diff --git a/R/conversion.R b/R/conversion.R index 9199a5d60af..1e9495e5efe 100644 --- a/R/conversion.R +++ b/R/conversion.R @@ -317,7 +317,7 @@ get.adjacency.sparse <- function(graph, type = c("both", "upper", "lower"), #' numeric. If the `sparse` argument is `FALSE`, then character is #' also allowed. The reason for the difference is that the `Matrix` #' package does not support character sparse matrices yet. -#' @param edges Logical scalar, whether to return the edge ids in the matrix. +#' @param edges `r lifecycle::badge("deprecated")` Logical scalar, whether to return the edge ids in the matrix. #' For non-existant edges zero is returned. #' @param names Logical constant, whether to assign row and column names #' to the matrix. These are only assigned if the `name` vertex attribute @@ -344,14 +344,14 @@ as_adjacency_matrix <- function(graph, type = c("both", "upper", "lower"), sparse = igraph_opt("sparsematrices")) { ensure_igraph(graph) - if (!missing(edges)) { - warning("The `edges` argument of `as_adjacency_matrix` is deprecated; it will be removed in igraph 1.4.0") + if (!missing(edges) && isTRUE(edges)) { + lifecycle::deprecate_stop("2.0.0", "as_adjacency_matrix(edges = )") } - if (!sparse) { - get.adjacency.dense(graph, type = type, attr = attr, weights = NULL, names = names) - } else { + if (sparse) { get.adjacency.sparse(graph, type = type, attr = attr, edges = edges, names = names) + } else { + get.adjacency.dense(graph, type = type, attr = attr, weights = NULL, names = names) } } diff --git a/man/as_adjacency_matrix.Rd b/man/as_adjacency_matrix.Rd index 94e27fcfbf1..101ffe0a0ec 100644 --- a/man/as_adjacency_matrix.Rd +++ b/man/as_adjacency_matrix.Rd @@ -45,7 +45,7 @@ numeric. If the \code{sparse} argument is \code{FALSE}, then character is also allowed. The reason for the difference is that the \code{Matrix} package does not support character sparse matrices yet.} -\item{edges}{Logical scalar, whether to return the edge ids in the matrix. +\item{edges}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} Logical scalar, whether to return the edge ids in the matrix. For non-existant edges zero is returned.} \item{names}{Logical constant, whether to assign row and column names diff --git a/man/get.adjacency.Rd b/man/get.adjacency.Rd index 28608d50bd6..20dfed6329e 100644 --- a/man/get.adjacency.Rd +++ b/man/get.adjacency.Rd @@ -35,7 +35,7 @@ numeric. If the \code{sparse} argument is \code{FALSE}, then character is also allowed. The reason for the difference is that the \code{Matrix} package does not support character sparse matrices yet.} -\item{edges}{Logical scalar, whether to return the edge ids in the matrix. +\item{edges}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} Logical scalar, whether to return the edge ids in the matrix. For non-existant edges zero is returned.} \item{names}{Logical constant, whether to assign row and column names diff --git a/revdep/README.md b/revdep/README.md index b5e0b0847bc..5aed4952e95 100644 --- a/revdep/README.md +++ b/revdep/README.md @@ -1,5 +1,17 @@ # Revdeps +## Failed to check (7) + +|package |version |error |warning |note | +|:----------|:-------|:-----|:-------|:----| +|geostan |0.5.3 |1 | | | +|HLSM |? | | | | +|Seurat |? | | | | +|streamDAG |? | | | | +|TDA |1.9 |1 | | | +|TestAnaAPP |0.1.5 |1 | | | +|treestats |1.0.3 |1 | | | + ## New problems (22) |package |version |error |warning |note | diff --git a/revdep/cran.md b/revdep/cran.md index 338b8967ac2..9f0c82b117c 100644 --- a/revdep/cran.md +++ b/revdep/cran.md @@ -1,9 +1,9 @@ ## revdepcheck results -We checked 22 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package. +We checked 30 reverse dependencies (29 from CRAN + 1 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package. * We saw 22 new problems - * We failed to check 0 packages + * We failed to check 6 packages Issues with CRAN packages are summarised below. @@ -80,3 +80,11 @@ Issues with CRAN packages are summarised below. * VertexSort checking examples ... ERROR +### Failed to check + +* geostan (NA) +* Seurat (NA) +* streamDAG (NA) +* TDA (NA) +* TestAnaAPP (NA) +* treestats (NA) diff --git a/revdep/failures.md b/revdep/failures.md index 9a207363396..9ee99086e33 100644 --- a/revdep/failures.md +++ b/revdep/failures.md @@ -1 +1,445 @@ -*Wow, no problems at all. :)* \ No newline at end of file +# geostan + +
+ +* Version: 0.5.3 +* GitHub: https://github.com/ConnorDonegan/geostan +* Source code: https://github.com/cran/geostan +* Date/Publication: 2023-11-24 22:30:02 UTC +* Number of recursive dependencies: 109 + +Run `revdepcheck::cloud_details(, "geostan")` for more info + +
+ +## In both + +* checking whether package ‘geostan’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/geostan/new/geostan.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘geostan’ ... +** package ‘geostan’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0’ +using C++17 + + +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:397, +... +/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:35:90: required from ‘Eigen::internal::evaluator >::evaluator(const XprType&) [with Lhs = Eigen::Product, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose > >, Eigen::Matrix, 0>; Rhs = Eigen::Matrix; int Options = 0; Eigen::internal::evaluator >::XprType = Eigen::Product, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose > >, Eigen::Matrix, 0>, Eigen::Matrix, 0>]’ +/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Product.h:132:22: required from ‘Eigen::internal::dense_product_base::operator const Scalar() const [with Lhs = Eigen::Product, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose > >, Eigen::Matrix, 0>; Rhs = Eigen::Matrix; int Option = 0; Eigen::internal::dense_product_base::Scalar = double]’ +/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_foundation_namespace::model_foundation; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ +/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here +/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:55:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__vector(2) double’} [-Wignored-attributes] +g++: fatal error: Killed signal terminated program cc1plus +compilation terminated. +make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_foundation.o] Error 1 +ERROR: compilation failed for package ‘geostan’ +* removing ‘/tmp/workdir/geostan/new/geostan.Rcheck/geostan’ + + +``` +### CRAN + +``` +* installing *source* package ‘geostan’ ... +** package ‘geostan’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0’ +using C++17 + + +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:397, +... +/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:35:90: required from ‘Eigen::internal::evaluator >::evaluator(const XprType&) [with Lhs = Eigen::Product, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose > >, Eigen::Matrix, 0>; Rhs = Eigen::Matrix; int Options = 0; Eigen::internal::evaluator >::XprType = Eigen::Product, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose > >, Eigen::Matrix, 0>, Eigen::Matrix, 0>]’ +/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Product.h:132:22: required from ‘Eigen::internal::dense_product_base::operator const Scalar() const [with Lhs = Eigen::Product, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose > >, Eigen::Matrix, 0>; Rhs = Eigen::Matrix; int Option = 0; Eigen::internal::dense_product_base::Scalar = double]’ +/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_foundation_namespace::model_foundation; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ +/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here +/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:55:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__vector(2) double’} [-Wignored-attributes] +g++: fatal error: Killed signal terminated program cc1plus +compilation terminated. +make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_foundation.o] Error 1 +ERROR: compilation failed for package ‘geostan’ +* removing ‘/tmp/workdir/geostan/old/geostan.Rcheck/geostan’ + + +``` +# HLSM + +
+ +* Version: NA +* GitHub: NA +* Source code: https://github.com/cran/HLSM +* Number of recursive dependencies: 13 + +Run `revdepcheck::cloud_details(, "HLSM")` for more info + +
+ +## Error before installation + +### Devel + +``` + + + + + + +``` +### CRAN + +``` + + + + + + +``` +# Seurat + +
+ +* Version: 5.0.1 +* GitHub: https://github.com/satijalab/seurat +* Source code: https://github.com/cran/Seurat +* Date/Publication: 2023-11-17 23:10:06 UTC +* Number of recursive dependencies: 264 + +Run `revdepcheck::cloud_details(, "Seurat")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/Seurat/new/Seurat.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 + GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 +* running under: Ubuntu 20.04.6 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘Seurat/DESCRIPTION’ ... OK +... +* checking for GNU extensions in Makefiles ... OK +* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK +* checking use of PKG_*FLAGS in Makefiles ... OK +* checking compiled code ... OK +* checking examples ... OK +* checking for unstated dependencies in ‘tests’ ... OK +* checking tests ... OK + Running ‘testthat.R’ +* DONE +Status: 3 NOTEs + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/Seurat/old/Seurat.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 + GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 +* running under: Ubuntu 20.04.6 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘Seurat/DESCRIPTION’ ... OK +... +* checking for GNU extensions in Makefiles ... OK +* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK +* checking use of PKG_*FLAGS in Makefiles ... OK +* checking compiled code ... OK +* checking examples ... OK +* checking for unstated dependencies in ‘tests’ ... OK +* checking tests ... OK + Running ‘testthat.R’ +* DONE +Status: 3 NOTEs + + + + + +``` +# streamDAG + +
+ +* Version: 1.5 +* GitHub: NA +* Source code: https://github.com/cran/streamDAG +* Date/Publication: 2023-10-06 18:50:02 UTC +* Number of recursive dependencies: 133 + +Run `revdepcheck::cloud_details(, "streamDAG")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/streamDAG/new/streamDAG.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 + GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 +* running under: Ubuntu 20.04.6 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘streamDAG/DESCRIPTION’ ... OK +* this is package ‘streamDAG’ version ‘1.5’ +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘asbio’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/streamDAG/old/streamDAG.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 + GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 +* running under: Ubuntu 20.04.6 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘streamDAG/DESCRIPTION’ ... OK +* this is package ‘streamDAG’ version ‘1.5’ +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘asbio’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +# TDA + +
+ +* Version: 1.9 +* GitHub: NA +* Source code: https://github.com/cran/TDA +* Date/Publication: 2023-02-04 18:42:30 UTC +* Number of recursive dependencies: 59 + +Run `revdepcheck::cloud_details(, "TDA")` for more info + +
+ +## In both + +* checking whether package ‘TDA’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/TDA/new/TDA.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘TDA’ ... +** package ‘TDA’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +/bin/sh: 1: clang++: not found +expr: syntax error: unexpected argument ‘50000’ +using C++ compiler: ‘g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0’ +using C++17 +/bin/sh: 1: clang++: not found +expr: syntax error: unexpected argument ‘50000’ +... + from ./gudhi/Simplex_tree/Simplex_tree_siblings.h:16, + from ./gudhi/Simplex_tree.h:15, + from ./tdautils/gudhiUtils.h:10, + from diag.cpp:19: +/opt/R/4.3.1/lib/R/site-library/BH/include/boost/move/detail/reverse_iterator.hpp:132:39: warning: inline function ‘bool boost::movelib::operator!=(const boost::movelib::reverse_iterator >**, true> >&, const boost::movelib::reverse_iterator >**, true> >&)’ used but never defined + 132 | BOOST_MOVE_FORCEINLINE friend bool operator!=(const reverse_iterator& l, const reverse_iterator& r) + | ^~~~~~~~ +make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:200: diag.o] Error 1 +ERROR: compilation failed for package ‘TDA’ +* removing ‘/tmp/workdir/TDA/new/TDA.Rcheck/TDA’ + + +``` +### CRAN + +``` +* installing *source* package ‘TDA’ ... +** package ‘TDA’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +/bin/sh: 1: clang++: not found +expr: syntax error: unexpected argument ‘50000’ +using C++ compiler: ‘g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0’ +using C++17 +/bin/sh: 1: clang++: not found +expr: syntax error: unexpected argument ‘50000’ +... + from ./gudhi/Simplex_tree/Simplex_tree_siblings.h:16, + from ./gudhi/Simplex_tree.h:15, + from ./tdautils/gudhiUtils.h:10, + from diag.cpp:19: +/opt/R/4.3.1/lib/R/site-library/BH/include/boost/move/detail/reverse_iterator.hpp:132:39: warning: inline function ‘bool boost::movelib::operator!=(const boost::movelib::reverse_iterator >**, true> >&, const boost::movelib::reverse_iterator >**, true> >&)’ used but never defined + 132 | BOOST_MOVE_FORCEINLINE friend bool operator!=(const reverse_iterator& l, const reverse_iterator& r) + | ^~~~~~~~ +make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:200: diag.o] Error 1 +ERROR: compilation failed for package ‘TDA’ +* removing ‘/tmp/workdir/TDA/old/TDA.Rcheck/TDA’ + + +``` +# TestAnaAPP + +
+ +* Version: 0.1.5 +* GitHub: https://github.com/jiangyouxiang/TestAnaAPP +* Source code: https://github.com/cran/TestAnaAPP +* Date/Publication: 2024-01-09 05:30:02 UTC +* Number of recursive dependencies: 238 + +Run `revdepcheck::cloud_details(, "TestAnaAPP")` for more info + +
+ +## In both + +* checking whether package ‘TestAnaAPP’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/TestAnaAPP/new/TestAnaAPP.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘TestAnaAPP’ ... +** package ‘TestAnaAPP’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘tidySEM’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + there is no package called ‘blavaan’ +Execution halted +ERROR: lazy loading failed for package ‘TestAnaAPP’ +* removing ‘/tmp/workdir/TestAnaAPP/new/TestAnaAPP.Rcheck/TestAnaAPP’ + + +``` +### CRAN + +``` +* installing *source* package ‘TestAnaAPP’ ... +** package ‘TestAnaAPP’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘tidySEM’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + there is no package called ‘blavaan’ +Execution halted +ERROR: lazy loading failed for package ‘TestAnaAPP’ +* removing ‘/tmp/workdir/TestAnaAPP/old/TestAnaAPP.Rcheck/TestAnaAPP’ + + +``` +# treestats + +
+ +* Version: 1.0.3 +* GitHub: https://github.com/thijsjanzen/treestats +* Source code: https://github.com/cran/treestats +* Date/Publication: 2024-01-12 16:30:02 UTC +* Number of recursive dependencies: 229 + +Run `revdepcheck::cloud_details(, "treestats")` for more info + +
+ +## In both + +* checking whether package ‘treestats’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/treestats/new/treestats.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘treestats’ ... +** package ‘treestats’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +Error: C++20 standard requested but CXX20 is not defined +* removing ‘/tmp/workdir/treestats/new/treestats.Rcheck/treestats’ + + +``` +### CRAN + +``` +* installing *source* package ‘treestats’ ... +** package ‘treestats’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +Error: C++20 standard requested but CXX20 is not defined +* removing ‘/tmp/workdir/treestats/old/treestats.Rcheck/treestats’ + + +``` diff --git a/revdep/problems.md b/revdep/problems.md index 0bd2c2882b4..a1e08c1d2b1 100644 --- a/revdep/problems.md +++ b/revdep/problems.md @@ -576,7 +576,7 @@ Run `revdepcheck::cloud_details(, "nbTransmission")` for more info 4. └─igraph::as_adjacency_matrix(...) 5. └─igraph:::get.adjacency.dense(...) - [ FAIL 1 | WARN 11 | SKIP 0 | PASS 136 ] + [ FAIL 1 | WARN 7 | SKIP 0 | PASS 136 ] Error: Test failures Execution halted ``` @@ -778,15 +778,15 @@ Run `revdepcheck::cloud_details(, "pcalg")` for more info Running ‘test_bicscore.R’ Running ‘test_causalEffect.R’ ... + > set.seed(37) + > rD.10.4 <- withCallingHandlers( + + rDAGall(10, 4) # "low-level warning" -- get it here and test it below + , warning = function(w) { + rDAG.warn <<- conditionMessage(w); invokeRestart("muffleWarning") }) > ## with a low-level warning: > ## IGNORE_RDIFF_BEGIN > rDAG.warn - [1] "The `edges` argument of `as_adjacency_matrix` is deprecated; it will be removed in igraph 1.4.0" - > ## IGNORE_RDIFF_END - > stopifnot(grepl("graph_molloy_.*Cannot shuffle graph", rDAG.warn)) - Error: grepl("graph_molloy_.*Cannot shuffle graph", rDAG.warn) is not TRUE + Error: object 'rDAG.warn' not found Execution halted ``` diff --git a/tests/testthat/test-indexing.R b/tests/testthat/test-indexing.R index 64c103c9409..42ce079ad27 100644 --- a/tests/testthat/test-indexing.R +++ b/tests/testthat/test-indexing.R @@ -176,50 +176,6 @@ test_that("[[ indexing is consistent with length()", { expect_that(length(g), equals(vcount(g))) }) -test_that("[ can query edge ids", { - g <- make_test_named_tree() - - expect_that(g[1, 2, edges = TRUE], equals(1)) - expect_that( - canonicalize_matrix(g[c(1, 1, 7), c(2, 3, 14), edges = TRUE]), - equals(vector_to_square_matrix(1, 1, 0, 2, 2, 0, 0, 0, 13)) - ) - expect_that( - canonicalize_matrix(g[c(1, 1, 7), c(5, 3, 12), edges = TRUE]), - equals(vector_to_square_matrix(0, 0, 0, 2, 2, 0, 0, 0, 0)) - ) - expect_that( - canonicalize_matrix(g[c(1, 1, 1, 1), c(2, 3, 2, 2), edges = TRUE]), - equals(vector_to_square_matrix(1, 1, 1, 1, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1)) - ) - expect_that( - canonicalize_matrix(g[c(8, 17), c(17, 8), edges = TRUE]), - equals(vector_to_square_matrix(16, 0, 0, 0)) - ) -}) - -test_that("[ can query edge ids with symbolic names", { - g <- make_test_named_tree() - - expect_that(g["a", "b", edges = TRUE], equals(1)) - expect_that( - canonicalize_matrix(g[c("a", "a", "g"), c("b", "c", "n"), edges = TRUE]), - equals(vector_to_square_matrix(1, 1, 0, 2, 2, 0, 0, 0, 13)) - ) - expect_that( - canonicalize_matrix(g[c("a", "a", "g"), c("e", "c", "l"), edges = TRUE]), - equals(vector_to_square_matrix(0, 0, 0, 2, 2, 0, 0, 0, 0)) - ) - expect_that( - canonicalize_matrix(g[c("a", "a", "a", "a"), c("b", "c", "b", "b"), edges = TRUE]), - equals(vector_to_square_matrix(1, 1, 1, 1, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1)) - ) - expect_that( - canonicalize_matrix(g[c("h", "q"), c("q", "h"), edges = TRUE]), - equals(vector_to_square_matrix(16, 0, 0, 0)) - ) -}) - test_that("[[ can query incident edges", { g <- make_test_named_tree()