From fee6655078f2ebce66e39ee90348e901f189d1a9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Kirill=20M=C3=BCller?= Date: Wed, 18 Sep 2024 06:45:37 +0200 Subject: [PATCH] chore: Results from revdepcheck --- revdep/README.md | 21 +++-- revdep/cran.md | 19 ++--- revdep/failures.md | 70 +++++++++++++++ revdep/problems.md | 208 +++++++++------------------------------------ 4 files changed, 124 insertions(+), 194 deletions(-) diff --git a/revdep/README.md b/revdep/README.md index 458a0d9024..eddd39c4cb 100644 --- a/revdep/README.md +++ b/revdep/README.md @@ -1,6 +1,6 @@ # Revdeps -## Failed to check (33) +## Failed to check (34) |package |version |error |warning |note | |:---------------------|:-------|:-----|:-------|:----| @@ -29,6 +29,7 @@ |ohun |? | | | | |pagoda2 |? | | | | |PathwaySpace |? | | | | +|pcvr |1.0.0 |1 | | | |piecewiseSEM |? | | | | |RGraphSpace |? | | | | |rTwig |1.1.0 |1 | | | @@ -38,15 +39,13 @@ |SubtypeDrug |? | | | | |topologyGSA |? | | | | -## New problems (7) +## New problems (5) -|package |version |error |warning |note | -|:---------|:-------|:------|:-------|:------| -|[isotracer](problems.md#isotracer)|1.1.6 |__+1__ |1 |3 | -|[manynet](problems.md#manynet)|1.0.5 |__+1__ | |2 | -|[MetaNet](problems.md#metanet)|0.1.2 |__+1__ | | | -|[netropy](problems.md#netropy)|0.1.0 |__+2__ | |__+1__ | -|[R6causal](problems.md#r6causal)|0.8.3 | |__+1__ | | -|[simcausal](problems.md#simcausal)|0.5.6 |__+1__ | |1 | -|[skynet](problems.md#skynet)|1.4.3 |__+1__ | |1 | +|package |version |error |warning |note | +|:---------|:-------|:------|:--------|:----| +|[CePa](problems.md#cepa)|0.8.0 | |1 __+1__ | | +|[manynet](problems.md#manynet)|1.0.5 |__+1__ | |2 | +|[MetaNet](problems.md#metanet)|0.1.2 |__+1__ | | | +|[simcausal](problems.md#simcausal)|0.5.6 |__+1__ | |1 | +|[skynet](problems.md#skynet)|1.4.3 |__+1__ | |1 | diff --git a/revdep/cran.md b/revdep/cran.md index 09b109734f..af80e0349b 100644 --- a/revdep/cran.md +++ b/revdep/cran.md @@ -1,17 +1,17 @@ ## revdepcheck results -We checked 851 reverse dependencies (846 from CRAN + 5 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package. +We checked 855 reverse dependencies (850 from CRAN + 5 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package. - * We saw 7 new problems - * We failed to check 28 packages + * We saw 5 new problems + * We failed to check 29 packages Issues with CRAN packages are summarised below. ### New problems (This reports the first line of each new failure) -* isotracer - checking tests ... ERROR +* CePa + checking Rd cross-references ... WARNING * manynet checking examples ... ERROR @@ -19,14 +19,6 @@ Issues with CRAN packages are summarised below. * MetaNet checking examples ... ERROR -* netropy - checking examples ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* R6causal - checking whether package ‘R6causal’ can be installed ... WARNING - * simcausal checking tests ... ERROR @@ -57,6 +49,7 @@ Issues with CRAN packages are summarised below. * NetworkChange (NA) * ohun (NA) * pagoda2 (NA) +* pcvr (NA) * rTwig (NA) * Seurat (NA) * speakeasyR (NA) diff --git a/revdep/failures.md b/revdep/failures.md index fa3a20cc02..4ab1cdbc1d 100644 --- a/revdep/failures.md +++ b/revdep/failures.md @@ -1648,6 +1648,76 @@ Run `revdepcheck::cloud_details(, "PathwaySpace")` for more info +``` +# pcvr + +
+ +* Version: 1.0.0 +* GitHub: https://github.com/danforthcenter/pcvr +* Source code: https://github.com/cran/pcvr +* Date/Publication: 2024-09-05 17:30:02 UTC +* Number of recursive dependencies: 189 + +Run `revdepcheck::cloud_details(, "pcvr")` for more info + +
+ +## In both + +* checking whether package ‘pcvr’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/pcvr/new/pcvr.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘pcvr’ ... +** package ‘pcvr’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Warning in check_dep_version() : + ABI version mismatch: +lme4 was built with Matrix ABI version 1 +Current Matrix ABI version is 0 +Please re-install lme4 from source or restore original ‘Matrix’ package +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘pcvr’ +* removing ‘/tmp/workdir/pcvr/new/pcvr.Rcheck/pcvr’ + + +``` +### CRAN + +``` +* installing *source* package ‘pcvr’ ... +** package ‘pcvr’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Warning in check_dep_version() : + ABI version mismatch: +lme4 was built with Matrix ABI version 1 +Current Matrix ABI version is 0 +Please re-install lme4 from source or restore original ‘Matrix’ package +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘pcvr’ +* removing ‘/tmp/workdir/pcvr/old/pcvr.Rcheck/pcvr’ + + ``` # piecewiseSEM diff --git a/revdep/problems.md b/revdep/problems.md index 67a5ebe9ec..6d4b6f5ff0 100644 --- a/revdep/problems.md +++ b/revdep/problems.md @@ -1,72 +1,55 @@ -# isotracer +# CePa
-* Version: 1.1.6 -* GitHub: NA -* Source code: https://github.com/cran/isotracer -* Date/Publication: 2024-05-15 08:50:07 UTC -* Number of recursive dependencies: 127 +* Version: 0.8.0 +* GitHub: https://github.com/jokergoo/CePa +* Source code: https://github.com/cran/CePa +* Date/Publication: 2022-06-11 21:30:06 UTC +* Number of recursive dependencies: 14 -Run `revdepcheck::cloud_details(, "isotracer")` for more info +Run `revdepcheck::cloud_details(, "CePa")` for more info
## Newly broken -* checking tests ... ERROR +* checking Rd cross-references ... WARNING ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(isotracer) - To automatically run isotracer in parallel on a multicore CPU, you can call: - options(mc.cores = parallel::detectCores()) - - - Attaching package: 'isotracer' - ... - ══ Failed tests ════════════════════════════════════════════════════════════════ - ── Failure ('test-steady-states-flows-pred.R:481:5'): Predictions for open network, single unit, one steady, one split ── - all(x[["from"]] - x[["to"]] < 1e-13) is not TRUE - - `actual`: FALSE - `expected`: TRUE - - [ FAIL 1 | WARN 0 | SKIP 0 | PASS 582 ] - Error: Test failures - Execution halted + Missing link or links in documentation object 'cepa.Rd': + ‘[igraph:igraph_test]{igraphtest}’ + + Missing link or links in documentation object 'cepa.ora.Rd': + ‘[igraph:igraph_test]{igraphtest}’ + + See section 'Cross-references' in the 'Writing R Extensions' manual. ``` ## In both -* checking whether package ‘isotracer’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: namespace ‘lubridate’ is not available and has been replaced - See ‘/tmp/workdir/isotracer/new/isotracer.Rcheck/00install.out’ for details. - ``` - -* checking installed package size ... NOTE - ``` - installed size is 95.1Mb - sub-directories of 1Mb or more: - R 1.5Mb - data 4.0Mb - doc 2.3Mb - libs 86.8Mb - ``` - -* checking dependencies in R code ... NOTE +* checking re-building of vignette outputs ... WARNING ``` - Namespace in Imports field not imported from: ‘rstantools’ - All declared Imports should be used. - ``` - -* checking for GNU extensions in Makefiles ... NOTE - ``` - GNU make is a SystemRequirements. + Error(s) in re-building vignettes: + --- re-building ‘CePa.Rnw’ using Sweave + Error: processing vignette 'CePa.Rnw' failed with diagnostics: + Running 'texi2dvi' on 'CePa.tex' failed. + LaTeX errors: + ! LaTeX Error: File `grfext.sty' not found. + + Type X to quit or to proceed, + or enter new name. (Default extension: sty) + + ... + l.179 \RequirePackage{grfext}\relax + ^^M + ! ==> Fatal error occurred, no output PDF file produced! + --- failed re-building ‘parsing-PID-pathway-data.Rnw’ + + SUMMARY: processing the following files failed: + ‘CePa.Rnw’ ‘analysis-p53.Rnw’ ‘parsing-PID-pathway-data.Rnw’ + + Error: Vignette re-building failed. + Execution halted ``` # manynet @@ -77,7 +60,7 @@ Run `revdepcheck::cloud_details(, "isotracer")` for more info * GitHub: https://github.com/stocnet/manynet * Source code: https://github.com/cran/manynet * Date/Publication: 2024-08-30 04:50:02 UTC -* Number of recursive dependencies: 152 +* Number of recursive dependencies: 147 Run `revdepcheck::cloud_details(, "manynet")` for more info @@ -163,121 +146,6 @@ Run `revdepcheck::cloud_details(, "MetaNet")` for more info Execution halted ``` -# netropy - -
- -* Version: 0.1.0 -* GitHub: NA -* Source code: https://github.com/cran/netropy -* Date/Publication: 2022-02-02 08:20:02 UTC -* Number of recursive dependencies: 85 - -Run `revdepcheck::cloud_details(, "netropy")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘netropy-Ex.R’ failed - The error most likely occurred in: - - > ### Name: assoc_graph - > ### Title: Association Graphs - > ### Aliases: assoc_graph - > - > ### ** Examples - > - > library(ggraph) - ... - + ifelse(df.att$age<=45,1,2)), - + practice = df.att$practice, - + lawschool= df.att$lawschool-1) - > - > # association graph based on cutoff 0.15 - > assoc_graph(df.att.ed, 0.15) - Error in igraph::distances(g) : - At vendor/cigraph/src/paths/dijkstra.c:128 : Weights must not contain NaN values. Invalid value - Calls: assoc_graph ... layout_with_stress -> .layout_with_stress_dim -> - Execution halted - ``` - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘joint_entropies.Rmd’ - ... - 21 0 4 45 - - > library(ggraph) - Loading required package: ggplot2 - - > assoc_graph(dyad.var, 0.15) - - When sourcing ‘joint_entropies.R’: - Error: At vendor/cigraph/src/paths/dijkstra.c:128 : Weights must not contain NaN values. Invalid value - Execution halted - - ‘joint_entropies.Rmd’ using ‘UTF-8’... failed - ‘prediction_power.Rmd’ using ‘UTF-8’... OK - ‘univariate_bivariate_trivariate.Rmd’ using ‘UTF-8’... OK - ‘variable_domains.Rmd’ using ‘UTF-8’... OK - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘joint_entropies.Rmd’ using rmarkdown - - Quitting from lines 96-98 [assoc_g] (joint_entropies.Rmd) - Error: processing vignette 'joint_entropies.Rmd' failed with diagnostics: - At vendor/cigraph/src/paths/dijkstra.c:128 : Weights must not contain NaN values. Invalid value - --- failed re-building ‘joint_entropies.Rmd’ - - --- re-building ‘prediction_power.Rmd’ using rmarkdown - ... - --- finished re-building ‘univariate_bivariate_trivariate.Rmd’ - - --- re-building ‘variable_domains.Rmd’ using rmarkdown - --- finished re-building ‘variable_domains.Rmd’ - - SUMMARY: processing the following file failed: - ‘joint_entropies.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# R6causal - -
- -* Version: 0.8.3 -* GitHub: NA -* Source code: https://github.com/cran/R6causal -* Date/Publication: 2024-03-14 16:10:02 UTC -* Number of recursive dependencies: 99 - -Run `revdepcheck::cloud_details(, "R6causal")` for more info - -
- -## Newly broken - -* checking whether package ‘R6causal’ can be installed ... WARNING - ``` - Found the following significant warnings: - Note: possible error in '.to(l[i])': unused argument (l[i]) - Note: possible error in '.from(l[i])': unused argument (l[i]) - See ‘/tmp/workdir/R6causal/new/R6causal.Rcheck/00install.out’ for details. - Information on the location(s) of code generating the ‘Note’s can be - obtained by re-running with environment variable R_KEEP_PKG_SOURCE set - to ‘yes’. - ``` - # simcausal