diff --git a/revdep/README.md b/revdep/README.md index 97459a2eb..8cbc119dd 100644 --- a/revdep/README.md +++ b/revdep/README.md @@ -1,10 +1,15 @@ # Revdeps -## Failed to check (3) +## Failed to check (2) -|package |version |error |warning |note | -|:---------|:-------|:-----|:-------|:----| -|clustree |? | | | | -|multinma |0.7.1 |1 | | | -|scDiffCom |? | | | | +|package |version |error |warning |note | +|:--------|:-------|:-----|:-------|:----| +|bayesCT |0.99.3 |1 | | | +|multinma |0.7.1 |1 | | | + +## New problems (1) + +|package |version |error |warning |note | +|:----------|:-------|:-----|:-------|:----| +|[preferably](problems.md#preferably)|0.4.1 | |__+1__ | | diff --git a/revdep/cran.md b/revdep/cran.md index b6089a30f..815b23a77 100644 --- a/revdep/cran.md +++ b/revdep/cran.md @@ -2,13 +2,19 @@ We checked 144 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package. - * We saw 0 new problems - * We failed to check 3 packages + * We saw 1 new problems + * We failed to check 2 packages Issues with CRAN packages are summarised below. +### New problems +(This reports the first line of each new failure) + +* preferably + checking whether package ‘preferably’ can be installed ... WARNING + I have submitted a patch at https://github.com/amirmasoudabdol/preferably/pull/19. + ### Failed to check -* clustree (NA) -* multinma (NA) -* scDiffCom (NA) +* bayesCT (NA) +* multinma (NA) diff --git a/revdep/failures.md b/revdep/failures.md index 39fb711e7..3cb79778a 100644 --- a/revdep/failures.md +++ b/revdep/failures.md @@ -1,76 +1,64 @@ -# clustree +# bayesCT
-* Version: 0.5.1 -* GitHub: https://github.com/lazappi/clustree -* Source code: https://github.com/cran/clustree -* Date/Publication: 2023-11-05 19:10:02 UTC -* Number of recursive dependencies: 192 +* Version: 0.99.3 +* GitHub: https://github.com/thevaachandereng/bayesCT +* Source code: https://github.com/cran/bayesCT +* Date/Publication: 2020-07-01 09:30:02 UTC +* Number of recursive dependencies: 122 -Run `revdepcheck::cloud_details(, "clustree")` for more info +Run `revdepcheck::cloud_details(, "bayesCT")` for more info
-## Error before installation - -### Devel +## In both -``` -* using log directory ‘/tmp/workdir/clustree/new/clustree.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 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘clustree/DESCRIPTION’ ... OK -... -* checking tests ... OK - Running ‘spelling.R’ - Running ‘testthat.R’ -* checking for unstated dependencies in vignettes ... OK -* checking package vignettes in ‘inst/doc’ ... OK -* checking running R code from vignettes ... OK - ‘clustree.Rmd’ using ‘UTF-8’... OK -* checking re-building of vignette outputs ... OK -* DONE -Status: 1 NOTE +* checking whether package ‘bayesCT’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/bayesCT/new/bayesCT.Rcheck/00install.out’ for details. + ``` +## Installation +### Devel +``` +* installing *source* package ‘bayesCT’ ... +** package ‘bayesCT’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +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 ‘bayesCT’ +* removing ‘/tmp/workdir/bayesCT/new/bayesCT.Rcheck/bayesCT’ ``` ### CRAN ``` -* using log directory ‘/tmp/workdir/clustree/old/clustree.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 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘clustree/DESCRIPTION’ ... OK -... -* checking tests ... OK - Running ‘spelling.R’ - Running ‘testthat.R’ -* checking for unstated dependencies in vignettes ... OK -* checking package vignettes in ‘inst/doc’ ... OK -* checking running R code from vignettes ... OK - ‘clustree.Rmd’ using ‘UTF-8’... OK -* checking re-building of vignette outputs ... OK -* DONE -Status: 1 NOTE - - - +* installing *source* package ‘bayesCT’ ... +** package ‘bayesCT’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +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 ‘bayesCT’ +* removing ‘/tmp/workdir/bayesCT/old/bayesCT.Rcheck/bayesCT’ ``` @@ -112,14 +100,14 @@ 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:205, ... -/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_survival_mspline_namespace::model_survival_mspline; 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:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_survival_param_namespace::model_survival_param; 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:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 654 | return internal::first_aligned::alignment),Derived>(m); | ^~~~~~~~~ g++: fatal error: Killed signal terminated program cc1plus compilation terminated. -make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_survival_mspline.o] Error 1 +make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_survival_param.o] Error 1 ERROR: compilation failed for package ‘multinma’ * removing ‘/tmp/workdir/multinma/new/multinma.Rcheck/multinma’ @@ -139,92 +127,16 @@ 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:205, ... -/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_survival_mspline_namespace::model_survival_mspline; 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:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_survival_param_namespace::model_survival_param; 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:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 654 | return internal::first_aligned::alignment),Derived>(m); | ^~~~~~~~~ g++: fatal error: Killed signal terminated program cc1plus compilation terminated. -make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_survival_mspline.o] Error 1 +make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_survival_param.o] Error 1 ERROR: compilation failed for package ‘multinma’ * removing ‘/tmp/workdir/multinma/old/multinma.Rcheck/multinma’ -``` -# scDiffCom - -
- -* Version: 1.0.0 -* GitHub: NA -* Source code: https://github.com/cran/scDiffCom -* Date/Publication: 2023-11-03 18:40:02 UTC -* Number of recursive dependencies: 259 - -Run `revdepcheck::cloud_details(, "scDiffCom")` for more info - -
- -## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/scDiffCom/new/scDiffCom.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 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘scDiffCom/DESCRIPTION’ ... OK -... -* this is package ‘scDiffCom’ version ‘1.0.0’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘Seurat’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -### CRAN - -``` -* using log directory ‘/tmp/workdir/scDiffCom/old/scDiffCom.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 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.4 LTS -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘scDiffCom/DESCRIPTION’ ... OK -... -* this is package ‘scDiffCom’ version ‘1.0.0’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘Seurat’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - ``` diff --git a/revdep/problems.md b/revdep/problems.md index 9a2073633..e995a4e05 100644 --- a/revdep/problems.md +++ b/revdep/problems.md @@ -1 +1,23 @@ -*Wow, no problems at all. :)* \ No newline at end of file +# preferably + +
+ +* Version: 0.4.1 +* GitHub: https://github.com/amirmasoudabdol/preferably +* Source code: https://github.com/cran/preferably +* Date/Publication: 2022-07-20 14:30:06 UTC +* Number of recursive dependencies: 53 + +Run `revdepcheck::cloud_details(, "preferably")` for more info + +
+ +## Newly broken + +* checking whether package ‘preferably’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: replacing previous import ‘knitr::clean_cache’ by ‘pkgdown::clean_cache’ when loading ‘preferably’ + See ‘/tmp/workdir/preferably/new/preferably.Rcheck/00install.out’ for details. + ``` +