Re: [R-pkg-devel] check cross-references error: Non-file package-anchored link(s)

2020-07-02 Thread William Dunlap
On Linux you can use 'ltrace' to get a list of all the environment variables that R looks up. E.g., do the following in 'script' so all the output is stored in a file ('typescript') and later look around in it for the getenv calls. $ R-devel --debugger=ltrace --debugger-args="-f -e getenv" ...

Re: [R-pkg-devel] check cross-references error: Non-file package-anchored link(s)

2020-07-02 Thread Duncan Murdoch
On 02/07/2020 10:41 a.m., Dr. Jens Oehlschlägel wrote: Thank you for the advice Duncan, But let's not get carried away here: we are talking about a *warning* that only arises if two packages are checked together that are never meant to be installed together. The new packages contain weeks of

Re: [R-pkg-devel] check cross-references error: Non-file package-anchored link(s)

2020-07-02 Thread Dr . Jens Oehlschlägel
Thank you for the advice Duncan, But let's not get carried away here: we are talking about a *warning* that only arises if two packages are checked together that are never meant to be installed together. The new packages contain weeks of improvement-work, and I am not going to add

Re: [R-pkg-devel] check cross-references error: Non-file package-anchored link(s)

2020-07-02 Thread Jan Gorecki
Thank you Gabor On Thu, Jul 2, 2020 at 10:20 AM Gábor Csárdi wrote: > > You can set the _R_CHECK_XREFS_MIND_SUSPECT_ANCHORS_=true env var and > use R-devel. > > Alternatively, and you don't need R-devel for this, you can run R CMD > --html INSTALL on your package, and then look for messages that

Re: [R-pkg-devel] check cross-references error: Non-file package-anchored link(s)

2020-07-02 Thread Duncan Murdoch
On 02/07/2020 7:49 a.m., Dr. Jens Oehlschlägel wrote: Duncan, One way is to make bit depend on a particular version of ff. That may cause a deadlock if both are being updated at once, but I think CRAN should be able to deal with it if they are informed of the issue. Exactly that I have

Re: [R-pkg-devel] check cross-references error: Non-file package-anchored link(s)

2020-07-02 Thread Dr . Jens Oehlschlägel
Duncan, > One way is to make bit depend on a particular version of ff. That may > cause a deadlock if both are being updated at once, but I think CRAN > should be able to deal with it if they are informed of the issue. Exactly that I have done: I submitted all three packages bit/bit64/ff in

Re: [R-pkg-devel] check cross-references error: Non-file package-anchored link(s)

2020-07-02 Thread Duncan Murdoch
There are a few ways to deal with this, but waiting for ff to be updated is probably easiest. However, maybe ff can't be updated until bit is updated. Here are some possibilities: One way is to make bit depend on a particular version of ff. That may cause a deadlock if both are being

Re: [R-pkg-devel] check cross-references error: Non-file package-anchored link(s)

2020-07-02 Thread Gábor Csárdi
Yes, this is one consequence of the newly enforced check. Now you can choose which version of the ff package you want to be compatible with. In the GH version a manual file was renamed and this is now a breaking change, so you cannot be compatible with both. Gabor On Thu, Jul 2, 2020 at 11:47 AM

Re: [R-pkg-devel] check cross-references error: Non-file package-anchored link(s)

2020-07-02 Thread Dr . Jens Oehlschlägel
Thanks Gabor and Duncan, > It's actually in ff/man/clone.rd, not clone.ff.rd. There is no > ff/man/clone.ff.rd file. but there *is* clone.ff.rd in the >= 4.0.0 versions of the packages bit/bit64/ff. Hence the check warning is a false alarm resulting from checking bit 4.0.2

Re: [R-pkg-devel] check cross-references error: Non-file package-anchored link(s)

2020-07-02 Thread Gábor Csárdi
You can set the _R_CHECK_XREFS_MIND_SUSPECT_ANCHORS_=true env var and use R-devel. Alternatively, and you don't need R-devel for this, you can run R CMD --html INSTALL on your package, and then look for messages that contain "treated as a topic", e.g. curl_fds

Re: [R-pkg-devel] check cross-references error: Non-file package-anchored link(s)

2020-07-02 Thread Jan Gorecki
Hi, What is the recommended way to test for those issues locally? If it is tested during cran submission, then seems reasonable to be enabled just by --as-cran switch. Is it? Thanks On Wed 17 Jun, 2020, 12:32 AM Wayne Oldford, wrote: > Thank you! > > -Original Message- > From: Gábor