such characters often occur when copying text from external programs (similar to the familiar problem with fancy quotes). If that is the case, Just changing the offending symbol to the two letters 'f' and 'l' should suffice. Georgi

Re: [Rd] [External] Something is wrong with the unserialize function

2020-10-29 Thread luke-tierney
I found that also; fixed in r79386 in the trunk. Will port to R-patched shortly. Best, luke On Thu, 29 Oct 2020, Martin Morgan wrote: This Index: src/main/altrep.c === --- src/main/altrep.c (revision 79385) +++

Re: [Rd] [External] Something is wrong with the unserialize function

2020-10-29 Thread Martin Morgan
This Index: src/main/altrep.c === --- src/main/altrep.c (revision 79385) +++ src/main/altrep.c (working copy) @@ -275,10 +275,11 @@ SEXP psym = ALTREP_SERIALIZED_CLASS_PKGSYM(info); SEXP class = LookupClass(csym,

Re: [Rd] [External] Something is wrong with the unserialize function

2020-10-29 Thread luke-tierney
Thanks for the report. Will look into it when I get a chance unless someone else gets there first. A simpler reprex: ## create and serialize a memmory-mapped file object filePath <- "x.dat" con <- file(filePath, "wrb") writeBin(rep(0.0,10),con) close(con) library(simplemmap) x <-

Re: [R-pkg-devel] checking PDF version of manual without hyperrefs or index ... ERROR

2020-10-29 Thread Duncan Murdoch
I don't know the best solution, but one workaround would be to replace "fl" in your Rd files with "fl". Duncan Murdoch On 29/10/2020 10:34 a.m., Anthony Hammond wrote: Hello, I'm attempting to upload a package to CRAN and although it passes the R CMD checks that I run, it doesn't pass the CRAN

[R-pkg-devel] checking PDF version of manual without hyperrefs or index ... ERROR

2020-10-29 Thread Anthony Hammond
Hello, I'm attempting to upload a package to CRAN and although it passes the R CMD checks that I run, it doesn't pass the CRAN check and the response I get is pasted below. I've looked online and found numerous solutions; some made no sense to me & others didn't work. I tried downloading and

[Rd] Something is wrong with the unserialize function

2020-10-29 Thread Jiefei Wang
Hi all, I am not able to export an ALTREP object when `gctorture` is on in the worker. The package simplemmap can be used to reproduce the problem. See the example below ``` ## Create a temporary file filePath <- tempfile() con <- file(filePath, "wrb") writeBin(rep(0.0,10),con) close(con)

Re: [Bioc-devel] Bioconductor Git Credentials

2020-10-29 Thread Turaga, Nitesh
Hi, It seems you’ve never activated your account. Please try https://git.bioconductor.org/BiocCredentials/account_activation first and then add an SSH key. Nitesh On Oct 28, 2020, at 2:48 PM, Wubing Zhang mailto:watson5bzh...@gmail.com>> wrote: Hi Nitesh, As you suggested, I tried the

Re: [Bioc-devel] Possible DNS issue?

2020-10-29 Thread Pages, Herve
Hi Damian, stringdb-static.org resolves to 185.111.60.15 on malbec1 like on nebbiolo1 and merida1. Also the following code runs with no problem in an interactive session on malbec1: > tmp <- tempfile() >