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REVDEP: 431 packages [ci skip]
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‎revdep/README.md

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|collate |en_US.UTF-8 |
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|ctype |en_US.UTF-8 |
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|tz |America/Los_Angeles |
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|date |2025-04-19 |
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|date |2025-04-20 |
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|pandoc |3.6.3 @ /software/c4/cbi/software/pandoc-3.6.3/bin/pandoc |
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|quarto |NA |
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# Dependencies
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|package |old |new |Δ |
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|:----------|:------|:-----------|:--|
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|future |1.40.0 |1.40.0-9102 |* |
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|future |1.40.0 |1.40.0-9109 |* |
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|codetools |0.2-20 |0.2-20 | |
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|digest |0.6.37 |0.6.37 | |
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|globals |0.17.0 |0.17.0 | |
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|lemna |1.0.2 | | | |
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|LexFindR |1.1.0 | | | |
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|lgr |0.4.4 | | | |
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|[lidR](problems.md#lidr) |4.1.2 |1 | |1 |
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|[lidR](problems.md#lidr) |4.1.2 |1 | |2 |
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|lightr |1.8.0 | | | |
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|lmtp |1.4.0 | | | |
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|LTFHPlus |2.1.2 | | | |
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|[OptimalGoldstandardDesigns](problems.md#optimalgoldstandarddesigns)|1.0.1 | | |1 |
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|optimLanduse |1.2.1 | | | |
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|origami |1.0.7 | | | |
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|[OutSeekR](problems.md#outseekr)|1.0.0 |1 | | |
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|OutSeekR |1.0.0 | | | |
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|[PAMpal](problems.md#pampal) |1.4.4 | |1 | |
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|[PAMscapes](problems.md#pamscapes)|0.11.3 | |1 | |
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|paramsim |0.1.0 | | | |
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|phylopath |1.3.0 | | | |
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|phylospatial |1.1.0 | | | |
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|[PINstimation](problems.md#pinstimation)|0.1.2 | | |1 |
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|[pliman](problems.md#pliman) |3.0.0 | | |1 |
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|[pliman](problems.md#pliman) |3.0.0 | | |4 |
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|[PLNmodels](problems.md#plnmodels)|1.2.2 | | |1 |
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|plumber |1.3.0 | | | |
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|polle |1.5 | | | |

‎revdep/problems.md

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@@ -235,7 +235,7 @@ Run `revdepcheck::revdep_details(, "batchtools")` for more info
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* checking dependencies in R code ... NOTE
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```
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[c4-n43:3626643] OPAL ERROR: Not initialized in file ext2x_client.c at line 112
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[c4-n43:1354832] OPAL ERROR: Not initialized in file ext2x_client.c at line 112
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--------------------------------------------------------------------------
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The application appears to have been direct launched using "srun",
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but OMPI was not built with SLURM's PMI support and therefore cannot
@@ -972,18 +972,15 @@ Run `revdepcheck::revdep_details(, "crossmap")` for more info
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> library(crossmap)
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>
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> test_check("crossmap")
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[ FAIL 2 | WARN 3 | SKIP 0 | PASS 264 ]
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[ FAIL 1 | WARN 3 | SKIP 0 | PASS 382 ]
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...
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7. └─future::ClusterFutureBackend(...)
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8. └─clusterRegistry$startCluster(...)
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9. └─future (local) makeCluster(workers, ...)
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10. ├─base::do.call(makeClusterPSOCK, args = args, quote = TRUE)
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11. └─parallelly (local) `<fn>`(base::quote(256L), rscript_libs = base::quote(`<chr>`))
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12. └─parallelly:::stopf(msg)
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══ Failed tests ════════════════════════════════════════════════════════════════
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── Failure ('test-errors.R:12:3'): require future ──────────────────────────────
979+
`future_xmap(list(1:3, 1:3), paste)` did not throw an error.
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985-
[ FAIL 2 | WARN 3 | SKIP 0 | PASS 264 ]
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[ FAIL 1 | WARN 3 | SKIP 0 | PASS 382 ]
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Error: Test failures
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In addition: There were 50 or more warnings (use warnings() to see the first 50)
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Execution halted
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```
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@@ -2143,17 +2140,17 @@ Run `revdepcheck::revdep_details(, "hacksig")` for more info
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Error(s) in re-building vignettes:
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--- re-building ‘hacksig.Rmd’ using rmarkdown
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Quitting from hacksig.Rmd:203-206 [unnamed-chunk-18]
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Quitting from hacksig.Rmd:215-225 [unnamed-chunk-19]
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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<error/rlang_error>
2149-
Error:
2150-
! Cannot create 256 parallel PSOCK nodes. Each node needs one connection, but there are only 123 connections left out of the maximum 128 available on this R installation. To increase this limit in R (>= 4.4.0), use command-line option '--max-connections=N' when launching R.
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Error in `msigdbr()`:
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! Unknown subcollection.
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---
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Backtrace:
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...
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Error: processing vignette 'hacksig.Rmd' failed with diagnostics:
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Cannot create 256 parallel PSOCK nodes. Each node needs one connection, but there are only 123 connections left out of the maximum 128 available on this R installation. To increase this limit in R (>= 4.4.0), use command-line option '--max-connections=N' when launching R.
2153+
Unknown subcollection.
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--- failed re-building ‘hacksig.Rmd’
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SUMMARY: processing the following file failed:
@@ -2232,7 +2229,7 @@ Run `revdepcheck::revdep_details(, "hero")` for more info
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* checking dependencies in R code ... NOTE
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```
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[c4-n43:1057183] OPAL ERROR: Not initialized in file ext2x_client.c at line 112
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[c4-n43:3011110] OPAL ERROR: Not initialized in file ext2x_client.c at line 112
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--------------------------------------------------------------------------
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The application appears to have been direct launched using "srun",
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but OMPI was not built with SLURM's PMI support and therefore cannot
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* checking installed package size ... NOTE
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```
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installed size is 6.1Mb
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installed size is 7.5Mb
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sub-directories of 1Mb or more:
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R 1.5Mb
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data 2.0Mb
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extdata 3.1Mb
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```
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* GitHub: https://github.com/r-lidar/lidR
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* Source code: https://github.com/cran/lidR
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* Date/Publication: 2024-07-09 08:40:02 UTC
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* Number of recursive dependencies: 146
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* Number of recursive dependencies: 154
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Run `revdepcheck::revdep_details(, "lidR")` for more info
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* checking tests ...
27212719
```
2722-
Running ‘testthat.R’/software/c4/cbi/software/_rocky8/R-4.4.3-gcc13/lib64/R/bin/BATCH: line 60: 20146 Aborted (core dumped) ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1
2720+
Running ‘testthat.R’/software/c4/cbi/software/_rocky8/R-4.4.3-gcc13/lib64/R/bin/BATCH: line 60: 4014933 Aborted (core dumped) ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1
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ERROR
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Running the tests in ‘tests/testthat.R’ failed.
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> test_check("lidR")
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Tests using raster: terra
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Tests using future: TRUE
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Tests using OpenMP thread: 128
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Tests using OpenMP thread: 48
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Tests using rlas: 1.8.0
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OGR: Unsupported geometry type
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OGR: Unsupported geometry type
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what(): basic_string::_M_create
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```
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* checking package dependencies ... NOTE
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```
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Package suggested but not available for checking: ‘mapedit’
2744+
```
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* checking installed package size ... NOTE
27442747
```
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installed size is 19.6Mb
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| ^
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```
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# OutSeekR
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<details>
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* Version: 1.0.0
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* GitHub: NA
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* Source code: https://github.com/cran/OutSeekR
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* Date/Publication: 2024-11-19 09:10:05 UTC
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* Number of recursive dependencies: 58
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Run `revdepcheck::revdep_details(, "OutSeekR")` for more info
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</details>
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## In both
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3723-
* checking re-building of vignette outputs ... ERROR
3724-
```
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Error(s) in re-building vignettes:
3726-
--- re-building ‘introduction.Rmd’ using rmarkdown
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Quitting from introduction.Rmd:101-117 [run-1]
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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<error/rlang_error>
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Error:
3732-
! Cannot create 256 parallel PSOCK nodes. Each node needs one connection, but there are only 123 connections left out of the maximum 128 available on this R installation. To increase this limit in R (>= 4.4.0), use command-line option '--max-connections=N' when launching R.
3733-
---
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Backtrace:
3735-
...
3736-
3737-
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
3738-
Cannot create 256 parallel PSOCK nodes. Each node needs one connection, but there are only 123 connections left out of the maximum 128 available on this R installation. To increase this limit in R (>= 4.4.0), use command-line option '--max-connections=N' when launching R.
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--- failed re-building ‘introduction.Rmd’
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SUMMARY: processing the following file failed:
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‘introduction.Rmd’
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3744-
Error: Vignette re-building failed.
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Execution halted
3746-
```
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# PAMpal
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<details>
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* GitHub: https://github.com/NA/NA
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* Source code: https://github.com/cran/pliman
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* Date/Publication: 2024-11-06 10:30:02 UTC
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* Number of recursive dependencies: 126
4061+
* Number of recursive dependencies: 134
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Run `revdepcheck::revdep_details(, "pliman")` for more info
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</details>
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## In both
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* checking package dependencies ... NOTE
4070+
```
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Package suggested but not available for checking: ‘mapedit’
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```
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* checking installed package size ... NOTE
41084075
```
41094076
installed size is 9.4Mb
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tmp_images 1.9Mb
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```
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* checking whether startup messages can be suppressed ... NOTE
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```
4085+
To use viewer = 'mapview', first install the required packages:mapedit
4086+
4087+
It looks like this package (or a package it requires) has a startup
4088+
message which cannot be suppressed: see ?packageStartupMessage.
4089+
```
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4091+
* checking Rd cross-references ... NOTE
4092+
```
4093+
Package unavailable to check Rd xrefs: ‘mapedit’
4094+
```
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41164096
# PLNmodels
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41184098
<details>
@@ -6566,22 +6546,22 @@ Run `revdepcheck::revdep_details(, "WeightedCluster")` for more info
65666546
```
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Error(s) in re-building vignettes:
65686548
--- re-building ‘BigDataSA.Rmd’ using rmarkdown
6549+
--- finished re-building ‘BigDataSA.Rmd’
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6551+
--- re-building ‘ClusterExternalValidSA.Rmd’ using rmarkdown
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--- finished re-building ‘ClusterExternalValidSA.Rmd’
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6554+
--- re-building ‘ClusterValidSA.Rmd’ using rmarkdown
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--- finished re-building ‘ClusterValidSA.Rmd’
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Quitting from BigDataSA.Rmd:73-77 [seqclaraex]
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
6572-
<error/rlang_error>
6573-
Error:
6574-
! Cannot create 256 parallel PSOCK nodes. Each node needs one connection, but there are only 123 connections left out of the maximum 128 available on this R installation. To increase this limit in R (>= 4.4.0), use command-line option '--max-connections=N' when launching R.
6575-
---
6576-
Backtrace:
65776557
...
6558+
l.85 \usepackage
65786559
{tikz}^^M
65796560
! ==> Fatal error occurred, no output PDF file produced!
65806561
--- failed re-building ‘WeightedClusterPreview.Rnw’
65816562
65826563
SUMMARY: processing the following files failed:
6583-
‘BigDataSA.Rmd’ ‘ClusterValidSA.Rmd’ ‘WeightedClusterFR.Rnw’
6584-
‘WeightedClusterPreview.Rnw’
6564+
‘WeightedClusterFR.Rnw’ ‘WeightedClusterPreview.Rnw’
65856565
65866566
Error: Vignette re-building failed.
65876567
Execution halted

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