diff --git a/revdep/.gitignore b/revdep/.gitignore
index 7fc8a4a0c1..a2b0d9bb97 100644
--- a/revdep/.gitignore
+++ b/revdep/.gitignore
@@ -1,2 +1,3 @@
/cloud.noindex
+/cloud
/review/
diff --git a/revdep/README.md b/revdep/README.md
index d7bf11c3b9..dd681ce38b 100644
--- a/revdep/README.md
+++ b/revdep/README.md
@@ -1,38 +1,21 @@
# Revdeps
-## Failed to check (22)
+## Failed to check (4)
-|package |version |error |warning |note |
-|:---------------------|:-------|:-----|:-------|:----|
-|bnlearn |? | | | |
-|CARBayes |6.1.1 |1 | | |
-|ConnectednessApproach |1.0.3 |1 | | |
-|datapack |1.4.1 |1 | | |
-|easybgm |0.1.2 |1 | | |
-|erah |2.0.1 |1 | | |
-|evolqg |0.3-4 |1 | | |
-|frechet |0.3.0 |1 | | |
-|kstMatrix |? | | | |
-|manet |2.0 |1 | | |
-|mlmts |1.1.2 |1 | | |
-|multinma |0.7.2 |1 | | |
-|netcmc |1.0.2 |1 | | |
-|NetworkChange |0.8 |1 | | |
-|PathwaySpace |? | | | |
-|pcvr |1.0.0 |1 | | |
-|piecewiseSEM |? | | | |
-|RGraphSpace |? | | | |
-|robber |? | | | |
-|rTwig |1.1.0 |1 | | |
-|Seurat |5.1.0 |1 | | |
-|streamDAG |? | | | |
+|package |version |error |warning |note |
+|:---------|:-------|:-----|:-------|:----|
+|bnlearn |5.0.1 |1 | | |
+|datapack |1.4.1 |1 | | |
+|multinma |0.7.2 |1 | | |
+|streamDAG |? | | | |
-## New problems (4)
+## New problems (5)
-|package |version |error |warning |note |
-|:---------|:-------|:------|:--------|:----|
-|[CePa](problems.md#cepa)|0.8.0 | |1 __+1__ | |
-|[MetaNet](problems.md#metanet)|0.1.2 |__+1__ | | |
-|[simcausal](problems.md#simcausal)|0.5.6 |__+1__ | |1 |
-|[skynet](problems.md#skynet)|1.4.3 |__+1__ | |1 |
+|package |version |error |warning |note |
+|:-----------|:-------|:------|:-------|:----|
+|[manynet](problems.md#manynet)|1.2.6 |__+1__ | |3 |
+|[MetaNet](problems.md#metanet)|0.1.2 |__+1__ | | |
+|[simcausal](problems.md#simcausal)|0.5.6 |__+1__ |1 | |
+|[skynet](problems.md#skynet)|1.4.3 |__+1__ | |1 |
+|[SpaDES.core](problems.md#spadescore)|2.1.0 |__+1__ | |1 |
diff --git a/revdep/cran.md b/revdep/cran.md
index c6677b86da..45665af972 100644
--- a/revdep/cran.md
+++ b/revdep/cran.md
@@ -1,17 +1,17 @@
## revdepcheck results
-We checked 858 reverse dependencies (853 from CRAN + 5 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package.
+We checked 868 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package.
- * We saw 4 new problems
- * We failed to check 17 packages
+ * We saw 5 new problems
+ * We failed to check 4 packages
Issues with CRAN packages are summarised below.
### New problems
(This reports the first line of each new failure)
-* CePa
- checking Rd cross-references ... WARNING
+* manynet
+ checking tests ... ERROR
* MetaNet
checking examples ... ERROR
@@ -22,22 +22,12 @@ Issues with CRAN packages are summarised below.
* skynet
checking tests ... ERROR
+* SpaDES.core
+ checking tests ... ERROR
+
### Failed to check
-* CARBayes (NA)
-* ConnectednessApproach (NA)
-* datapack (NA)
-* easybgm (NA)
-* erah (NA)
-* evolqg (NA)
-* frechet (NA)
-* manet (NA)
-* mlmts (NA)
-* multinma (NA)
-* netcmc (NA)
-* NetworkChange (NA)
-* pcvr (NA)
-* robber (NA)
-* rTwig (NA)
-* Seurat (NA)
-* streamDAG (NA)
+* bnlearn (NA)
+* datapack (NA)
+* multinma (NA)
+* streamDAG (NA)
diff --git a/revdep/failures.md b/revdep/failures.md
index ac1f1ad079..cb6fa09c26 100644
--- a/revdep/failures.md
+++ b/revdep/failures.md
@@ -2,57 +2,22 @@
-* Version: NA
+* Version: 5.0.1
* GitHub: NA
* Source code: https://github.com/cran/bnlearn
+* Date/Publication: 2024-08-19 17:40:11 UTC
* Number of recursive dependencies: 36
Run `revdepcheck::cloud_details(, "bnlearn")` for more info
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# CARBayes
-
-
-
-* Version: 6.1.1
-* GitHub: https://github.com/duncanplee/CARBayes
-* Source code: https://github.com/cran/CARBayes
-* Date/Publication: 2024-03-08 13:20:02 UTC
-* Number of recursive dependencies: 137
-
-Run `revdepcheck::cloud_details(, "CARBayes")` for more info
-
-
-
## In both
-* checking whether package ‘CARBayes’ can be installed ... ERROR
+* checking whether package ‘bnlearn’ can be installed ... ERROR
```
Installation failed.
- See ‘/tmp/workdir/CARBayes/new/CARBayes.Rcheck/00install.out’ for details.
+ See ‘/tmp/workdir/bnlearn/new/bnlearn.Rcheck/00install.out’ for details.
```
## Installation
@@ -60,110 +25,54 @@ Run `revdepcheck::cloud_details(, "CARBayes")` for more info
### Devel
```
-* installing *source* package ‘CARBayes’ ...
-** package ‘CARBayes’ successfully unpacked and MD5 sums checked
+* installing *source* package ‘bnlearn’ ...
+** package ‘bnlearn’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
-using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
-g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c CARBayes.cpp -o CARBayes.o
-g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o
-g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o CARBayes.so CARBayes.o RcppExports.o -L/opt/R/4.3.1/lib/R/lib -lR
-installing to /tmp/workdir/CARBayes/new/CARBayes.Rcheck/00LOCK-CARBayes/00new/CARBayes/libs
-** 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
+using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
+gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c arcs/arcs2amat.c -o arcs/arcs2amat.o
+gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c arcs/arcs2elist.c -o arcs/arcs2elist.o
+gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c arcs/bind.c -o arcs/bind.o
+gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c arcs/filter.arcs.c -o arcs/filter.arcs.o
+gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c arcs/hash.c -o arcs/hash.o
+...
+*** installing help indices
+** building package indices
+** testing if installed package can be loaded from temporary location
+Error: package or namespace load failed for ‘bnlearn’ in dyn.load(file, DLLpath = DLLpath, ...):
+ unable to load shared object '/tmp/workdir/bnlearn/new/bnlearn.Rcheck/00LOCK-bnlearn/00new/bnlearn/libs/bnlearn.so':
+ /tmp/workdir/bnlearn/new/bnlearn.Rcheck/00LOCK-bnlearn/00new/bnlearn/libs/bnlearn.so: undefined symbol: allocLang
+Error: loading failed
Execution halted
-ERROR: lazy loading failed for package ‘CARBayes’
-* removing ‘/tmp/workdir/CARBayes/new/CARBayes.Rcheck/CARBayes’
+ERROR: loading failed
+* removing ‘/tmp/workdir/bnlearn/new/bnlearn.Rcheck/bnlearn’
```
### CRAN
```
-* installing *source* package ‘CARBayes’ ...
-** package ‘CARBayes’ successfully unpacked and MD5 sums checked
+* installing *source* package ‘bnlearn’ ...
+** package ‘bnlearn’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
-using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
-g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c CARBayes.cpp -o CARBayes.o
-g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o
-g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o CARBayes.so CARBayes.o RcppExports.o -L/opt/R/4.3.1/lib/R/lib -lR
-installing to /tmp/workdir/CARBayes/old/CARBayes.Rcheck/00LOCK-CARBayes/00new/CARBayes/libs
-** 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 ‘CARBayes’
-* removing ‘/tmp/workdir/CARBayes/old/CARBayes.Rcheck/CARBayes’
-
-
-```
-# ConnectednessApproach
-
-
-
-* Version: 1.0.3
-* GitHub: NA
-* Source code: https://github.com/cran/ConnectednessApproach
-* Date/Publication: 2024-06-16 16:20:02 UTC
-* Number of recursive dependencies: 131
-
-Run `revdepcheck::cloud_details(, "ConnectednessApproach")` for more info
-
-
-
-## In both
-
-* checking whether package ‘ConnectednessApproach’ can be installed ... ERROR
- ```
- Installation failed.
- See ‘/tmp/workdir/ConnectednessApproach/new/ConnectednessApproach.Rcheck/00install.out’ for details.
- ```
-
-## Installation
-
-### Devel
-
-```
-* installing *source* package ‘ConnectednessApproach’ ...
-** package ‘ConnectednessApproach’ 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 ‘ConnectednessApproach’
-* removing ‘/tmp/workdir/ConnectednessApproach/new/ConnectednessApproach.Rcheck/ConnectednessApproach’
-
-
-```
-### CRAN
-
-```
-* installing *source* package ‘ConnectednessApproach’ ...
-** package ‘ConnectednessApproach’ 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
+using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
+gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c arcs/arcs2amat.c -o arcs/arcs2amat.o
+gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c arcs/arcs2elist.c -o arcs/arcs2elist.o
+gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c arcs/bind.c -o arcs/bind.o
+gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c arcs/filter.arcs.c -o arcs/filter.arcs.o
+gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c arcs/hash.c -o arcs/hash.o
+...
+*** installing help indices
+** building package indices
+** testing if installed package can be loaded from temporary location
+Error: package or namespace load failed for ‘bnlearn’ in dyn.load(file, DLLpath = DLLpath, ...):
+ unable to load shared object '/tmp/workdir/bnlearn/old/bnlearn.Rcheck/00LOCK-bnlearn/00new/bnlearn/libs/bnlearn.so':
+ /tmp/workdir/bnlearn/old/bnlearn.Rcheck/00LOCK-bnlearn/00new/bnlearn/libs/bnlearn.so: undefined symbol: allocLang
+Error: loading failed
Execution halted
-ERROR: lazy loading failed for package ‘ConnectednessApproach’
-* removing ‘/tmp/workdir/ConnectednessApproach/old/ConnectednessApproach.Rcheck/ConnectednessApproach’
+ERROR: loading failed
+* removing ‘/tmp/workdir/bnlearn/old/bnlearn.Rcheck/bnlearn’
```
@@ -201,7 +110,7 @@ Run `revdepcheck::cloud_details(, "datapack")` for more info
** inst
** byte-compile and prepare package for lazy loading
Error in dyn.load(file, DLLpath = DLLpath, ...) :
- unable to load shared object '/opt/R/4.3.1/lib/R/site-library/redland/libs/redland.so':
+ unable to load shared object '/opt/R/4.4.0/lib/R/site-library/redland/libs/redland.so':
librdf.so.0: cannot open shared object file: No such file or directory
Calls: ... namespaceImport -> loadNamespace -> library.dynam -> dyn.load
Execution halted
@@ -220,7 +129,7 @@ ERROR: lazy loading failed for package ‘datapack’
** inst
** byte-compile and prepare package for lazy loading
Error in dyn.load(file, DLLpath = DLLpath, ...) :
- unable to load shared object '/opt/R/4.3.1/lib/R/site-library/redland/libs/redland.so':
+ unable to load shared object '/opt/R/4.4.0/lib/R/site-library/redland/libs/redland.so':
librdf.so.0: cannot open shared object file: No such file or directory
Calls: ... namespaceImport -> loadNamespace -> library.dynam -> dyn.load
Execution halted
@@ -229,84 +138,26 @@ ERROR: lazy loading failed for package ‘datapack’
```
-# easybgm
-
-
-
-* Version: 0.1.2
-* GitHub: https://github.com/KarolineHuth/easybgm
-* Source code: https://github.com/cran/easybgm
-* Date/Publication: 2024-03-13 13:40:02 UTC
-* Number of recursive dependencies: 175
-
-Run `revdepcheck::cloud_details(, "easybgm")` for more info
-
-
-
-## In both
-
-* checking whether package ‘easybgm’ can be installed ... ERROR
- ```
- Installation failed.
- See ‘/tmp/workdir/easybgm/new/easybgm.Rcheck/00install.out’ for details.
- ```
-
-## Installation
-
-### Devel
-
-```
-* installing *source* package ‘easybgm’ ...
-** package ‘easybgm’ successfully unpacked and MD5 sums checked
-** using staged installation
-** R
-** 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 ‘easybgm’
-* removing ‘/tmp/workdir/easybgm/new/easybgm.Rcheck/easybgm’
-
-
-```
-### CRAN
-
-```
-* installing *source* package ‘easybgm’ ...
-** package ‘easybgm’ successfully unpacked and MD5 sums checked
-** using staged installation
-** R
-** 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 ‘easybgm’
-* removing ‘/tmp/workdir/easybgm/old/easybgm.Rcheck/easybgm’
-
-
-```
-# erah
+# multinma
-* Version: 2.0.1
-* GitHub: https://github.com/xdomingoal/erah-devel
-* Source code: https://github.com/cran/erah
-* Date/Publication: 2023-12-20 10:10:02 UTC
-* Number of recursive dependencies: 91
+* Version: 0.7.2
+* GitHub: https://github.com/dmphillippo/multinma
+* Source code: https://github.com/cran/multinma
+* Date/Publication: 2024-09-16 12:20:02 UTC
+* Number of recursive dependencies: 152
-Run `revdepcheck::cloud_details(, "erah")` for more info
+Run `revdepcheck::cloud_details(, "multinma")` for more info
## In both
-* checking whether package ‘erah’ can be installed ... ERROR
+* checking whether package ‘multinma’ can be installed ... ERROR
```
Installation failed.
- See ‘/tmp/workdir/erah/new/erah.Rcheck/00install.out’ for details.
+ See ‘/tmp/workdir/multinma/new/multinma.Rcheck/00install.out’ for details.
```
## Installation
@@ -314,968 +165,56 @@ Run `revdepcheck::cloud_details(, "erah")` for more info
### Devel
```
-* installing *source* package ‘erah’ ...
-** package ‘erah’ successfully unpacked and MD5 sums checked
+* installing *source* package ‘multinma’ ...
+** package ‘multinma’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
-using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
-gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c registerDynamicSymbol.c -o registerDynamicSymbol.o
-gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c runfunc.c -o runfunc.o
-gcc -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o erah.so registerDynamicSymbol.o runfunc.o -L/opt/R/4.3.1/lib/R/lib -lR
-installing to /tmp/workdir/erah/new/erah.Rcheck/00LOCK-erah/00new/erah/libs
-** 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 ‘erah’
-* removing ‘/tmp/workdir/erah/new/erah.Rcheck/erah’
-
+using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
+using C++17
-```
-### CRAN
-```
-* installing *source* package ‘erah’ ...
-** package ‘erah’ successfully unpacked and MD5 sums checked
-** using staged installation
-** libs
-using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
-gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c registerDynamicSymbol.c -o registerDynamicSymbol.o
-gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c runfunc.c -o runfunc.o
-gcc -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o erah.so registerDynamicSymbol.o runfunc.o -L/opt/R/4.3.1/lib/R/lib -lR
-installing to /tmp/workdir/erah/old/erah.Rcheck/00LOCK-erah/00new/erah/libs
-** R
+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,
...
-** 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 ‘erah’
-* removing ‘/tmp/workdir/erah/old/erah.Rcheck/erah’
-
-
-```
-# evolqg
-
-
-
-* Version: 0.3-4
-* GitHub: https://github.com/lem-usp/evolqg
-* Source code: https://github.com/cran/evolqg
-* Date/Publication: 2023-12-05 15:20:12 UTC
-* Number of recursive dependencies: 111
-
-Run `revdepcheck::cloud_details(, "evolqg")` for more info
-
-
-
-## In both
-
-* checking whether package ‘evolqg’ can be installed ... ERROR
- ```
- Installation failed.
- See ‘/tmp/workdir/evolqg/new/evolqg.Rcheck/00install.out’ for details.
- ```
-
-## Installation
-
-### Devel
-
-```
-* installing *source* package ‘evolqg’ ...
-** package ‘evolqg’ successfully unpacked and MD5 sums checked
-** using staged installation
-** libs
-using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
-g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o
-g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c fast_RS.cpp -o fast_RS.o
-g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o evolqg.so RcppExports.o fast_RS.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR
-installing to /tmp/workdir/evolqg/new/evolqg.Rcheck/00LOCK-evolqg/00new/evolqg/libs
-** R
-** data
-** 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 ‘evolqg’
-* removing ‘/tmp/workdir/evolqg/new/evolqg.Rcheck/evolqg’
+/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/4.4.0/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’
```
### CRAN
```
-* installing *source* package ‘evolqg’ ...
-** package ‘evolqg’ successfully unpacked and MD5 sums checked
+* installing *source* package ‘multinma’ ...
+** package ‘multinma’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
-g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o
-g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c fast_RS.cpp -o fast_RS.o
-g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o evolqg.so RcppExports.o fast_RS.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR
-installing to /tmp/workdir/evolqg/old/evolqg.Rcheck/00LOCK-evolqg/00new/evolqg/libs
-** R
-** data
-** 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 ‘evolqg’
-* removing ‘/tmp/workdir/evolqg/old/evolqg.Rcheck/evolqg’
-
-
-```
-# frechet
-
-
-
-* Version: 0.3.0
-* GitHub: https://github.com/functionaldata/tFrechet
-* Source code: https://github.com/cran/frechet
-* Date/Publication: 2023-12-09 15:50:08 UTC
-* Number of recursive dependencies: 111
-
-Run `revdepcheck::cloud_details(, "frechet")` for more info
-
-
-
-## In both
-
-* checking whether package ‘frechet’ can be installed ... ERROR
- ```
- Installation failed.
- See ‘/tmp/workdir/frechet/new/frechet.Rcheck/00install.out’ for details.
- ```
-
-## Installation
-
-### Devel
-
-```
-* installing *source* package ‘frechet’ ...
-** package ‘frechet’ successfully unpacked and MD5 sums checked
-** using staged installation
-** R
-** 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 >= 1.6.1 is required
-Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace
-Execution halted
-ERROR: lazy loading failed for package ‘frechet’
-* removing ‘/tmp/workdir/frechet/new/frechet.Rcheck/frechet’
-
-
-```
-### CRAN
-
-```
-* installing *source* package ‘frechet’ ...
-** package ‘frechet’ successfully unpacked and MD5 sums checked
-** using staged installation
-** R
-** 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 >= 1.6.1 is required
-Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace
-Execution halted
-ERROR: lazy loading failed for package ‘frechet’
-* removing ‘/tmp/workdir/frechet/old/frechet.Rcheck/frechet’
-
-
-```
-# kstMatrix
-
-
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/kstMatrix
-* Number of recursive dependencies: 35
-
-Run `revdepcheck::cloud_details(, "kstMatrix")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# manet
-
-
-
-* Version: 2.0
-* GitHub: NA
-* Source code: https://github.com/cran/manet
-* Date/Publication: 2018-08-23 15:02:15 UTC
-* Number of recursive dependencies: 21
+using C++17
-Run `revdepcheck::cloud_details(, "manet")` for more info
-
-
-## In both
-
-* checking whether package ‘manet’ can be installed ... ERROR
- ```
- Installation failed.
- See ‘/tmp/workdir/manet/new/manet.Rcheck/00install.out’ for details.
- ```
-
-## Installation
-
-### Devel
-
-```
-* installing *source* package ‘manet’ ...
-** package ‘manet’ 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 ‘MCMCpack’ 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 ‘manet’
-* removing ‘/tmp/workdir/manet/new/manet.Rcheck/manet’
-
-
-```
-### CRAN
-
-```
-* installing *source* package ‘manet’ ...
-** package ‘manet’ 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 ‘MCMCpack’ 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 ‘manet’
-* removing ‘/tmp/workdir/manet/old/manet.Rcheck/manet’
-
-
-```
-# mlmts
-
-
-
-* Version: 1.1.2
-* GitHub: NA
-* Source code: https://github.com/cran/mlmts
-* Date/Publication: 2024-08-18 08:40:06 UTC
-* Number of recursive dependencies: 242
-
-Run `revdepcheck::cloud_details(, "mlmts")` for more info
-
-
-
-## In both
-
-* checking whether package ‘mlmts’ can be installed ... ERROR
- ```
- Installation failed.
- See ‘/tmp/workdir/mlmts/new/mlmts.Rcheck/00install.out’ for details.
- ```
-
-## Installation
-
-### Devel
-
-```
-* installing *source* package ‘mlmts’ ...
-** package ‘mlmts’ 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 ‘quantspec’ 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
-Error: unable to load R code in package ‘mlmts’
-Execution halted
-ERROR: lazy loading failed for package ‘mlmts’
-* removing ‘/tmp/workdir/mlmts/new/mlmts.Rcheck/mlmts’
-
-
-```
-### CRAN
-
-```
-* installing *source* package ‘mlmts’ ...
-** package ‘mlmts’ 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 ‘quantspec’ 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
-Error: unable to load R code in package ‘mlmts’
-Execution halted
-ERROR: lazy loading failed for package ‘mlmts’
-* removing ‘/tmp/workdir/mlmts/old/mlmts.Rcheck/mlmts’
-
-
-```
-# multinma
-
-
-
-* Version: 0.7.2
-* GitHub: https://github.com/dmphillippo/multinma
-* Source code: https://github.com/cran/multinma
-* Date/Publication: 2024-09-16 12:20:02 UTC
-* Number of recursive dependencies: 152
-
-Run `revdepcheck::cloud_details(, "multinma")` for more info
-
-
-
-## In both
-
-* checking whether package ‘multinma’ can be installed ... ERROR
- ```
- Installation failed.
- See ‘/tmp/workdir/multinma/new/multinma.Rcheck/00install.out’ for details.
- ```
-
-## Installation
-
-### Devel
-
-```
-* installing *source* package ‘multinma’ ...
-** package ‘multinma’ successfully unpacked and MD5 sums checked
-** using staged installation
-** libs
-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
-ERROR: compilation failed for package ‘multinma’
-* removing ‘/tmp/workdir/multinma/new/multinma.Rcheck/multinma’
-
-
-```
-### CRAN
-
-```
-* installing *source* package ‘multinma’ ...
-** package ‘multinma’ successfully unpacked and MD5 sums checked
-** using staged installation
-** libs
-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,
-...
-/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_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’
-```
-# netcmc
-
-
-
-* Version: 1.0.2
-* GitHub: NA
-* Source code: https://github.com/cran/netcmc
-* Date/Publication: 2022-11-08 22:30:15 UTC
-* Number of recursive dependencies: 61
-
-Run `revdepcheck::cloud_details(, "netcmc")` for more info
-
-
-
-## In both
-
-* checking whether package ‘netcmc’ can be installed ... ERROR
- ```
- Installation failed.
- See ‘/tmp/workdir/netcmc/new/netcmc.Rcheck/00install.out’ for details.
- ```
-
-## Installation
-
-### Devel
-
-```
-* installing *source* package ‘netcmc’ ...
-** package ‘netcmc’ successfully unpacked and MD5 sums checked
-** using staged installation
-** libs
-using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
-using C++11
-g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o
-g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c choleskyDecompositionRcppConversion.cpp -o choleskyDecompositionRcppConversion.o
-g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c doubleMatrixMultiplicationRcpp.cpp -o doubleMatrixMultiplicationRcpp.o
-g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c doubleVectorMultiplicationRcpp.cpp -o doubleVectorMultiplicationRcpp.o
-...
-g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c vectorVectorTransposeMultiplicationRcpp.cpp -o vectorVectorTransposeMultiplicationRcpp.o
-g++ -std=gnu++11 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o netcmc.so RcppExports.o choleskyDecompositionRcppConversion.o doubleMatrixMultiplicationRcpp.o doubleVectorMultiplicationRcpp.o eigenValuesRcppConversion.o getDiagonalMatrix.o getExp.o getExpDividedByOnePlusExp.o getMeanCenteredRandomEffects.o getMultivariateBinomialNetworkLerouxDIC.o getMultivariateBinomialNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getMultivariateGaussianNetworkLerouxDIC.o getMultivariateGaussianNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getMultivariatePoissonNetworkLerouxDIC.o getMultivariatePoissonNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getNonZeroEntries.o getSubvector.o getSubvectorIndecies.o getSumExpNetwork.o getSumExpNetworkIndecies.o getSumExpNetworkLeroux.o getSumExpNetworkLerouxIndecies.o getSumLogExp.o getSumLogExpIndecies.o getSumVector.o getTripletForm.o getUnivariateBinomialNetworkLerouxDIC.o getUnivariateBinomialNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getUnivariateGaussianNetworkLerouxDIC.o getUnivariateGaussianNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getUnivariatePoissonNetworkDIC.o getUnivariatePoissonNetworkFittedValuesAndLikelihoodForDICEveryIteration.o getUnivariatePoissonNetworkLerouxDIC.o getUnivariatePoissonNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getVectorMean.o matrixInverseRcppConversion.o matrixMatrixAdditionRcpp.o matrixMatrixSubtractionRcpp.o matrixVectorMultiplicationRcpp.o multivariateBinomialNetworkLerouxAllUpdate.o multivariateBinomialNetworkLerouxBetaUpdate.o multivariateBinomialNetworkLerouxRhoUpdate.o multivariateBinomialNetworkLerouxSingleUpdate.o multivariateBinomialNetworkLerouxSpatialRandomEffectsUpdate.o multivariateBinomialNetworkLerouxTauSquaredUpdate.o multivariateBinomialNetworkLerouxURandomEffectsUpdate.o multivariateBinomialNetworkLerouxVRandomEffectsUpdate.o multivariateBinomialNetworkLerouxVarianceCovarianceUUpdate.o multivariateBinomialNetworkRandAllUpdate.o multivariateBinomialNetworkRandSingleUpdate.o multivariateGaussianNetworkLerouxAllMHUpdate.o multivariateGaussianNetworkLerouxBetaUpdate.o multivariateGaussianNetworkLerouxRhoUpdate.o multivariateGaussianNetworkLerouxSigmaSquaredEUpdate.o multivariateGaussianNetworkLerouxSingleMHUpdate.o multivariateGaussianNetworkLerouxSpatialRandomEffectsMHUpdate.o multivariateGaussianNetworkLerouxTauSquaredUpdate.o multivariateGaussianNetworkLerouxURandomEffectsUpdate.o multivariateGaussianNetworkLerouxVarianceCovarianceUUpdate.o multivariateGaussianNetworkRandAllUpdate.o multivariateGaussianNetworkRandSingleUpdate.o multivariateGaussianNetworkRandVRandomEffectsUpdate.o multivariatePoissonNetworkLerouxAllUpdate.o multivariatePoissonNetworkLerouxBetaUpdate.o multivariatePoissonNetworkLerouxRhoUpdate.o multivariatePoissonNetworkLerouxSingleUpdate.o multivariatePoissonNetworkLerouxSpatialRandomEffectsUpdate.o multivariatePoissonNetworkLerouxTauSquaredUpdate.o multivariatePoissonNetworkLerouxURandomEffectsUpdate.o multivariatePoissonNetworkLerouxVRandomEffectsUpdate.o multivariatePoissonNetworkLerouxVarianceCovarianceUUpdate.o multivariatePoissonNetworkRandAllUpdate.o multivariatePoissonNetworkRandSingleUpdate.o sumMatrix.o univariateBinomialNetworkLerouxAllUpdate.o univariateBinomialNetworkLerouxBetaUpdate.o univariateBinomialNetworkLerouxRhoUpdate.o univariateBinomialNetworkLerouxSigmaSquaredUpdate.o univariateBinomialNetworkLerouxSingleUpdate.o univariateBinomialNetworkLerouxSpatialRandomEffectsUpdate.o univariateBinomialNetworkLerouxTauSquaredUpdate.o univariateBinomialNetworkLerouxURandomEffectsUpdate.o univariateGaussianNetworkLerouxAllMHUpdate.o univariateGaussianNetworkLerouxBetaUpdate.o univariateGaussianNetworkLerouxRhoUpdate.o univariateGaussianNetworkLerouxSigmaSquaredEUpdate.o univariateGaussianNetworkLerouxSigmaSquaredUUpdate.o univariateGaussianNetworkLerouxSingleMHUpdate.o univariateGaussianNetworkLerouxSpatialRandomEffectsMHUpdate.o univariateGaussianNetworkLerouxTauSquaredUpdate.o univariateGaussianNetworkLerouxURandomEffectsUpdate.o univariatePoissonNetworkLerouxAllUpdate.o univariatePoissonNetworkLerouxBetaUpdate.o univariatePoissonNetworkLerouxRhoUpdate.o univariatePoissonNetworkLerouxSigmaSquaredUpdate.o univariatePoissonNetworkLerouxSingleUpdate.o univariatePoissonNetworkLerouxSpatialRandomEffectsUpdate.o univariatePoissonNetworkLerouxTauSquaredUpdate.o univariatePoissonNetworkLerouxURandomEffectsUpdate.o vectorTransposeVectorMultiplicationRcpp.o vectorVectorTransposeMultiplicationRcpp.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR
-installing to /tmp/workdir/netcmc/new/netcmc.Rcheck/00LOCK-netcmc/00new/netcmc/libs
-** R
-** byte-compile and prepare package for lazy loading
-Error: package or namespace load failed for ‘MCMCpack’ 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 ‘netcmc’
-* removing ‘/tmp/workdir/netcmc/new/netcmc.Rcheck/netcmc’
-
-
-```
-### CRAN
-
-```
-* installing *source* package ‘netcmc’ ...
-** package ‘netcmc’ successfully unpacked and MD5 sums checked
-** using staged installation
-** libs
-using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
-using C++11
-g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o
-g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c choleskyDecompositionRcppConversion.cpp -o choleskyDecompositionRcppConversion.o
-g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c doubleMatrixMultiplicationRcpp.cpp -o doubleMatrixMultiplicationRcpp.o
-g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c doubleVectorMultiplicationRcpp.cpp -o doubleVectorMultiplicationRcpp.o
-...
-g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c vectorVectorTransposeMultiplicationRcpp.cpp -o vectorVectorTransposeMultiplicationRcpp.o
-g++ -std=gnu++11 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o netcmc.so RcppExports.o choleskyDecompositionRcppConversion.o doubleMatrixMultiplicationRcpp.o doubleVectorMultiplicationRcpp.o eigenValuesRcppConversion.o getDiagonalMatrix.o getExp.o getExpDividedByOnePlusExp.o getMeanCenteredRandomEffects.o getMultivariateBinomialNetworkLerouxDIC.o getMultivariateBinomialNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getMultivariateGaussianNetworkLerouxDIC.o getMultivariateGaussianNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getMultivariatePoissonNetworkLerouxDIC.o getMultivariatePoissonNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getNonZeroEntries.o getSubvector.o getSubvectorIndecies.o getSumExpNetwork.o getSumExpNetworkIndecies.o getSumExpNetworkLeroux.o getSumExpNetworkLerouxIndecies.o getSumLogExp.o getSumLogExpIndecies.o getSumVector.o getTripletForm.o getUnivariateBinomialNetworkLerouxDIC.o getUnivariateBinomialNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getUnivariateGaussianNetworkLerouxDIC.o getUnivariateGaussianNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getUnivariatePoissonNetworkDIC.o getUnivariatePoissonNetworkFittedValuesAndLikelihoodForDICEveryIteration.o getUnivariatePoissonNetworkLerouxDIC.o getUnivariatePoissonNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getVectorMean.o matrixInverseRcppConversion.o matrixMatrixAdditionRcpp.o matrixMatrixSubtractionRcpp.o matrixVectorMultiplicationRcpp.o multivariateBinomialNetworkLerouxAllUpdate.o multivariateBinomialNetworkLerouxBetaUpdate.o multivariateBinomialNetworkLerouxRhoUpdate.o multivariateBinomialNetworkLerouxSingleUpdate.o multivariateBinomialNetworkLerouxSpatialRandomEffectsUpdate.o multivariateBinomialNetworkLerouxTauSquaredUpdate.o multivariateBinomialNetworkLerouxURandomEffectsUpdate.o multivariateBinomialNetworkLerouxVRandomEffectsUpdate.o multivariateBinomialNetworkLerouxVarianceCovarianceUUpdate.o multivariateBinomialNetworkRandAllUpdate.o multivariateBinomialNetworkRandSingleUpdate.o multivariateGaussianNetworkLerouxAllMHUpdate.o multivariateGaussianNetworkLerouxBetaUpdate.o multivariateGaussianNetworkLerouxRhoUpdate.o multivariateGaussianNetworkLerouxSigmaSquaredEUpdate.o multivariateGaussianNetworkLerouxSingleMHUpdate.o multivariateGaussianNetworkLerouxSpatialRandomEffectsMHUpdate.o multivariateGaussianNetworkLerouxTauSquaredUpdate.o multivariateGaussianNetworkLerouxURandomEffectsUpdate.o multivariateGaussianNetworkLerouxVarianceCovarianceUUpdate.o multivariateGaussianNetworkRandAllUpdate.o multivariateGaussianNetworkRandSingleUpdate.o multivariateGaussianNetworkRandVRandomEffectsUpdate.o multivariatePoissonNetworkLerouxAllUpdate.o multivariatePoissonNetworkLerouxBetaUpdate.o multivariatePoissonNetworkLerouxRhoUpdate.o multivariatePoissonNetworkLerouxSingleUpdate.o multivariatePoissonNetworkLerouxSpatialRandomEffectsUpdate.o multivariatePoissonNetworkLerouxTauSquaredUpdate.o multivariatePoissonNetworkLerouxURandomEffectsUpdate.o multivariatePoissonNetworkLerouxVRandomEffectsUpdate.o multivariatePoissonNetworkLerouxVarianceCovarianceUUpdate.o multivariatePoissonNetworkRandAllUpdate.o multivariatePoissonNetworkRandSingleUpdate.o sumMatrix.o univariateBinomialNetworkLerouxAllUpdate.o univariateBinomialNetworkLerouxBetaUpdate.o univariateBinomialNetworkLerouxRhoUpdate.o univariateBinomialNetworkLerouxSigmaSquaredUpdate.o univariateBinomialNetworkLerouxSingleUpdate.o univariateBinomialNetworkLerouxSpatialRandomEffectsUpdate.o univariateBinomialNetworkLerouxTauSquaredUpdate.o univariateBinomialNetworkLerouxURandomEffectsUpdate.o univariateGaussianNetworkLerouxAllMHUpdate.o univariateGaussianNetworkLerouxBetaUpdate.o univariateGaussianNetworkLerouxRhoUpdate.o univariateGaussianNetworkLerouxSigmaSquaredEUpdate.o univariateGaussianNetworkLerouxSigmaSquaredUUpdate.o univariateGaussianNetworkLerouxSingleMHUpdate.o univariateGaussianNetworkLerouxSpatialRandomEffectsMHUpdate.o univariateGaussianNetworkLerouxTauSquaredUpdate.o univariateGaussianNetworkLerouxURandomEffectsUpdate.o univariatePoissonNetworkLerouxAllUpdate.o univariatePoissonNetworkLerouxBetaUpdate.o univariatePoissonNetworkLerouxRhoUpdate.o univariatePoissonNetworkLerouxSigmaSquaredUpdate.o univariatePoissonNetworkLerouxSingleUpdate.o univariatePoissonNetworkLerouxSpatialRandomEffectsUpdate.o univariatePoissonNetworkLerouxTauSquaredUpdate.o univariatePoissonNetworkLerouxURandomEffectsUpdate.o vectorTransposeVectorMultiplicationRcpp.o vectorVectorTransposeMultiplicationRcpp.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR
-installing to /tmp/workdir/netcmc/old/netcmc.Rcheck/00LOCK-netcmc/00new/netcmc/libs
-** R
-** byte-compile and prepare package for lazy loading
-Error: package or namespace load failed for ‘MCMCpack’ 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 ‘netcmc’
-* removing ‘/tmp/workdir/netcmc/old/netcmc.Rcheck/netcmc’
-
-
-```
-# NetworkChange
-
-
-
-* Version: 0.8
-* GitHub: https://github.com/jongheepark/NetworkChange
-* Source code: https://github.com/cran/NetworkChange
-* Date/Publication: 2022-03-04 07:30:02 UTC
-* Number of recursive dependencies: 133
-
-Run `revdepcheck::cloud_details(, "NetworkChange")` for more info
-
-
-
-## In both
-
-* checking whether package ‘NetworkChange’ can be installed ... ERROR
- ```
- Installation failed.
- See ‘/tmp/workdir/NetworkChange/new/NetworkChange.Rcheck/00install.out’ for details.
- ```
-
-## Installation
-
-### Devel
-
-```
-* installing *source* package ‘NetworkChange’ ...
-** package ‘NetworkChange’ successfully unpacked and MD5 sums checked
-** using staged installation
-** R
-** data
-** byte-compile and prepare package for lazy loading
-Error: package or namespace load failed for ‘MCMCpack’ 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 ‘NetworkChange’
-* removing ‘/tmp/workdir/NetworkChange/new/NetworkChange.Rcheck/NetworkChange’
-
-
-```
-### CRAN
-
-```
-* installing *source* package ‘NetworkChange’ ...
-** package ‘NetworkChange’ successfully unpacked and MD5 sums checked
-** using staged installation
-** R
-** data
-** byte-compile and prepare package for lazy loading
-Error: package or namespace load failed for ‘MCMCpack’ 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 ‘NetworkChange’
-* removing ‘/tmp/workdir/NetworkChange/old/NetworkChange.Rcheck/NetworkChange’
-
-
-```
-# PathwaySpace
-
-
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/PathwaySpace
-* Number of recursive dependencies: 70
-
-Run `revdepcheck::cloud_details(, "PathwaySpace")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# pcvr
-
-
-
-* Version: 1.0.0
-* GitHub: https://github.com/danforthcenter/pcvr
-* Source code: https://github.com/cran/pcvr
-* Date/Publication: 2024-09-05 17:30:02 UTC
-* Number of recursive dependencies: 189
-
-Run `revdepcheck::cloud_details(, "pcvr")` for more info
-
-
-
-## In both
-
-* checking whether package ‘pcvr’ can be installed ... ERROR
- ```
- Installation failed.
- See ‘/tmp/workdir/pcvr/new/pcvr.Rcheck/00install.out’ for details.
- ```
-
-## Installation
-
-### Devel
-
-```
-* installing *source* package ‘pcvr’ ...
-** package ‘pcvr’ successfully unpacked and MD5 sums checked
-** using staged installation
-** R
-** inst
-** byte-compile and prepare package for lazy loading
-Warning in check_dep_version() :
- ABI version mismatch:
-lme4 was built with Matrix ABI version 1
-Current Matrix ABI version is 0
-Please re-install lme4 from source or restore original ‘Matrix’ package
-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 ‘pcvr’
-* removing ‘/tmp/workdir/pcvr/new/pcvr.Rcheck/pcvr’
-
-
-```
-### CRAN
-
-```
-* installing *source* package ‘pcvr’ ...
-** package ‘pcvr’ successfully unpacked and MD5 sums checked
-** using staged installation
-** R
-** inst
-** byte-compile and prepare package for lazy loading
-Warning in check_dep_version() :
- ABI version mismatch:
-lme4 was built with Matrix ABI version 1
-Current Matrix ABI version is 0
-Please re-install lme4 from source or restore original ‘Matrix’ package
-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 ‘pcvr’
-* removing ‘/tmp/workdir/pcvr/old/pcvr.Rcheck/pcvr’
-
-
-```
-# piecewiseSEM
-
-
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/piecewiseSEM
-* Number of recursive dependencies: 108
-
-Run `revdepcheck::cloud_details(, "piecewiseSEM")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# RGraphSpace
-
-
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/RGraphSpace
-* Number of recursive dependencies: 65
-
-Run `revdepcheck::cloud_details(, "RGraphSpace")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# robber
-
-
-
-* Version: 0.2.4
-* GitHub: https://github.com/Chabert-Liddell/robber
-* Source code: https://github.com/cran/robber
-* Date/Publication: 2024-02-07 13:50:02 UTC
-* Number of recursive dependencies: 144
-
-Run `revdepcheck::cloud_details(, "robber")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-* using log directory ‘/tmp/workdir/robber/new/robber.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 ‘robber/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
- ‘topological-analysis.Rmd’ using ‘UTF-8’... OK
-* checking re-building of vignette outputs ... OK
-* DONE
-Status: OK
-
-
-
-
-
-```
-### CRAN
-
-```
-* using log directory ‘/tmp/workdir/robber/old/robber.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 ‘robber/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
- ‘topological-analysis.Rmd’ using ‘UTF-8’... OK
-* checking re-building of vignette outputs ... OK
-* DONE
-Status: OK
-
-
-
-
-
-```
-# rTwig
-
-
-
-* Version: 1.1.0
-* GitHub: https://github.com/aidanmorales/rTwig
-* Source code: https://github.com/cran/rTwig
-* Date/Publication: 2024-08-21 00:50:02 UTC
-* Number of recursive dependencies: 147
-
-Run `revdepcheck::cloud_details(, "rTwig")` for more info
-
-
-
-## In both
-
-* checking whether package ‘rTwig’ can be installed ... ERROR
- ```
- Installation failed.
- See ‘/tmp/workdir/rTwig/new/rTwig.Rcheck/00install.out’ for details.
- ```
-
-## Installation
-
-### Devel
-
-```
-* installing *source* package ‘rTwig’ ...
-** package ‘rTwig’ successfully unpacked and MD5 sums checked
-** using staged installation
-** libs
-using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
-g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o
-g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c box_counting.cpp -o box_counting.o
-g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c colors.cpp -o colors.o
-g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c convex_hull.cpp -o convex_hull.o
-g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c cylinder_mesh.cpp -o cylinder_mesh.o
-...
-** 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 ‘rTwig’
-* removing ‘/tmp/workdir/rTwig/new/rTwig.Rcheck/rTwig’
-
-
-```
-### CRAN
-
-```
-* installing *source* package ‘rTwig’ ...
-** package ‘rTwig’ successfully unpacked and MD5 sums checked
-** using staged installation
-** libs
-using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
-g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o
-g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c box_counting.cpp -o box_counting.o
-g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c colors.cpp -o colors.o
-g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c convex_hull.cpp -o convex_hull.o
-g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c cylinder_mesh.cpp -o cylinder_mesh.o
-...
-** 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 ‘rTwig’
-* removing ‘/tmp/workdir/rTwig/old/rTwig.Rcheck/rTwig’
-
-
-```
-# Seurat
-
-
-
-* Version: 5.1.0
-* GitHub: https://github.com/satijalab/seurat
-* Source code: https://github.com/cran/Seurat
-* Date/Publication: 2024-05-10 17:23:17 UTC
-* Number of recursive dependencies: 267
-
-Run `revdepcheck::cloud_details(, "Seurat")` for more info
-
-
-
-## In both
-
-* checking whether package ‘Seurat’ can be installed ... ERROR
- ```
- Installation failed.
- See ‘/tmp/workdir/Seurat/new/Seurat.Rcheck/00install.out’ for details.
- ```
-
-## Installation
-
-### Devel
-
-```
-* installing *source* package ‘Seurat’ ...
-** package ‘Seurat’ successfully unpacked and MD5 sums checked
-** using staged installation
-** libs
-using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
-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'/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/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c ModularityOptimizer.cpp -o ModularityOptimizer.o
-g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -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/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c RModularityOptimizer.cpp -o RModularityOptimizer.o
-In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205,
-...
-** R
-** data
-*** moving datasets to lazyload DB
-** inst
-** 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 ‘Seurat’
-* removing ‘/tmp/workdir/Seurat/new/Seurat.Rcheck/Seurat’
-
-
-```
-### CRAN
-
-```
-* installing *source* package ‘Seurat’ ...
-** package ‘Seurat’ successfully unpacked and MD5 sums checked
-** using staged installation
-** libs
-using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
-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'/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/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c ModularityOptimizer.cpp -o ModularityOptimizer.o
-g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -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/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c RModularityOptimizer.cpp -o RModularityOptimizer.o
-In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205,
-...
-** R
-** data
-*** moving datasets to lazyload DB
-** inst
-** 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 ‘Seurat’
-* removing ‘/tmp/workdir/Seurat/old/Seurat.Rcheck/Seurat’
-
-
```
# streamDAG
@@ -1297,8 +236,8 @@ Run `revdepcheck::cloud_details(, "streamDAG")` for more info
```
* 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)
+* using R version 4.4.0 (2024-04-24)
+* using platform: x86_64-pc-linux-gnu
* 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
@@ -1325,8 +264,8 @@ Status: 1 ERROR
```
* 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)
+* using R version 4.4.0 (2024-04-24)
+* using platform: x86_64-pc-linux-gnu
* 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
diff --git a/revdep/problems.md b/revdep/problems.md
index d01bf7142e..bfc121d4d2 100644
--- a/revdep/problems.md
+++ b/revdep/problems.md
@@ -1,55 +1,62 @@
-# CePa
+# manynet
-* Version: 0.8.0
-* GitHub: https://github.com/jokergoo/CePa
-* Source code: https://github.com/cran/CePa
-* Date/Publication: 2022-06-11 21:30:06 UTC
-* Number of recursive dependencies: 14
+* Version: 1.2.6
+* GitHub: https://github.com/stocnet/manynet
+* Source code: https://github.com/cran/manynet
+* Date/Publication: 2024-10-05 16:40:01 UTC
+* Number of recursive dependencies: 146
-Run `revdepcheck::cloud_details(, "CePa")` for more info
+Run `revdepcheck::cloud_details(, "manynet")` for more info
## Newly broken
-* checking Rd cross-references ... WARNING
+* checking tests ... ERROR
```
- Missing link or links in documentation object 'cepa.Rd':
- ‘[igraph:igraph_test]{igraphtest}’
-
- Missing link or links in documentation object 'cepa.ora.Rd':
- ‘[igraph:igraph_test]{igraphtest}’
-
- See section 'Cross-references' in the 'Writing R Extensions' manual.
+ Running ‘testthat.R’
+ Running the tests in ‘tests/testthat.R’ failed.
+ Complete output:
+ > library(testthat)
+ > library(manynet)
+ >
+ > test_check("manynet")
+ Starting 2 test processes
+ [ FAIL 7 | WARN 18643 | SKIP 21 | PASS 558 ]
+
+ ...
+ `expected`: 0.2 0.1 0.1
+ ── Failure ('test-measure_centrality.R:79:3'): two mode eigenvector centrality calculated correctly ──
+ top3(node_eigenvector(test_igr, normalized = TRUE)) (`actual`) not equal to c(0.4505, 0.4248, 0.5) (`expected`).
+
+ `actual`: 1.3 1.2 1.4
+ `expected`: 0.5 0.4 0.5
+
+ [ FAIL 7 | WARN 18643 | SKIP 21 | PASS 558 ]
+ Error: Test failures
+ Execution halted
```
## In both
-* checking re-building of vignette outputs ... WARNING
+* checking package dependencies ... NOTE
```
- Error(s) in re-building vignettes:
- --- re-building ‘CePa.Rnw’ using Sweave
- Error: processing vignette 'CePa.Rnw' failed with diagnostics:
- Running 'texi2dvi' on 'CePa.tex' failed.
- LaTeX errors:
- ! LaTeX Error: File `grfext.sty' not found.
-
- Type X to quit or to proceed,
- or enter new name. (Default extension: sty)
-
- ...
- l.179 \RequirePackage{grfext}\relax
- ^^M
- ! ==> Fatal error occurred, no output PDF file produced!
- --- failed re-building ‘parsing-PID-pathway-data.Rnw’
-
- SUMMARY: processing the following files failed:
- ‘CePa.Rnw’ ‘analysis-p53.Rnw’ ‘parsing-PID-pathway-data.Rnw’
-
- Error: Vignette re-building failed.
- Execution halted
+ Package which this enhances but not available for checking: ‘Rgraphviz’
+ ```
+
+* checking installed package size ... NOTE
+ ```
+ installed size is 5.2Mb
+ sub-directories of 1Mb or more:
+ R 1.5Mb
+ tutorials 1.8Mb
+ ```
+
+* checking data for non-ASCII characters ... NOTE
+ ```
+ Note: found 7 marked UTF-8 strings
```
# MetaNet
@@ -122,21 +129,21 @@ Run `revdepcheck::cloud_details(, "simcausal")` for more info
+ ## --- Setup ---
+
...
- In addition: Warning messages:
- 1: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
- RNGkind: Marsaglia-Multicarry has poor statistical properties
+ ℹ Please use `as_directed()` instead.
2: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
- RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
- 3: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: Marsaglia-Multicarry has poor statistical properties
+ 3: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
+ RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
4: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
+ RNGkind: Marsaglia-Multicarry has poor statistical properties
+ 5: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
Execution halted
```
## In both
-* checking re-building of vignette outputs ... NOTE
+* checking re-building of vignette outputs ... WARNING
```
Error(s) in re-building vignettes:
...
@@ -186,18 +193,18 @@ Run `revdepcheck::cloud_details(, "skynet")` for more info
> library(skynet)
>
> test_check("skynet")
- [ FAIL 1 | WARN 24 | SKIP 4 | PASS 69 ]
+ [ FAIL 1 | WARN 25 | SKIP 4 | PASS 69 ]
══ Skipped tests (4) ═══════════════════════════════════════════════════════════
...
14. │ └─base::lapply(...)
15. │ └─rlang (local) FUN(X[[i]], ...)
16. └─igraph (local) from(V(x)[y])
- 17. └─lifecycle::deprecate_stop("2.0.4", "from()", ".from()")
+ 17. └─lifecycle::deprecate_stop("2.1.0", "from()", ".from()")
18. └─lifecycle:::deprecate_stop0(msg)
19. └─rlang::cnd_signal(...)
- [ FAIL 1 | WARN 24 | SKIP 4 | PASS 69 ]
+ [ FAIL 1 | WARN 25 | SKIP 4 | PASS 69 ]
Error: Test failures
Execution halted
```
@@ -210,3 +217,53 @@ Run `revdepcheck::cloud_details(, "skynet")` for more info
All declared Imports should be used.
```
+# SpaDES.core
+
+
+
+* Version: 2.1.0
+* GitHub: https://github.com/PredictiveEcology/SpaDES.core
+* Source code: https://github.com/cran/SpaDES.core
+* Date/Publication: 2024-06-02 11:02:47 UTC
+* Number of recursive dependencies: 136
+
+Run `revdepcheck::cloud_details(, "SpaDES.core")` for more info
+
+
+
+## Newly broken
+
+* checking tests ... ERROR
+ ```
+ Running ‘test-all.R’
+ Running the tests in ‘tests/test-all.R’ failed.
+ Complete output:
+ > library(testthat)
+ > aa <- options(spades.debug = FALSE)
+ > options("spades.temp.debug" = aa)
+ > if (FALSE) {
+ + ff <- list()
+ + runTestsWithTimings("ff")
+ + }
+ ...
+ Backtrace:
+ ▆
+ 1. └─SpaDES.core::saveSimList(mySim, filename = tmpfile[2]) at test-save.R:208:3
+ 2. └─SpaDES.core:::archiveWrite(filename, relFns, verbose)
+ 3. └─archive::archive_write_files(...)
+ 4. └─archive:::assert(...)
+
+ [ FAIL 1 | WARN 0 | SKIP 29 | PASS 532 ]
+ Error: Test failures
+ Execution halted
+ ```
+
+## In both
+
+* checking installed package size ... NOTE
+ ```
+ installed size is 9.3Mb
+ sub-directories of 1Mb or more:
+ R 7.5Mb
+ ```
+
diff --git a/revdep/run-all.R b/revdep/run-all.R
new file mode 100644
index 0000000000..d94f11b059
--- /dev/null
+++ b/revdep/run-all.R
@@ -0,0 +1,15 @@
+me <- unname(desc::desc_get("Package"))
+
+last <- dir(pattern = paste0("^", me, "_.*[.]tar[.]gz$"))
+stopifnot(length(last) == 1)
+last
+
+strong <- unlist(tools::package_dependencies(me, which = "most", reverse = TRUE), use.names = FALSE)
+# second <- unlist(tools::package_dependencies(strong, reverse = TRUE, recursive = TRUE), use.names = FALSE)
+second <- unlist(tools::package_dependencies(strong, reverse = TRUE), use.names = FALSE)
+bad <- c("streamDAG", "Seurat", "bsts")
+packages <- unique(c(strong, second))
+
+revdepcheck::cloud_check(tarball = last, revdep_packages = packages, r_version = "4.4.0")
+revdepcheck::cloud_status()
+revdepcheck::cloud_report()
diff --git a/revdep/run-broken.R b/revdep/run-broken.R
index 2dea728b98..e42161ccd0 100644
--- a/revdep/run-broken.R
+++ b/revdep/run-broken.R
@@ -1,9 +1,16 @@
+me <- unname(desc::desc_get("Package"))
+
+last <- dir(pattern = paste0("^", me, "_.*[.]tar[.]gz$"))
+stopifnot(length(last) == 1)
+last
+
problems <- gsub("^# ", "", grep("^# ", readLines("revdep/problems.md"), value = TRUE))
# broken <- revdepcheck::cloud_broken(install_failures = TRUE, timeout_failures = TRUE)
failed <- revdepcheck::cloud_failed()
failures <- gsub("^# ", "", grep("^# ", readLines("revdep/failures.md"), value = TRUE))
-packages <- c(problems, failed, failures)
-revdepcheck::cloud_check(revdep_packages = packages)
+broken <- c(problems, failed, failures)
+
+revdepcheck::cloud_check(tarball = last, revdep_packages = broken, r_version = "4.4.0")
revdepcheck::cloud_status()
revdepcheck::cloud_report()
diff --git a/revdep/run.R b/revdep/run.R
index 45602c1a1e..22bfb48805 100644
--- a/revdep/run.R
+++ b/revdep/run.R
@@ -1,10 +1,9 @@
me <- unname(desc::desc_get("Package"))
-strong <- unlist(tools::package_dependencies(me, which = "most", reverse = TRUE), use.names = FALSE)
-# second <- unlist(tools::package_dependencies(strong, reverse = TRUE, recursive = TRUE), use.names = FALSE)
-second <- unlist(tools::package_dependencies(strong, reverse = TRUE), use.names = FALSE)
-bad <- c("streamDAG", "Seurat", "bsts")
-packages <- unique(c(strong, second))
-revdepcheck::cloud_check(revdep_packages = packages)
+last <- dir(pattern = paste0("^", me, "_.*[.]tar[.]gz$"))
+stopifnot(length(last) == 1)
+last
+
+revdepcheck::cloud_check(tarball = last, r_version = "4.4.0")
revdepcheck::cloud_status()
revdepcheck::cloud_report()