From 86a713579fd338245978107a6e4844c8f3319488 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Kirill=20M=C3=BCller?= Date: Tue, 15 Oct 2024 04:34:42 +0200 Subject: [PATCH] chore: Results of downstream checks --- revdep/.gitignore | 1 + revdep/README.md | 47 +- revdep/cran.md | 34 +- revdep/failures.md | 1221 +++---------------------------------------- revdep/problems.md | 149 ++++-- revdep/run-all.R | 15 + revdep/run-broken.R | 11 +- revdep/run.R | 11 +- 8 files changed, 240 insertions(+), 1249 deletions(-) create mode 100644 revdep/run-all.R 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()