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R-lava: drop explicit test dependencies due to possible CI failures #20736

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merged 1 commit into from
Oct 9, 2023

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barracuda156
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Description

Nothing will be added here.

(This PR does not depend on recommended packages update one. It can be merged once CI pass.)

Type(s)
  • bugfix
  • enhancement
  • security fix
Tested on

macOS 10.6
Xcode 3.2

Verification

Have you

  • followed our Commit Message Guidelines?
  • squashed and minimized your commits?
  • checked that there aren't other open pull requests for the same change?
  • referenced existing tickets on Trac with full URL?
  • checked your Portfile with port lint --nitpick?
  • tried existing tests with sudo port test?
  • tried a full install with sudo port -vst install?
  • tested basic functionality of all binary files?
  • checked that the Portfile's most important variants haven't been broken?

@barracuda156
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@cjones051073 Hmm, we keep getting failures here for dependencies (unchanged ones, which were fine earlier). Not sure what goes wrong, since logs do not show what exactly fails.

@barracuda156
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barracuda156 commented Oct 6, 2023

@cjones051073 So it appears that the whole thing is still pretty broken for whatever reason.

I guess, let me try allowing gcc13 (without revbumps of ports). At least we may know whether it works or not.

@barracuda156 barracuda156 marked this pull request as draft October 6, 2023 09:17
@cjones051073
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Everything looks fine to me locally.

@cjones051073
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Isn't the problem here the number of R updates you are squeezing into one PR, and then the timeout is hit ?

Please try reducing the number of updates to just one or two, and see what then happens.

@cjones051073
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cjones051073 commented Oct 6, 2023

One thing you should bear in mind is the default variants on all R ports have now changed, from +gfortran to +gcc12. This means all R ports will automatically get rebuilt as binary installs for the new default variants do not exist.

I think it would be useful to manually trigger rebuilds on the buildbots (I can do this without a rev bump) hjust to get all the ports built with the new variants.

@barracuda156
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@cjones051073 Everything worked fine for me locally too, but…

Anyway, I will try splitting this. Maybe heavier that usual dependencies. (Usually 27–28 commits per R-related PR are all fine.)

@cjones051073
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@cjones051073 Everything worked fine for me locally too, but…

Anyway, I will try splitting this. Maybe heavier that usual dependencies. (Usually 27–28 commits per R-related PR are all fine.)

I suspect the issue is all the dependencies currently need to be rebuilt on the ci, due to the default variant change, and this is just pushing things over the timeout limit.

@cjones051073
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I've triggered a rebuild of all R-<X> ports on the builders. will take a little time to go through so suggest you wait until that is done before trying here again with any ci tests.

@barracuda156
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@cjones051073 Thank you very much! Yeah, I will wait for a while with pushing an update.

@cjones051073
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@cjones051073 Thank you very much! Yeah, I will wait for a while with pushing an update.

There are quite a number of ports to build, 700 odd, but each seems reasonably fast so hopefully will not take too long, perhaps a day or two, for each builder to work through the list.

@cjones051073
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https://build.macports.org/waterfall

progress can be tracked there

@cjones051073
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Interesting to note though we have ended up doing precisely what pegging the ports to gcc12 was supposed to prevent, having to rebuild them all via a rev-bump.

At least, after this the R ecosystem will have control itself of which gcc/clang it wishes to use, and won't just automatically migrate when a new compiler is released.

Side note, I have seen a few R ports (and R itself) checking for recent C++ standard support. c++20 and c++23 even. Clang 15, and gcc 12 not being the most recent releases, do not have great support for these standards so I do think you might want to as a second step do a mass migration to updated versions, clang-17 and gcc-13..

@barracuda156
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@cjones051073 For gcc13 all should be good, I believe: there were no drastic changes, AFAIK. With clang17 someone has to verify it works; I recall we have initially blacklisted clang16 because there were build failures with it on CI.
Otherwise if we do not revbump anything for compiler change, testing will happen with updates’ PR, but we won’t be sure unupdated ports still build.

@cjones051073
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cjones051073 commented Oct 6, 2023

@cjones051073 For gcc13 all should be good, I believe: there were no drastic changes, AFAIK. With clang17 someone has to verify it works; I recall we have initially blacklisted clang16 because there were build failures with it on CI. Otherwise if we do not revbump anything for compiler change, testing will happen with updates’ PR, but we won’t be sure unupdated ports still build.

According to

https://trac.macports.org/ticket/67144

which is the ticket referenced where the clang blacklisting is done, the reason for it was not because the builds would fail with the newer compiler, but because of the issue of builds failing to find the right clang compiler, because of a mis-match between what R was built with and what the R-X port was trying to use.

This therefore does not mean if you switch to a newer clang, and then rev-bump everything, R and all the R-X ports they wouldn't work just fine.

@barracuda156
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barracuda156 commented Oct 6, 2023

@cjones051073 Great. Then we can move to a newer clang and newer gcc at once.

@i0ntempest What do you think about switching to clang17? My concern is gcc, and it is desirable not to require to build an extra one (which is currently the case), but it makes sense to revbump ports once for both compilers together. (Not it this PR, of course.)

@barracuda156
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Still same silly failures: notice, the message itself is off – dependencies do install (OK status for all), but then reported as failed:

Cleaning up between ports
[16079](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16114)
Installing dependencies for R-geostan
[16080](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16115)
  Installing 91 dependencies of R-geostan:
[16081](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16116)
  R-BH 
[16082](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16117)
  R-Rcpp 
[16083](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16118)
  R-RcppEigen +gcc12
[16084](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16119)
  R-RcppParallel 
[16085](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16120)
  R-StanHeaders 
[16086](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16121)
  R-cli 
[16087](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16122)
  R-glue 
[16088](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16123)
  R-rlang 
[16089](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16124)
  R-lifecycle 
[16090](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16125)
  R-gtable 
[16091](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16126)
  R-isoband 
[16092](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16127)
  R-R6 
[16093](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16128)
  R-RColorBrewer 
[16094](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16129)
  R-farver 
[16095](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16130)
  R-labeling 
[16096](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16131)
  R-colorspace 
[16097](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16132)
  R-munsell 
[16098](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16133)
  R-viridisLite 
[16099](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16134)
  R-scales 
[16100](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16135)
  R-fansi 
[16101](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16136)
  R-magrittr 
[16102](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16137)
  R-utf8 
[16103](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16138)
  R-vctrs 
[16104](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16139)
  R-pillar 
[16105](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16140)
  R-pkgconfig 
[16106](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16141)
  R-tibble 
[16107](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16142)
  R-withr 
[16108](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16143)
  R-ggplot2 
[16109](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16144)
  R-gridExtra 
[16110](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16145)
  R-jsonlite 
[16111](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16146)
  R-QuickJSR 
[16112](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16147)
  R-inline 
[16113](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16148)
  R-backports 
[16114](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16149)
  R-checkmate 
[16115](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16150)
  R-matrixStats 
[16116](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16151)
  R-loo 
[16117](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16152)
  R-ps 
[16118](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16153)
  R-processx 
[16119](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16154)
  R-callr 
[16120](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16155)
  R-crayon 
[16121](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16156)
  R-rprojroot 
[16122](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16157)
  R-desc 
[16123](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16158)
  R-prettyunits 
[16124](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16159)
  R-pkgbuild 
[16125](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16160)
  R-rstan 
[16126](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16161)
  R-rstantools 
[16127](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16162)
  R-DBI 
[16128](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16163)
  R-proxy 
[16129](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16164)
  R-e1071 
[16130](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16165)
  R-classInt +gcc12
[16131](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16166)
  R-wk 
[16132](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16167)
  R-s2 
[16133](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16168)
  cunit 
[16134](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16169)
  udunits2 
[16135](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16170)
  R-units 
[16136](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16171)
  lzo2 
[16137](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16172)
  snappy 
[16138](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16173)
  blosc 
[16139](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16174)
  brunsli 
[16140](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16175)
  charls 
[16141](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16176)
  giflib 
[16142](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16177)
  libcomerr 
[16143](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16178)
  lmdb 
[16144](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16179)
  kerberos5 
[16145](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16180)
  libxslt 
[16146](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16181)
  postgresql_select 
[16147](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16182)
  postgresql15 
[16148](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16183)
  proj9 +tiff
[16149](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16184)
  qhull 
[16150](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16185)
  minizip 
[16151](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16186)
  freexl 
[16152](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16187)
  geos 
[16153](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16188)
  librttopo 
[16154](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16189)
  spatialite +proj9
[16155](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16190)
  webp 
[16156](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16191)
  gdal +postgresql15+proj9
[16157](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16192)
  proj 
[16158](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16193)
  R-sf 
[16159](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16194)
  R-signs 
[16160](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16195)
  gcc12-libcxx +clang14
[16161](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16196)
  gcc_select 
[16162](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16197)
  gmp 
[16163](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16198)
  isl 
[16164](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16199)
  mpfr 
[16165](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16200)
  libmpc 
[16166](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16201)
  gcc12 +stdlib_flag
[16167](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16202)
  R-deldir +gcc12
[16168](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16203)
  R-sp 
[16169](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16204)
  R-spData 
[16170](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16205)
  R-spdep +gcc12
[16171](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16206)
  R-truncnorm 
[16172](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16207)
  
[16173](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16208)
  Installing dependency (1 of 91) 'R-BH' with variants '' ... [OK]
[16174](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16209)
  Installing dependency (2 of 91) 'R-Rcpp' with variants '' ... [OK]
[16175](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16210)
  Installing dependency (3 of 91) 'R-RcppEigen' with variants '+gcc12' ... [OK]
[16176](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16211)
  Installing dependency (4 of 91) 'R-RcppParallel' with variants '' ... [OK]
[16177](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16212)
  Installing dependency (5 of 91) 'R-StanHeaders' with variants '' ... [OK]
[16178](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16213)
  Installing dependency (6 of 91) 'R-cli' with variants '' ... [OK]
[16179](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16214)
  Installing dependency (7 of 91) 'R-glue' with variants '' ... [OK]
[16180](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16215)
  Installing dependency (8 of 91) 'R-rlang' with variants '' ... [OK]
[16181](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16216)
  Installing dependency (9 of 91) 'R-lifecycle' with variants '' ... [OK]
[16182](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16217)
  Installing dependency (10 of 91) 'R-gtable' with variants '' ... [OK]
[16183](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16218)
  Installing dependency (11 of 91) 'R-isoband' with variants '' ... [OK]
[16184](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16219)
  Installing dependency (12 of 91) 'R-R6' with variants '' ... [OK]
[16185](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16220)
  Installing dependency (13 of 91) 'R-RColorBrewer' with variants '' ... [OK]
[16186](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16221)
  Installing dependency (14 of 91) 'R-farver' with variants '' ... [OK]
[16187](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16222)
  Installing dependency (15 of 91) 'R-labeling' with variants '' ... [OK]
[16188](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16223)
  Installing dependency (16 of 91) 'R-colorspace' with variants '' ... [OK]
[16189](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16224)
  Installing dependency (17 of 91) 'R-munsell' with variants '' ... [OK]
[16190](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16225)
  Installing dependency (18 of 91) 'R-viridisLite' with variants '' ... [OK]
[16191](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16226)
  Installing dependency (19 of 91) 'R-scales' with variants '' ... [OK]
[16192](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16227)
  Installing dependency (20 of 91) 'R-fansi' with variants '' ... [OK]
[16193](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16228)
  Installing dependency (21 of 91) 'R-magrittr' with variants '' ... [OK]
[16194](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16229)
  Installing dependency (22 of 91) 'R-utf8' with variants '' ... [OK]
[16195](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16230)
  Installing dependency (23 of 91) 'R-vctrs' with variants '' ... [OK]
[16196](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16231)
  Installing dependency (24 of 91) 'R-pillar' with variants '' ... [OK]
[16197](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16232)
  Installing dependency (25 of 91) 'R-pkgconfig' with variants '' ... [OK]
[16198](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16233)
  Installing dependency (26 of 91) 'R-tibble' with variants '' ... [OK]
[16199](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16234)
  Installing dependency (27 of 91) 'R-withr' with variants '' ... [OK]
[16200](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16235)
  Installing dependency (28 of 91) 'R-ggplot2' with variants '' ... [OK]
[16201](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16236)
  Installing dependency (29 of 91) 'R-gridExtra' with variants '' ... [OK]
[16202](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16237)
  Installing dependency (30 of 91) 'R-jsonlite' with variants '' ... [OK]
[16203](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16238)
  Installing dependency (31 of 91) 'R-QuickJSR' with variants '' ... [OK]
[16204](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16239)
  Installing dependency (32 of 91) 'R-inline' with variants '' ... [OK]
[16205](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16240)
  Installing dependency (33 of 91) 'R-backports' with variants '' ... [OK]
[16206](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16241)
  Installing dependency (34 of 91) 'R-checkmate' with variants '' ... [OK]
[16207](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16242)
  Installing dependency (35 of 91) 'R-matrixStats' with variants '' ... [OK]
[16208](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16243)
  Installing dependency (36 of 91) 'R-loo' with variants '' ... [OK]
[16209](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16244)
  Installing dependency (37 of 91) 'R-ps' with variants '' ... [OK]
[16210](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16245)
  Installing dependency (38 of 91) 'R-processx' with variants '' ... [OK]
[16211](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16246)
  Installing dependency (39 of 91) 'R-callr' with variants '' ... [OK]
[16212](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16247)
  Installing dependency (40 of 91) 'R-crayon' with variants '' ... [OK]
[16213](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16248)
  Installing dependency (41 of 91) 'R-rprojroot' with variants '' ... [OK]
[16214](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16249)
  Installing dependency (42 of 91) 'R-desc' with variants '' ... [OK]
[16215](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16250)
  Installing dependency (43 of 91) 'R-prettyunits' with variants '' ... [OK]
[16216](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16251)
  Installing dependency (44 of 91) 'R-pkgbuild' with variants '' ... [OK]
[16217](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16252)
  Installing dependency (45 of 91) 'R-rstan' with variants '' ... [OK]
[16218](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16253)
  Installing dependency (46 of 91) 'R-rstantools' with variants '' ... [OK]
[16219](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16254)
  Installing dependency (47 of 91) 'R-DBI' with variants '' ... [OK]
[16220](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16255)
  Installing dependency (48 of 91) 'R-proxy' with variants '' ... [OK]
[16221](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16256)
  Installing dependency (49 of 91) 'R-e1071' with variants '' ... [OK]
[16222](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16257)
  Installing dependency (50 of 91) 'R-classInt' with variants '+gcc12' ... [OK]
[16223](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16258)
  Installing dependency (51 of 91) 'R-wk' with variants '' ... [OK]
[16224](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16259)
  Installing dependency (52 of 91) 'R-s2' with variants '' ... [OK]
[16225](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16260)
  Installing dependency (53 of 91) 'cunit' with variants '' ... [OK]
[16226](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16261)
  Installing dependency (54 of 91) 'udunits2' with variants '' ... [OK]
[16227](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16262)
  Installing dependency (55 of 91) 'R-units' with variants '' ... [OK]
[16228](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16263)
  Installing dependency (56 of 91) 'lzo2' with variants '' ... [OK]
[16229](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16264)
  Installing dependency (57 of 91) 'snappy' with variants '' ... [OK]
[16230](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16265)
  Installing dependency (58 of 91) 'blosc' with variants '' ... [OK]
[16231](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16266)
  Installing dependency (59 of 91) 'brunsli' with variants '' ... [OK]
[16232](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16267)
  Installing dependency (60 of 91) 'charls' with variants '' ... [OK]
[16233](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16268)
  Installing dependency (61 of 91) 'giflib' with variants '' ... [OK]
[16234](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16269)
  Installing dependency (62 of 91) 'libcomerr' with variants '' ... [OK]
[16235](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16270)
  Installing dependency (63 of 91) 'lmdb' with variants '' ... [OK]
[16236](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16271)
  Installing dependency (64 of 91) 'kerberos5' with variants '' ... [OK]
[16237](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16272)
  Installing dependency (65 of 91) 'libxslt' with variants '' ... [OK]
[16238](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16273)
  Installing dependency (66 of 91) 'postgresql_select' with variants '' ... [OK]
[16239](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16274)
  Installing dependency (67 of 91) 'postgresql15' with variants '' ... [OK]
[16240](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16275)
  Installing dependency (68 of 91) 'proj9' with variants '+tiff' ... [OK]
[16241](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16276)
  Installing dependency (69 of 91) 'qhull' with variants '' ... [OK]
[16242](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16277)
  Installing dependency (70 of 91) 'minizip' with variants '' ... [OK]
[16243](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16278)
  Installing dependency (71 of 91) 'freexl' with variants '' ... [OK]
[16244](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16279)
  Installing dependency (72 of 91) 'geos' with variants '' ... [OK]
[16245](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16280)
  Installing dependency (73 of 91) 'librttopo' with variants '' ... [OK]
[16246](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16281)
  Installing dependency (74 of 91) 'spatialite' with variants '+proj9' ... [OK]
[16247](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16282)
  Installing dependency (75 of 91) 'webp' with variants '' ... [OK]
[16248](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16283)
  Installing dependency (76 of 91) 'gdal' with variants '+postgresql15+proj9' ... [OK]
[16249](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16284)
  Installing dependency (77 of 91) 'proj' with variants '' ... [OK]
[16250](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16285)
  Installing dependency (78 of 91) 'R-sf' with variants '' ... [OK]
[16251](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16286)
  Installing dependency (79 of 91) 'R-signs' with variants '' ... [OK]
[16252](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16287)
  Installing dependency (80 of 91) 'gcc12-libcxx' with variants '+clang14' ... [OK]
[16253](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16288)
  Installing dependency (81 of 91) 'gcc_select' with variants '' ... [OK]
[16254](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16289)
  Installing dependency (82 of 91) 'gmp' with variants '' ... [OK]
[16255](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16290)
  Installing dependency (83 of 91) 'isl' with variants '' ... [OK]
[16256](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16291)
  Installing dependency (84 of 91) 'mpfr' with variants '' ... [OK]
[16257](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16292)
  Installing dependency (85 of 91) 'libmpc' with variants '' ... [OK]
[16258](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16293)
  Installing dependency (86 of 91) 'gcc12' with variants '+stdlib_flag' ... [OK]
[16259](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16294)
  Installing dependency (87 of 91) 'R-deldir' with variants '+gcc12' ... [OK]
[16260](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16295)
  Installing dependency (88 of 91) 'R-sp' with variants '' ... [OK]
[16261](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16296)
  Installing dependency (89 of 91) 'R-spData' with variants '' ... [OK]
[16262](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16297)
  Installing dependency (90 of 91) 'R-spdep' with variants '+gcc12' ... [OK]
[16263](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16298)
  Installing dependency (91 of 91) 'R-truncnorm' with variants '' ... [OK]
[16264](https://github.com/macports/macports-ports/actions/runs/6434864324/job/17474944460?pr=20736#step:8:16300)
Error: Failed to install dependencies for R-geostan

Gonna leave it until tomorrow.

@cjones051073
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cjones051073 commented Oct 6, 2023

As I said before please do not run any more ci tests until the buildbots have finished the ongoing rebuilds…

@barracuda156
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@cjones051073 Is there a way to know when they are done or some estimate? (Sorry, I just never dealt with this matter.)

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@cjones051073 Is there a way to know when they are done or some estimate? (Sorry, I just never dealt with this matter.)

Just keep an eye on the link i sent before…

@barracuda156
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@cjones051073 I am afraid we are in trouble. Take a look:

36-125% sudo port -v upgrade R-cpfa
Error: R-glmnet: Variant gcc12 conflicts with gfortran
Error: Unable to open port: Error evaluating variants
Error: Follow https://guide.macports.org/#project.tickets if you believe there
is a bug.
36-125% sudo port -v -n upgrade R-cpfa 
sudo: ignoring time stamp from the future
Password:
Warning: configured user/group macports does not exist, will build as root
--->  Computing dependencies for R-cpfa.
--->  Fetching distfiles for R-cpfa

If the port has been installed previously, it fails to be updated normally. I did not notice that earlier, because used -n flag to avoid rebuilding unrelated stuff (with -n it works fine).
What could we do?

@barracuda156
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@cjones051073 (Also, while maybe this is just because of some delays in communication between buildbots and CI, but macos-13 but have finished rebuilding R stuff some time ago, but macos-13 CI still fails with all the same inexplicable (to me) errors. I.e. on dependencies, as before.
If it is indeed merely due to delays, please ignore this comment.)

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@cjones051073 BTW, we can revbump only those R ports which use gfortran, that will fix the problem. Unless you have a better idea.

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cjones051073 commented Oct 7, 2023

@cjones051073 (Also, while maybe this is just because of some delays in communication between buildbots and CI, but macos-13 but have finished rebuilding R stuff some time ago, but macos-13 CI still fails with all the same inexplicable (to me) errors. I.e. on dependencies, as before. If it is indeed merely due to delays, please ignore this comment.

I have no clue why you see the errors, timeouts was just a suggestion.

but, having all these updates in one PR makes understanding things hard. Please, if only as a test, update this to update a single port and lets see what that does.

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cjones051073 commented Oct 9, 2023

Which in turn uses the mpbb script
https://github.com/macports/mpbb
Finally note that project is also what the buildbots use, so any issues there are also in principle something they would suffer from.

Is it used from the master? If so, maybe something was broken by macports/mpbb@c48853e ?

I believe so yes. If the above is causing what you see you will have to ask someone who knows their way around mpbb like @jmroot

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cjones051073 commented Oct 9, 2023

@catap We do not need to enable it though. As with numerous other ports, test variant is not built by default.

The issue happens only on CI, not even buildbots. But even on buildbots non-default variants are not built. Locally it works fine, and anyone who wants to test it will have to invoke it locally. I cannot see why creating unknown number of additional shim ports is a good idea.
UPD. I rather remove tests option from wherever the issue occurs, if / until the base is not fixed.

It's only your opinion that this is a bug in base (or the mpbb script I pointed you at). This is not proven and I remain unconvinced it is until you do.

@cjones051073

  1. What is the alternative explanation for the following?
Error: The following dependencies were not installed because all of them have unmet dependencies (likely due to a dependency cycle): libiconv
Build of dependency 'libtextstyle' with variants '' failed, aborting.
  1. If you have an idea of what you will consider a convincing test case, please suggest that.

It is still though triggered by the attempt to build R-lava

2023-10-09T17:28:54.1622480Z Installing dependency (1 of 158) 'bzip2' with variants '' ... [OK]
2023-10-09T17:28:54.1622980Z Installing dependency (2 of 158) 'expat' with variants '' ... [OK]
2023-10-09T17:28:54.1623510Z Installing dependency (3 of 158) 'cmake-bootstrap' with variants '' ... [OK]
2023-10-09T17:28:54.1624010Z Installing dependency (4 of 158) 'brotli' with variants '' ... [OK]
2023-10-09T17:28:54.1624500Z Installing dependency (5 of 158) 'gperf' with variants '' ... [OK]
2023-10-09T17:28:54.1624990Z Installing dependency (6 of 158) 'libiconv' with variants '' ... [OK]
2023-10-09T17:28:54.1625490Z Installing dependency (7 of 158) 'gettext-runtime' with variants '' ... [OK]
2023-10-09T17:28:54.1626000Z Installing dependency (8 of 158) 'ncurses' with variants '' ... [OK]
2023-10-09T17:28:54.1626510Z Installing dependency (9 of 158) 'libtextstyle' with variants '' ... [FAIL]
2023-10-09T17:28:54.1919190Z ##[endgroup]
2023-10-09T17:28:54.1948960Z ##[error]Failed to install dependencies for R-lava

and we already know for a fact R-lava has a circular dependency (when you take test deps into account).

@barracuda156
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@jmroot Could you please take a look? Could the errors we get be related your recent commits to mpbb?

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barracuda156 commented Oct 9, 2023

and we already know for a fact R-lava has a circular dependency (when you take test reps into account).

@cjones051073 Yes, but unless logs lie (reported sequence is unrelated to actual), that happens prior to installing anything R-related, in fact much much earlier. If we assume that R-lava causes the problem, and it was failing very consistently, how so we suddenly get a failure with libiconv?
Also, an actual circular dependency is supposed to be circular for all three macos versions (there are no special settings for macos-13 in any R ports or R PG). But only one failed here. It should not be random, right?

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and we already know for a fact R-lava has a circular dependency (when you take test reps into account).

@cjones051073 Yes, but unless logs lie (reported sequence is unrelated to actual), that happens prior to installing anything R-related, in fact much much earlier. If we assume that R-lava causes the problem, and it was failing very consistently, how so we suddenly get a failure with libiconv?

That I cannot explain, but then I don’t really know enough about what precisely the ci and/or mpbb scripts do to be able to.

barracuda156 referenced this pull request in macports/mpbb Oct 9, 2023
Doing this instead of using registry::run_target saves running another
mportopen for each dependency, so should perform better. This wasn't
originally possible due to the workaround for
https://trac.macports.org/ticket/24857.
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barracuda156 commented Oct 9, 2023

@cjones051073 @kencu If we are okay with committing c75100f I will drop the last commit (which was for testing). I have no objections in principle against a non-default tests variant as long as we do not do that for every R port.
This does not mean I think the bug either the base or mpbb script should be left unfixed, but I rather have CI for R ports working sooner than later or being suspended indefinitely. Unfortunately, I cannot fix the base or script myself.

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@cjones051073 @kencu If we are okay with committing c75100f I will drop the last commit (which was for testing). I have no objections in principle against a non-default tests variant as long as we do not do that for every R port.

This does not mean I think the bug either the base or mpbb script should be left unfixed, but I rather have CI for R ports working sooner than later or being suspended indefinitely. Unfortunately, I cannot fix the base or script myself.

check is not really a good name for this variant, test would be better.

That aside I would prefer if you moved this into a subport rather than a variant, for the very reason the variant still has the circular dependency issue and when ports are built in the buildbots all variants are parsed, if not built, so potentially this issue will still be hit.

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@cjones051073 I do not find subports to be a neat solution. Also, removing subports is more problematic than dropping a variant (which hopefully can be done once the problem is actually fixed).

I used check due to R CMD check, but let me rename it to test, no issue here.

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@cjones051073 I do not find subports to be a neat solution. Also, removing subports is more problematic than dropping a variant (which hopefully can be done once the problem is actually fixed).

Before you assume there is anything to fix we need feedback from those more familiar with the ci and buildbot scripts. Your workaround might have to be more long lived than you are assuming, and I will still worry about the same circular dependency issues hitting the buildbots even if you move it to a none default variant, as as I said all variants are tested, if not built.

So putting your tastes aside you might have to move away from using a variant for this.

I used check due to R CMD check, but let me rename it to test, no issue here.

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barracuda156 commented Oct 9, 2023

@cjones051073 Well, if now you consider CI unreliable (they all passed earlier), I can just remove test option here and make a note to be displayed to a user upon port install.

Let us wait until CI results (for the record, so that we know if success is reproducible and not random), and then I can remove testing option from this port.

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@cjones051073 Well, if now you consider CI unreliable (they all passed earlier), I can just remove test option here and make a note to be displayed to a user upon port install.

Let us wait until CI results (for the record, so that we know if success is reproducible and not random), and then I can remove testing option from this port.

Removing the test entirely also works for me, as that is also a way to completely remove the possibility of the circular dependency rearing its ugly head. If, later on it is concluded there is indeed something in ci/base/mpbb that needs fixing then you can reenable it once that update is available wherever it needs to be.

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@cjones051073 CI passed.

Well, okay, I remove test option then, add a note for a user with a list of ports needed for tests, and let us merge this.

@barracuda156 barracuda156 marked this pull request as ready for review October 9, 2023 20:11
@barracuda156 barracuda156 changed the title R: updates R-lava: drop explicit test dependencies due to possible CI failures Oct 9, 2023
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@cjones051073 CI passed (expectedly); if you are okay with this version, please help with merging this, so that I can deal with delayed updates to other R ports. (If the same issue happens with some other R port, I will replicate this solution.)

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@cjones051073 @kencu If anything still to be changed, please ping me here.

@cjones051073 cjones051073 merged commit caaa1f7 into macports:master Oct 9, 2023
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@barracuda156 barracuda156 deleted the r_updates branch October 9, 2023 21:04
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@cjones051073 Thank you

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cjones051073 commented Oct 11, 2023

@barracuda156 with the resolution in https://trac.macports.org/ticket/68408 could you, if you have not already, open an MR that reverts the changes here, so remove the notes and put back the original test dependencies? Lets see if that fixes the issues you had here.

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jmroot commented Oct 11, 2023

Certainly nothing in the CI config or mpbb has ever looked at depends_test, except maybe the distfile mirroring.

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@cjones051073 @jmroot Thank you, sure.

@barracuda156 barracuda156 mentioned this pull request Oct 11, 2023
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barracuda156 added a commit to barracuda156/macports-ports-powerpc that referenced this pull request Oct 11, 2023
cjones051073 pushed a commit that referenced this pull request Oct 11, 2023
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