Check revdeps

r-lib · Sep 17, 2024 · ae56105 · ae56105
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diff --git 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
@@ -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
@@ -1,76 +1,64 @@
-# clustree
+# bayesCT
 
 <details>
 
-* 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
 
 </details>
 
-## 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: <Anonymous> ... 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: <Anonymous> ... 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<Model, BaseRNG>::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<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >]’
+/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<Model, BaseRNG>::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<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >]’
 /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<double>::type’ {aka ‘__m128d’} [-Wignored-attributes]
  654 | return internal::first_aligned<int(unpacket_traits<DefaultPacketType>::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<Model, BaseRNG>::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<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >]’
+/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<Model, BaseRNG>::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<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >]’
 /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<double>::type’ {aka ‘__m128d’} [-Wignored-attributes]
  654 | return internal::first_aligned<int(unpacket_traits<DefaultPacketType>::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
-
-<details>
-
-* 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
-
-</details>
-
-## 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
@@ -1 +1,23 @@
-*Wow, no problems at all. :)*
+# preferably
+
+<details>
+
+* 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
+
+</details>
+
+## 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.
+ ```
+