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‎revdep/README.md

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# Revdeps
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## Failed to check (3)
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## Failed to check (2)
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|package |version |error |warning |note |
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|:---------|:-------|:-----|:-------|:----|
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|clustree |? | | | |
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|multinma |0.7.1 |1 | | |
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|scDiffCom |? | | | |
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|package |version |error |warning |note |
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|:--------|:-------|:-----|:-------|:----|
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|bayesCT |0.99.3 |1 | | |
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|multinma |0.7.1 |1 | | |
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## New problems (1)
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|package |version |error |warning |note |
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|:----------|:-------|:-----|:-------|:----|
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|[preferably](problems.md#preferably)|0.4.1 | |__+1__ | |
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‎revdep/cran.md

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We checked 144 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package.
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* We saw 0 new problems
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* We failed to check 3 packages
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* We saw 1 new problems
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* We failed to check 2 packages
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Issues with CRAN packages are summarised below.
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### New problems
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(This reports the first line of each new failure)
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* preferably
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checking whether package ‘preferably’ can be installed ... WARNING
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I have submitted a patch at https://github.com/amirmasoudabdol/preferably/pull/19.
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### Failed to check
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* clustree (NA)
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* multinma (NA)
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* scDiffCom (NA)
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* bayesCT (NA)
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* multinma (NA)

‎revdep/failures.md

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# clustree
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# bayesCT
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<details>
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* Version: 0.5.1
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* GitHub: https://github.com/lazappi/clustree
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* Source code: https://github.com/cran/clustree
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* Date/Publication: 2023-11-05 19:10:02 UTC
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* Number of recursive dependencies: 192
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* Version: 0.99.3
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* GitHub: https://github.com/thevaachandereng/bayesCT
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* Source code: https://github.com/cran/bayesCT
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* Date/Publication: 2020-07-01 09:30:02 UTC
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* Number of recursive dependencies: 122
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Run `revdepcheck::cloud_details(, "clustree")` for more info
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Run `revdepcheck::cloud_details(, "bayesCT")` for more info
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</details>
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## Error before installation
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### Devel
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## In both
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```
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* using log directory ‘/tmp/workdir/clustree/new/clustree.Rcheck’
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* using R version 4.3.1 (2023-06-16)
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* using platform: x86_64-pc-linux-gnu (64-bit)
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* R was compiled by
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gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
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GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
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* running under: Ubuntu 22.04.4 LTS
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* using session charset: UTF-8
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* using option ‘--no-manual’
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* checking for file ‘clustree/DESCRIPTION’ ... OK
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...
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* checking tests ... OK
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Running ‘spelling.R’
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Running ‘testthat.R’
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* checking for unstated dependencies in vignettes ... OK
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* checking package vignettes in ‘inst/doc’ ... OK
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* checking running R code from vignettes ... OK
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‘clustree.Rmd’ using ‘UTF-8’... OK
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* checking re-building of vignette outputs ... OK
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* DONE
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Status: 1 NOTE
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* checking whether package ‘bayesCT’ can be installed ... ERROR
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```
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Installation failed.
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See ‘/tmp/workdir/bayesCT/new/bayesCT.Rcheck/00install.out’ for details.
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```
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## Installation
4224
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### Devel
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```
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* installing *source* package ‘bayesCT’ ...
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** package ‘bayesCT’ successfully unpacked and MD5 sums checked
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** using staged installation
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** R
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** data
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*** moving datasets to lazyload DB
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** inst
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** byte-compile and prepare package for lazy loading
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Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
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namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required
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Calls: <Anonymous> ... namespaceImportFrom -> asNamespace -> loadNamespace
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Execution halted
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ERROR: lazy loading failed for package ‘bayesCT’
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* removing ‘/tmp/workdir/bayesCT/new/bayesCT.Rcheck/bayesCT’
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```
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### CRAN
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```
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* using log directory ‘/tmp/workdir/clustree/old/clustree.Rcheck’
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* using R version 4.3.1 (2023-06-16)
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* using platform: x86_64-pc-linux-gnu (64-bit)
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* R was compiled by
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gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
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GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
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* running under: Ubuntu 22.04.4 LTS
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* using session charset: UTF-8
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* using option ‘--no-manual’
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* checking for file ‘clustree/DESCRIPTION’ ... OK
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...
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* checking tests ... OK
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Running ‘spelling.R’
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Running ‘testthat.R’
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* checking for unstated dependencies in vignettes ... OK
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* checking package vignettes in ‘inst/doc’ ... OK
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* checking running R code from vignettes ... OK
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‘clustree.Rmd’ using ‘UTF-8’... OK
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* checking re-building of vignette outputs ... OK
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* DONE
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Status: 1 NOTE
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73-
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* installing *source* package ‘bayesCT’ ...
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** package ‘bayesCT’ successfully unpacked and MD5 sums checked
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** using staged installation
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** R
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** data
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*** moving datasets to lazyload DB
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** inst
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** byte-compile and prepare package for lazy loading
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Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
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namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required
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Calls: <Anonymous> ... namespaceImportFrom -> asNamespace -> loadNamespace
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Execution halted
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ERROR: lazy loading failed for package ‘bayesCT’
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* removing ‘/tmp/workdir/bayesCT/old/bayesCT.Rcheck/bayesCT’
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```
@@ -112,14 +100,14 @@ using C++17
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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
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In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205,
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...
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/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> >]’
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/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> >]’
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/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
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/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]
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654 | return internal::first_aligned<int(unpacket_traits<DefaultPacketType>::alignment),Derived>(m);
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| ^~~~~~~~~
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g++: fatal error: Killed signal terminated program cc1plus
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compilation terminated.
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make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_survival_mspline.o] Error 1
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make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_survival_param.o] Error 1
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ERROR: compilation failed for package ‘multinma’
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* removing ‘/tmp/workdir/multinma/new/multinma.Rcheck/multinma’
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@@ -139,92 +127,16 @@ using C++17
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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
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In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205,
141129
...
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/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> >]’
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/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> >]’
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/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
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/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]
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| ^~~~~~~~~
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g++: fatal error: Killed signal terminated program cc1plus
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compilation terminated.
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make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_survival_mspline.o] Error 1
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make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_survival_param.o] Error 1
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ERROR: compilation failed for package ‘multinma’
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* removing ‘/tmp/workdir/multinma/old/multinma.Rcheck/multinma’
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```
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# scDiffCom
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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/scDiffCom
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* Date/Publication: 2023-11-03 18:40:02 UTC
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* Number of recursive dependencies: 259
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Run `revdepcheck::cloud_details(, "scDiffCom")` for more info
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</details>
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## Error before installation
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### Devel
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```
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* using log directory ‘/tmp/workdir/scDiffCom/new/scDiffCom.Rcheck’
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* using R version 4.3.1 (2023-06-16)
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* using platform: x86_64-pc-linux-gnu (64-bit)
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* R was compiled by
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gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
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GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
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* running under: Ubuntu 22.04.4 LTS
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* using session charset: UTF-8
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* using option ‘--no-manual’
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* checking for file ‘scDiffCom/DESCRIPTION’ ... OK
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...
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* this is package ‘scDiffCom’ version ‘1.0.0’
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* package encoding: UTF-8
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* checking package namespace information ... OK
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* checking package dependencies ... ERROR
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Package required but not available: ‘Seurat’
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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manual.
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* DONE
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Status: 1 ERROR
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```
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### CRAN
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```
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* using log directory ‘/tmp/workdir/scDiffCom/old/scDiffCom.Rcheck’
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* using R version 4.3.1 (2023-06-16)
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* using platform: x86_64-pc-linux-gnu (64-bit)
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* R was compiled by
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gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
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GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
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* running under: Ubuntu 22.04.4 LTS
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* using session charset: UTF-8
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* using option ‘--no-manual’
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* checking for file ‘scDiffCom/DESCRIPTION’ ... OK
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...
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* this is package ‘scDiffCom’ version ‘1.0.0’
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* package encoding: UTF-8
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* checking package namespace information ... OK
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* checking package dependencies ... ERROR
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Package required but not available: ‘Seurat’
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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manual.
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* DONE
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Status: 1 ERROR
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```

‎revdep/problems.md

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*Wow, no problems at all. :)*
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# preferably
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<details>
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* Version: 0.4.1
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* GitHub: https://github.com/amirmasoudabdol/preferably
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* Source code: https://github.com/cran/preferably
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* Date/Publication: 2022-07-20 14:30:06 UTC
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* Number of recursive dependencies: 53
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Run `revdepcheck::cloud_details(, "preferably")` for more info
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</details>
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## Newly broken
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* checking whether package ‘preferably’ can be installed ... WARNING
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```
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Found the following significant warnings:
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Warning: replacing previous import ‘knitr::clean_cache’ by ‘pkgdown::clean_cache’ when loading ‘preferably’
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See ‘/tmp/workdir/preferably/new/preferably.Rcheck/00install.out’ for details.
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```
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