diff --git a/revdep/README.md b/revdep/README.md index 03755c9..fbe07c6 100644 --- a/revdep/README.md +++ b/revdep/README.md @@ -1,31 +1,26 @@ # Revdeps -## Failed to check (8) +## Failed to check (3) |package |version |error |warning |note | |:----------------|:-------|:------|:-------|:----| -|censored |? | | | | -|covid19india |0.1.4 |1 | | | |multinma |0.7.2 |1 | | | -|OVtool |1.0.3 |1 | | | |[params](failures.md#params)|0.7.3 |__+1__ | | | -|scCustomize |2.1.2 |1 | |1 | -|shinyTempSignal |0.0.8 |1 | | | |TriDimRegression |1.0.2 |1 | | | ## New problems (11) -|package |version |error |warning |note | -|:------------------|:-------|:--------|:-------|:--------| -|[adoptr](problems.md#adoptr)|1.1.0 |1 __+2__ | |__+1__ | -|[atrrr](problems.md#atrrr)|0.0.3 |__+1__ | | | -|[codebook](problems.md#codebook)|0.9.2 |1 | |3 __+1__ | -|[gtreg](problems.md#gtreg)|0.4.0 |__+2__ | | | -|[gtsummary](problems.md#gtsummary)|2.0.2 |__+2__ | |__+1__ | -|[logger](problems.md#logger)|0.3.0 |__+1__ |1 |1 | -|[odin](problems.md#odin)|1.2.5 |1 __+2__ | |__+1__ | -|[roxytypes](problems.md#roxytypes)|0.1.0 |__+2__ | |1 | -|[shinyCohortBuilder](problems.md#shinycohortbuilder)|0.2.1 |__+2__ | |__+1__ | -|[sqltargets](problems.md#sqltargets)|0.2.0 |__+1__ | | | -|[table.glue](problems.md#tableglue)|0.0.3 |__+3__ | |__+1__ | +|package |version |error |warning |note | +|:------------------|:-------|:------|:-------|:----| +|[adoptr](problems.md#adoptr)|1.1.0 |__+3__ | | | +|[atrrr](problems.md#atrrr)|0.0.3 |__+1__ | | | +|[codebook](problems.md#codebook)|0.9.2 |__+1__ | |3 | +|[gtreg](problems.md#gtreg)|0.4.0 |__+2__ | | | +|[gtsummary](problems.md#gtsummary)|2.0.2 |__+2__ | | | +|[logger](problems.md#logger)|0.3.0 |__+1__ | |1 | +|[odin](problems.md#odin)|1.2.5 |__+3__ | | | +|[roxytypes](problems.md#roxytypes)|0.1.0 |__+2__ | |1 | +|[shinyCohortBuilder](problems.md#shinycohortbuilder)|0.2.1 |__+2__ | |1 | +|[sqltargets](problems.md#sqltargets)|0.2.0 |__+1__ | | | +|[table.glue](problems.md#tableglue)|0.0.3 |__+3__ | |1 | diff --git a/revdep/cran.md b/revdep/cran.md index 3125af2..3988e1e 100644 --- a/revdep/cran.md +++ b/revdep/cran.md @@ -1,9 +1,9 @@ ## revdepcheck results -We checked 802 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package. +We checked 803 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package. * We saw 11 new problems - * We failed to check 8 packages + * We failed to check 3 packages Issues with CRAN packages are summarised below. @@ -13,13 +13,13 @@ Issues with CRAN packages are summarised below. * adoptr checking examples ... ERROR checking tests ... ERROR - checking re-building of vignette outputs ... NOTE + checking re-building of vignette outputs ... ERROR * atrrr checking tests ... ERROR * codebook - checking re-building of vignette outputs ... NOTE + checking re-building of vignette outputs ... ERROR * gtreg checking examples ... ERROR @@ -27,8 +27,7 @@ Issues with CRAN packages are summarised below. * gtsummary checking examples ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE + checking re-building of vignette outputs ... ERROR * logger checking tests ... ERROR @@ -36,7 +35,7 @@ Issues with CRAN packages are summarised below. * odin checking examples ... ERROR checking tests ... ERROR - checking re-building of vignette outputs ... NOTE + checking re-building of vignette outputs ... ERROR * roxytypes checking examples ... ERROR @@ -44,8 +43,7 @@ Issues with CRAN packages are summarised below. * shinyCohortBuilder checking examples ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE + checking re-building of vignette outputs ... ERROR * sqltargets checking tests ... ERROR @@ -53,16 +51,10 @@ Issues with CRAN packages are summarised below. * table.glue checking examples ... ERROR checking tests ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE + checking re-building of vignette outputs ... ERROR ### Failed to check -* censored (NA) -* covid19india (NA) * multinma (NA) -* OVtool (NA) * params (NA) -* scCustomize (NA) -* shinyTempSignal (NA) * TriDimRegression (NA) diff --git a/revdep/failures.md b/revdep/failures.md index d13218b..d5daef7 100644 --- a/revdep/failures.md +++ b/revdep/failures.md @@ -1,141 +1,3 @@ -# censored - -
- -* Version: 0.3.2 -* GitHub: https://github.com/tidymodels/censored -* Source code: https://github.com/cran/censored -* Date/Publication: 2024-06-11 18:10:02 UTC -* Number of recursive dependencies: 164 - -Run `revdepcheck::cloud_details(, "censored")` for more info - -
- -## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/censored/new/censored.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 ‘censored/DESCRIPTION’ ... OK -... -* this is package ‘censored’ version ‘0.3.2’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required and available but unsuitable version: ‘survival’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -### CRAN - -``` -* using log directory ‘/tmp/workdir/censored/old/censored.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 ‘censored/DESCRIPTION’ ... OK -... -* this is package ‘censored’ version ‘0.3.2’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required and available but unsuitable version: ‘survival’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -# covid19india - -
- -* Version: 0.1.4 -* GitHub: https://github.com/maxsal/covid19india -* Source code: https://github.com/cran/covid19india -* Date/Publication: 2021-10-09 15:00:30 UTC -* Number of recursive dependencies: 95 - -Run `revdepcheck::cloud_details(, "covid19india")` for more info - -
- -## In both - -* checking whether package ‘covid19india’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/covid19india/new/covid19india.Rcheck/00install.out’ for details. - ``` - -## Installation - -### Devel - -``` -* installing *source* package ‘covid19india’ ... -** package ‘covid19india’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** 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 ‘covid19india’ -* removing ‘/tmp/workdir/covid19india/new/covid19india.Rcheck/covid19india’ - - -``` -### CRAN - -``` -* installing *source* package ‘covid19india’ ... -** package ‘covid19india’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** 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 ‘covid19india’ -* removing ‘/tmp/workdir/covid19india/old/covid19india.Rcheck/covid19india’ - - -``` # multinma
@@ -171,17 +33,17 @@ using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ 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:205, +g++ -std=gnu++17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.4.0/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/4.4.0/lib/R/site-library/BH/include' -I'/opt/R/4.4.0/lib/R/site-library/Rcpp/include' -I'/opt/R/4.4.0/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.4.0/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.4.0/lib/R/site-library/rstan/include' -I'/opt/R/4.4.0/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.4.0/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/4.4.0/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_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] +/opt/R/4.4.0/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/4.4.0/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here +/opt/R/4.4.0/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_param.o] Error 1 +make: *** [/opt/R/4.4.0/lib/R/etc/Makeconf:202: stanExports_survival_param.o] Error 1 ERROR: compilation failed for package ‘multinma’ * removing ‘/tmp/workdir/multinma/new/multinma.Rcheck/multinma’ @@ -198,83 +60,21 @@ using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ 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:205, +g++ -std=gnu++17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.4.0/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/4.4.0/lib/R/site-library/BH/include' -I'/opt/R/4.4.0/lib/R/site-library/Rcpp/include' -I'/opt/R/4.4.0/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.4.0/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.4.0/lib/R/site-library/rstan/include' -I'/opt/R/4.4.0/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.4.0/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/4.4.0/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_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] +/opt/R/4.4.0/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/4.4.0/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here +/opt/R/4.4.0/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_param.o] Error 1 +make: *** [/opt/R/4.4.0/lib/R/etc/Makeconf:202: stanExports_survival_param.o] Error 1 ERROR: compilation failed for package ‘multinma’ * removing ‘/tmp/workdir/multinma/old/multinma.Rcheck/multinma’ -``` -# OVtool - -
- -* Version: 1.0.3 -* GitHub: NA -* Source code: https://github.com/cran/OVtool -* Date/Publication: 2021-11-02 08:10:07 UTC -* Number of recursive dependencies: 157 - -Run `revdepcheck::cloud_details(, "OVtool")` for more info - -
- -## In both - -* checking whether package ‘OVtool’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/OVtool/new/OVtool.Rcheck/00install.out’ for details. - ``` - -## Installation - -### Devel - -``` -* installing *source* package ‘OVtool’ ... -** package ‘OVtool’ 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: package or namespace load failed for ‘twang’ 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 -Execution halted -ERROR: lazy loading failed for package ‘OVtool’ -* removing ‘/tmp/workdir/OVtool/new/OVtool.Rcheck/OVtool’ - - -``` -### CRAN - -``` -* installing *source* package ‘OVtool’ ... -** package ‘OVtool’ 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: package or namespace load failed for ‘twang’ 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 -Execution halted -ERROR: lazy loading failed for package ‘OVtool’ -* removing ‘/tmp/workdir/OVtool/old/OVtool.Rcheck/OVtool’ - - ``` # params @@ -342,131 +142,6 @@ ERROR: loading failed * DONE (params) -``` -# scCustomize - -
- -* Version: 2.1.2 -* GitHub: https://github.com/samuel-marsh/scCustomize -* Source code: https://github.com/cran/scCustomize -* Date/Publication: 2024-02-28 19:40:02 UTC -* Number of recursive dependencies: 267 - -Run `revdepcheck::cloud_details(, "scCustomize")` for more info - -
- -## In both - -* checking whether package ‘scCustomize’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/scCustomize/new/scCustomize.Rcheck/00install.out’ for details. - ``` - -* checking package dependencies ... NOTE - ``` - Package suggested but not available for checking: ‘Nebulosa’ - ``` - -## Installation - -### Devel - -``` -* installing *source* package ‘scCustomize’ ... -** package ‘scCustomize’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘SeuratObject’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.4 is required -Execution halted -ERROR: lazy loading failed for package ‘scCustomize’ -* removing ‘/tmp/workdir/scCustomize/new/scCustomize.Rcheck/scCustomize’ - - -``` -### CRAN - -``` -* installing *source* package ‘scCustomize’ ... -** package ‘scCustomize’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘SeuratObject’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.4 is required -Execution halted -ERROR: lazy loading failed for package ‘scCustomize’ -* removing ‘/tmp/workdir/scCustomize/old/scCustomize.Rcheck/scCustomize’ - - -``` -# shinyTempSignal - -
- -* Version: 0.0.8 -* GitHub: https://github.com/YuLab-SMU/shinyTempSignal -* Source code: https://github.com/cran/shinyTempSignal -* Date/Publication: 2024-03-06 08:00:02 UTC -* Number of recursive dependencies: 137 - -Run `revdepcheck::cloud_details(, "shinyTempSignal")` for more info - -
- -## In both - -* checking whether package ‘shinyTempSignal’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/shinyTempSignal/new/shinyTempSignal.Rcheck/00install.out’ for details. - ``` - -## Installation - -### Devel - -``` -* installing *source* package ‘shinyTempSignal’ ... -** package ‘shinyTempSignal’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** 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 ‘shinyTempSignal’ -* removing ‘/tmp/workdir/shinyTempSignal/new/shinyTempSignal.Rcheck/shinyTempSignal’ - - -``` -### CRAN - -``` -* installing *source* package ‘shinyTempSignal’ ... -** package ‘shinyTempSignal’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** 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 ‘shinyTempSignal’ -* removing ‘/tmp/workdir/shinyTempSignal/old/shinyTempSignal.Rcheck/shinyTempSignal’ - - ``` # TriDimRegression diff --git a/revdep/problems.md b/revdep/problems.md index f56b29f..44e36d6 100644 --- a/revdep/problems.md +++ b/revdep/problems.md @@ -61,39 +61,12 @@ Run `revdepcheck::cloud_details(, "adoptr")` for more info Execution halted ``` -* checking re-building of vignette outputs ... NOTE +* checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: --- re-building ‘adoptr.Rmd’ using rmarkdown ``` -## In both - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘adoptr_jss.Rmd’ - ... - - > ess <- ExpectedSampleSize(dist = datadist, prior = alternative) - - > initial_design <- get_initial_design(theta = 0.3, - + alpha = 0.025, beta = 0.1, type = "two-stage", dist = datadist, - + order = 7) - - ... - ! is.environment(.envir) is not TRUE - Execution halted - - ‘adoptr.Rmd’ using ‘UTF-8’... OK - ‘adoptr_jss.Rmd’ using ‘UTF-8’... failed - ‘composite-scores.Rmd’ using ‘UTF-8’... OK - ‘conditional-scores.Rmd’ using ‘UTF-8’... failed - ‘defining-new-scores.Rmd’ using ‘UTF-8’... OK - ‘other-endpoints.Rmd’ using ‘UTF-8’... OK - ‘working-with-priors.Rmd’ using ‘UTF-8’... failed - ``` - # atrrr
@@ -151,7 +124,7 @@ Run `revdepcheck::cloud_details(, "codebook")` for more info ## Newly broken -* checking re-building of vignette outputs ... NOTE +* checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: --- re-building ‘codebook.Rmd’ using rmarkdown @@ -178,31 +151,6 @@ Run `revdepcheck::cloud_details(, "codebook")` for more info ## In both -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘codebook.Rmd’ - ... - - - - - - Quitting from lines 17-22 [rmdpartial-1] - - ... - Quitting from lines 17-22 [rmdpartial-1] - - When sourcing ‘codebook_tutorial.R’: - Error: is.environment(.envir) is not TRUE - Execution halted - - ‘codebook.Rmd’ using ‘UTF-8’... failed - ‘codebook_qualtrics.Rmd’ using ‘UTF-8’... failed - ‘codebook_sav.Rmd’ using ‘UTF-8’... failed - ‘codebook_tutorial.Rmd’ using ‘UTF-8’... failed - ``` - * checking package dependencies ... NOTE ``` Package suggested but not available for checking: ‘userfriendlyscience’ @@ -327,26 +275,7 @@ Run `revdepcheck::cloud_details(, "gtsummary")` for more info Execution halted ``` -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘gtsummary_definition.Rmd’ - ... - + tbl_regression() %>% bold_p(t = 0.5) - - > tbl_summary_ex <- trial %>% select(trt, age, grade, - + response) %>% tbl_summary(by = trt) - - When sourcing ‘gtsummary_definition.R’: - Error: ℹ In argument: `stat = as.character(...)`. - Caused by error in `glue_data()`: - ! is.environment(.envir) is not TRUE - Execution halted - - ‘gtsummary_definition.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE +* checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: ... @@ -409,31 +338,6 @@ Run `revdepcheck::cloud_details(, "logger")` for more info ## In both -* checking running R code from vignettes ... WARNING - ``` - Errors in running code in vignettes: - when running code in ‘migration.Rmd’ - ... - > oldconf <- list(threshold = log_threshold(), layout = log_layout(), - + formatter = log_formatter(), appender = log_appender()) - - > log_appender(appender_stdout) - - > library(futile.logger) - - ... - Error: there is no package called ‘futile.logger’ - Execution halted - - ‘Intro.Rmd’ using ‘UTF-8’... OK - ‘anatomy.Rmd’ using ‘UTF-8’... OK - ‘customize_logger.Rmd’ using ‘UTF-8’... OK - ‘migration.Rmd’ using ‘UTF-8’... failed - ‘performance.Rmd’ using ‘UTF-8’... OK - ‘r_packages.Rmd’ using ‘UTF-8’... OK - ‘write_custom_extensions.Rmd’ using ‘UTF-8’... OK - ``` - * checking package dependencies ... NOTE ``` Packages which this enhances but not available for checking: @@ -506,7 +410,7 @@ Run `revdepcheck::cloud_details(, "odin")` for more info Execution halted ``` -* checking re-building of vignette outputs ... NOTE +* checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: ... @@ -531,33 +435,6 @@ Run `revdepcheck::cloud_details(, "odin")` for more info Execution halted ``` -## In both - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘discrete.Rmd’ - ... - beta <- user(0.2) - gamma <- user(0.1) - ``` - - > sir_generator <- odin::odin(path_sir_model) - Loading required namespace: pkgbuild - - ... - > generator <- odin::odin(path_logistic) - Loading required namespace: pkgbuild - - When sourcing ‘odin.R’: - Error: is.environment(.envir) is not TRUE - Execution halted - - ‘discrete.Rmd’ using ‘UTF-8’... failed - ‘functions.Rmd’ using ‘UTF-8’... OK - ‘odin.Rmd’ using ‘UTF-8’... failed - ``` - # params
@@ -732,30 +609,7 @@ Run `revdepcheck::cloud_details(, "shinyCohortBuilder")` for more info Execution halted ``` -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘gui-filter-layer.Rmd’ - ... - $ get_params :function (name) - $ get_data :function (data_object) - $ get_defaults:function (data_object, cache_object) - - > .pre_post_stats_text(name = c("A", "B"), current = 1:2, - + previous = 3:4, stats = c("pre", "post")) - - When sourcing ‘gui-filter-layer.R’: - Error: is.environment(.envir) is not TRUE - Execution halted - - ‘custom-gui-layer.Rmd’ using ‘UTF-8’... OK - ‘gui-filter-layer.Rmd’ using ‘UTF-8’... failed - ‘package-options.Rmd’ using ‘UTF-8’... OK - ‘shinyCohortBuilder.Rmd’ using ‘UTF-8’... OK - ‘updating-source.Rmd’ using ‘UTF-8’... OK - ``` - -* checking re-building of vignette outputs ... NOTE +* checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: ... @@ -780,6 +634,33 @@ Run `revdepcheck::cloud_details(, "shinyCohortBuilder")` for more info Execution halted ``` +## In both + +* checking Rd files ... NOTE + ``` + checkRd: (-1) gui-filter-layer.Rd:40: Lost braces in \itemize; meant \describe ? + checkRd: (-1) gui-filter-layer.Rd:41: Lost braces in \itemize; meant \describe ? + checkRd: (-1) gui-filter-layer.Rd:42: Lost braces in \itemize; meant \describe ? + checkRd: (-1) gui-filter-layer.Rd:43: Lost braces in \itemize; meant \describe ? + checkRd: (-1) gui-filter-layer.Rd:44-45: Lost braces in \itemize; meant \describe ? + checkRd: (-1) gui-filter-layer.Rd:46-49: Lost braces in \itemize; meant \describe ? + checkRd: (-1) rendering-step-attrition.Rd:34: Lost braces in \itemize; meant \describe ? + checkRd: (-1) rendering-step-attrition.Rd:35: Lost braces in \itemize; meant \describe ? + checkRd: (-1) source-gui-layer.Rd:22: Lost braces in \itemize; meant \describe ? + checkRd: (-1) source-gui-layer.Rd:23: Lost braces in \itemize; meant \describe ? + ... + checkRd: (-1) trigger-action.Rd:39: Lost braces in \itemize; meant \describe ? + checkRd: (-1) trigger-action.Rd:40: Lost braces in \itemize; meant \describe ? + checkRd: (-1) trigger-action.Rd:41: Lost braces in \itemize; meant \describe ? + checkRd: (-1) trigger-action.Rd:42: Lost braces in \itemize; meant \describe ? + checkRd: (-1) trigger-action.Rd:43: Lost braces in \itemize; meant \describe ? + checkRd: (-1) trigger-action.Rd:44: Lost braces in \itemize; meant \describe ? + checkRd: (-1) trigger-action.Rd:45: Lost braces in \itemize; meant \describe ? + checkRd: (-1) trigger-action.Rd:46: Lost braces in \itemize; meant \describe ? + checkRd: (-1) trigger-action.Rd:47: Lost braces in \itemize; meant \describe ? + checkRd: (-1) trigger-action.Rd:48: Lost braces in \itemize; meant \describe ? + ``` + # sqltargets
@@ -885,32 +766,7 @@ Run `revdepcheck::cloud_details(, "table.glue")` for more info Execution halted ``` -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘default_rounder.Rmd’ - ... - > names(rspec) <- paste("table.glue", names(rspec), - + sep = ".") - - > options(rspec) - - > table_value(pi) - - ... - {height_upr})")`. - ℹ In group 1: `sex = "female"`. - Caused by error: - ! Failed to evaluate glue component {..f(height_est)} - Caused by error in `glue_data()`: - ! is.environment(.envir) is not TRUE - Execution halted - - ‘default_rounder.Rmd’ using ‘UTF-8’... failed - ‘table_guide.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE +* checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: --- re-building ‘default_rounder.Rmd’ using rmarkdown @@ -935,3 +791,18 @@ Run `revdepcheck::cloud_details(, "table.glue")` for more info Execution halted ``` +## In both + +* checking Rd files ... NOTE + ``` + checkRd: (-1) table_ester.Rd:32: Lost braces; missing escapes or markup? + 32 | inside of curly brackets, i.e., { } . For instance, if estimate = 1.23 + | ^ + checkRd: (-1) table_ester.Rd:33: Lost braces; missing escapes or markup? + 33 | and error = 0.45, then \code{form} = "{estimate} ({error})" will return + | ^ + checkRd: (-1) table_ester.Rd:33: Lost braces; missing escapes or markup? + 33 | and error = 0.45, then \code{form} = "{estimate} ({error})" will return + | ^ + ``` +