diff --git a/cran-comments.md b/cran-comments.md index 03e05b8f06..eb0da8b790 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,8 +1,7 @@ New release with many bug fixes and new features. -We checked 23 reverse dependencies (22 from CRAN + 1 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package. +We checked 39 reverse dependencies (37 from CRAN + 2 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package. * We saw 1 new problems - * We failed to check 9 packages -The new failing package is luz, and a new version will be submitted shortly after. \ No newline at end of file +The new problem is in torchvisionlib and we'll submit a fixed version of it shortly after the torch release. \ No newline at end of file diff --git a/revdep/README.md b/revdep/README.md index 19d0b7f221..994ac21558 100644 --- a/revdep/README.md +++ b/revdep/README.md @@ -2,57 +2,57 @@ |field |value | |:--------|:---------------------------------| -|version |R version 4.2.2 (2022-10-31) | -|os |macOS Ventura 13.1 | +|version |R version 4.4.1 (2024-06-14) | +|os |macOS 15.1.1 | |system |aarch64, darwin20 | |ui |X11 | |language |(EN) | |collate |en_US.UTF-8 | |ctype |en_US.UTF-8 | -|tz |Europe/Rome | -|date |2023-06-06 | +|tz |America/Sao_Paulo | +|date |2025-01-30 | |pandoc |2.19.2 @ /opt/homebrew/bin/pandoc | # Dependencies -|package |old |new |Δ | -|:---------|:------|:-----------|:--| -|torch |0.10.0 |0.10.0.9000 |* | -|bit |4.0.5 |4.0.5 | | -|bit64 |4.0.5 |4.0.5 | | -|callr |3.7.3 |3.7.3 | | -|cli |3.6.1 |3.6.1 | | -|coro |1.0.3 |1.0.3 | | -|desc |1.4.2 |1.4.2 | | -|ellipsis |0.3.2 |0.3.2 | | -|glue |1.6.2 |1.6.2 | | -|magrittr |2.0.3 |2.0.3 | | -|processx |3.8.1 |3.8.1 | | -|ps |1.7.5 |1.7.5 | | -|R6 |2.5.1 |2.5.1 | | -|Rcpp |1.0.10 |1.0.10 | | -|rlang |1.1.1 |1.1.1 | | -|rprojroot |2.0.3 |2.0.3 | | -|withr |2.5.0 |2.5.0 | | +|package |old |new |Δ | +|:------------|:-------|:-------|:--| +|torch |0.13.0 |0.14.0 |* | +|bit |4.5.0.1 |4.5.0.1 | | +|bit64 |4.6.0-1 |4.6.0-1 | | +|callr |3.7.6 |3.7.6 | | +|cli |3.6.3 |3.6.3 | | +|colorspace |NA |2.1-1 |* | +|coro |1.1.0 |1.1.0 | | +|desc |1.4.3 |1.4.3 | | +|ellipsis |0.3.2 |NA |* | +|farver |NA |2.1.2 |* | +|glue |1.8.0 |1.8.0 | | +|jsonlite |1.8.9 |1.8.9 | | +|labeling |NA |0.4.3 |* | +|lifecycle |NA |1.0.4 |* | +|magrittr |2.0.3 |2.0.3 | | +|munsell |NA |0.5.1 |* | +|processx |3.8.5 |3.8.5 | | +|ps |1.8.1 |1.8.1 | | +|R6 |2.5.1 |2.5.1 | | +|RColorBrewer |NA |1.1-3 |* | +|Rcpp |1.0.14 |1.0.14 | | +|rlang |1.1.5 |1.1.5 | | +|safetensors |0.1.2 |0.1.2 | | +|scales |NA |1.3.0 |* | +|viridisLite |NA |0.4.2 |* | +|withr |3.0.2 |3.0.2 | | # Revdeps -## Failed to check (8) - -|package |version |error |warning |note | -|:-------------|:-------|:-----------|:-------|:----| -|PLNmodels |1.0.1 |1 | | | -|proteus |1.1.0 |1 | | | -|scDHA |1.2.1 |1 | | | -|sits |1.4.0 |1 | | | -|SPQR |0.1.0 |1 | | | -|[targets](failures.md#targets)|1.1.3 |__+1__ | | | -|torchdatasets |0.3.0 |1 | | | -|[torchvision](failures.md#torchvision)|0.5.1 |1 -1 __+1__ | | | - -## New problems (1) +## Failed to check (5) |package |version |error |warning |note | |:--------------|:-------|:------|:-------|:----| -|[torchvisionlib](problems.md#torchvisionlib)|0.4.0 |__+1__ | | | +|COTAN |2.6.2 |2 | |3 | +|proteus |1.1.4 |1 | | | +|tabnet |0.6.0 |2 | | | +|torchdatasets |0.3.1 |1 | | | +|[torchvisionlib](failures.md#torchvisionlib)|0.5.0 |__+1__ | | | diff --git a/revdep/cran.md b/revdep/cran.md index b0869d3ef8..f8bfa10065 100644 --- a/revdep/cran.md +++ b/revdep/cran.md @@ -1,25 +1,15 @@ ## revdepcheck results -We checked 25 reverse dependencies (24 from CRAN + 1 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package. +We checked 39 reverse dependencies (37 from CRAN + 2 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package. - * We saw 1 new problems - * We failed to check 8 packages + * We saw 0 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) - -* torchvisionlib - checking tests ... - ### Failed to check -* PLNmodels (NA) -* proteus (NA) -* scDHA (NA) -* sits (NA) -* SPQR (NA) -* targets (NA) -* torchdatasets (NA) -* torchvision (NA) +* proteus (NA) +* tabnet (NA) +* torchdatasets (NA) +* torchvisionlib (NA) diff --git a/revdep/failures.md b/revdep/failures.md index 51a8fe2d57..45363ae6b9 100644 --- a/revdep/failures.md +++ b/revdep/failures.md @@ -1,90 +1,97 @@ -# PLNmodels +# COTAN
-* Version: 1.0.1 -* GitHub: https://github.com/pln-team/PLNmodels -* Source code: https://github.com/cran/PLNmodels -* Date/Publication: 2023-02-12 14:42:07 UTC -* Number of recursive dependencies: 147 +* Version: 2.6.2 +* GitHub: https://github.com/seriph78/COTAN +* Source code: https://github.com/cran/COTAN +* Date/Publication: 2025-01-19 +* Number of recursive dependencies: 276 -Run `revdepcheck::revdep_details(, "PLNmodels")` for more info +Run `revdepcheck::revdep_details(, "COTAN")` for more info
## In both -* checking whether package ‘PLNmodels’ can be installed ... ERROR +* checking examples ... ERROR ``` - Installation failed. - See ‘/Users/dfalbel/Documents/posit/torch/revdep/checks.noindex/PLNmodels/new/PLNmodels.Rcheck/00install.out’ for details. + Running examples in ‘COTAN-Ex.R’ failed + The error most likely occurred in: + + > ### Name: COTAN_ObjectCreation + > ### Title: 'COTAN' shortcuts + > ### Aliases: COTAN_ObjectCreation COTAN proceedToCoex,COTAN-method + > ### proceedToCoex automaticCOTANObjectCreation + > + > ### ** Examples + > + ... + Cotan genes' coex estimation started + Warning in canUseTorch(optimizeForSpeed, deviceStr) : + The `torch` library could not find any `CUDA` device + Warning in canUseTorch(optimizeForSpeed, deviceStr) : + Falling back to CPU calculations + Calculate genes coex (torch) on device cpu: START + Error in cpp_cuda_empty_cache() : + `cuda_empty_cache` is only supported on CUDA runtimes. + Calls: automaticCOTANObjectCreation ... calculateCoex_Torch -> -> cpp_cuda_empty_cache + Execution halted ``` -## Installation - -### Devel - -``` -* installing *source* package ‘PLNmodels’ ... -** package ‘PLNmodels’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/include" -DNDEBUG -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/new/Rcpp/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/PLNmodels/RcppArmadillo/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/PLNmodels/nloptr/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o -clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/include" -DNDEBUG -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/new/Rcpp/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/PLNmodels/RcppArmadillo/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/PLNmodels/nloptr/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c nlopt_wrapper.cpp -o nlopt_wrapper.o -clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/include" -DNDEBUG -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/new/Rcpp/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/PLNmodels/RcppArmadillo/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/PLNmodels/nloptr/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c optim_diag_cov.cpp -o optim_diag_cov.o -clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/include" -DNDEBUG -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/new/Rcpp/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/PLNmodels/RcppArmadillo/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/PLNmodels/nloptr/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c optim_fixed_cov.cpp -o optim_fixed_cov.o -clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/include" -DNDEBUG -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/new/Rcpp/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/PLNmodels/RcppArmadillo/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/PLNmodels/nloptr/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c optim_full_cov.cpp -o optim_full_cov.o -clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/include" -DNDEBUG -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/new/Rcpp/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/PLNmodels/RcppArmadillo/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/PLNmodels/nloptr/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c optim_genet_cov.cpp -o optim_genet_cov.o -... -1 warning generated. -1 warning generated. -clang++ -arch arm64 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib -L/opt/R/arm64/lib -o PLNmodels.so RcppExports.o nlopt_wrapper.o optim_diag_cov.o optim_fixed_cov.o optim_full_cov.o optim_genet_cov.o optim_rank_cov.o optim_spherical.o packing.o -L/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib -lRblas -L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1 -L/opt/R/arm64/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/Versions/4.2-arm64 -framework R -Wl,-framework -Wl,CoreFoundation -ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1' -ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib' -ld: library not found for -lgfortran -clang: error: linker command failed with exit code 1 (use -v to see invocation) -make: *** [PLNmodels.so] Error 1 -ERROR: compilation failed for package ‘PLNmodels’ -* removing ‘/Users/dfalbel/Documents/posit/torch/revdep/checks.noindex/PLNmodels/new/PLNmodels.Rcheck/PLNmodels’ - +* R CMD check timed out + -``` -### CRAN +* checking installed package size ... NOTE + ``` + installed size is 13.7Mb + sub-directories of 1Mb or more: + doc 11.8Mb + ``` -``` -* installing *source* package ‘PLNmodels’ ... -** package ‘PLNmodels’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/include" -DNDEBUG -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/old/Rcpp/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/PLNmodels/RcppArmadillo/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/PLNmodels/nloptr/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o -clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/include" -DNDEBUG -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/old/Rcpp/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/PLNmodels/RcppArmadillo/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/PLNmodels/nloptr/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c nlopt_wrapper.cpp -o nlopt_wrapper.o -clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/include" -DNDEBUG -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/old/Rcpp/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/PLNmodels/RcppArmadillo/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/PLNmodels/nloptr/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c optim_diag_cov.cpp -o optim_diag_cov.o -clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/include" -DNDEBUG -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/old/Rcpp/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/PLNmodels/RcppArmadillo/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/PLNmodels/nloptr/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c optim_fixed_cov.cpp -o optim_fixed_cov.o -clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/include" -DNDEBUG -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/old/Rcpp/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/PLNmodels/RcppArmadillo/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/PLNmodels/nloptr/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c optim_full_cov.cpp -o optim_full_cov.o -clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/include" -DNDEBUG -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/old/Rcpp/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/PLNmodels/RcppArmadillo/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/PLNmodels/nloptr/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c optim_genet_cov.cpp -o optim_genet_cov.o -... -1 warning generated. -1 warning generated. -clang++ -arch arm64 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib -L/opt/R/arm64/lib -o PLNmodels.so RcppExports.o nlopt_wrapper.o optim_diag_cov.o optim_fixed_cov.o optim_full_cov.o optim_genet_cov.o optim_rank_cov.o optim_spherical.o packing.o -L/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib -lRblas -L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1 -L/opt/R/arm64/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/Versions/4.2-arm64 -framework R -Wl,-framework -Wl,CoreFoundation -ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1' -ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib' -ld: library not found for -lgfortran -clang: error: linker command failed with exit code 1 (use -v to see invocation) -make: *** [PLNmodels.so] Error 1 -ERROR: compilation failed for package ‘PLNmodels’ -* removing ‘/Users/dfalbel/Documents/posit/torch/revdep/checks.noindex/PLNmodels/old/PLNmodels.Rcheck/PLNmodels’ +* checking dependencies in R code ... NOTE + ``` + 'library' or 'require' call to ‘torch’ in package code. + Please use :: or requireNamespace() instead. + See section 'Suggested packages' in the 'Writing R Extensions' manual. + Unexported object imported by a ':::' call: ‘ggplot2:::ggname’ + See the note in ?`:::` about the use of this operator. + ``` +* checking R code for possible problems ... NOTE + ``` + mergeUniformCellsClusters : fromMergedName: warning in + vapply(currentClNames, function(clName, mergedName) {: partial + argument match of 'FUN.VAL' to 'FUN.VALUE' + mergeUniformCellsClusters : fromMergedName: warning in + return(str_detect(mergedName, clName)): partial argument match of + 'FUN.VAL' to 'FUN.VALUE' + mergeUniformCellsClusters : fromMergedName: warning in }, FUN.VAL = + logical(1L), mergedClName): partial argument match of 'FUN.VAL' to + 'FUN.VALUE' + ECDPlot: no visible binding for global variable ‘.’ + ... + ‘clusterData’ + Undefined global functions or variables: + . .x CellNumber Cluster Condition ExpGenes GCS GDI PC1 PC2 UDEPLot a + bGroupGenesPlot cl1 cl2 clName1 clName2 clusterData clusters coex + condName conditions expectedN expectedNN expectedNY expectedYN + expectedYY g2 group hk keys lambda means mit.percentage n nu nuPlot + obj objSeurat observedNN observedNY observedY observedYN observedYY + pcaCellsPlot permMap rankGenes rawNorm secondaryMarkers sum.raw.norm + type types useTorch usedMaxResolution values violinwidth width x xmax + xmaxv xminv y zoomedNuPlot + ``` -``` # proteus
-* Version: 1.1.0 +* Version: 1.1.4 * GitHub: NA * Source code: https://github.com/cran/proteus -* Date/Publication: 2023-03-08 09:20:05 UTC -* Number of recursive dependencies: 123 +* Date/Publication: 2023-10-21 17:40:02 UTC +* Number of recursive dependencies: 137 Run `revdepcheck::revdep_details(, "proteus")` for more info @@ -95,168 +102,89 @@ Run `revdepcheck::revdep_details(, "proteus")` for more info * R CMD check timed out -# scDHA +# tabnet
-* Version: 1.2.1 -* GitHub: https://github.com/duct317/scDHA -* Source code: https://github.com/cran/scDHA -* Date/Publication: 2023-04-04 12:10:02 UTC -* Number of recursive dependencies: 62 +* Version: 0.6.0 +* GitHub: https://github.com/mlverse/tabnet +* Source code: https://github.com/cran/tabnet +* Date/Publication: 2024-06-15 18:20:02 UTC +* Number of recursive dependencies: 173 -Run `revdepcheck::revdep_details(, "scDHA")` for more info +Run `revdepcheck::revdep_details(, "tabnet")` for more info
## In both -* checking whether package ‘scDHA’ can be installed ... ERROR +* checking tests ... ``` - Installation failed. - See ‘/Users/dfalbel/Documents/posit/torch/revdep/checks.noindex/scDHA/new/scDHA.Rcheck/00install.out’ for details. + Running ‘spelling.R’ + Running ‘testthat.R’ + ERROR + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 4. └─testthat:::test_files_parallel(...) + 5. ├─withr::with_dir(...) + 6. │ └─base::force(code) + 7. ├─testthat::with_reporter(...) + 8. │ └─base::tryCatch(...) + ... + 9. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) + 10. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) + 11. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) + 12. └─testthat:::parallel_event_loop_chunky(queue, reporters, ".") + 13. └─queue$poll(Inf) + 14. └─base::lapply(...) + 15. └─testthat (local) FUN(X[[i]], ...) + 16. └─private$handle_error(msg, i) + 17. └─rlang::abort(...) + Execution halted ``` -## Installation - -### Devel - -``` -* installing *source* package ‘scDHA’ ... -** package ‘scDHA’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/new/Rcpp/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/scDHA/RcppArmadillo/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/scDHA/RcppParallel/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/scDHA/RcppAnnoy/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o -clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/new/Rcpp/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/scDHA/RcppArmadillo/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/scDHA/RcppParallel/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/scDHA/RcppAnnoy/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Support.cpp -o Support.o -clang++ -arch arm64 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib -L/opt/R/arm64/lib -o scDHA.so RcppExports.o Support.o -L/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib -lRblas -L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1 -L/opt/R/arm64/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/Versions/4.2-arm64 -framework R -Wl,-framework -Wl,CoreFoundation -ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1' -ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib' -ld: library not found for -lgfortran -clang: error: linker command failed with exit code 1 (use -v to see invocation) -make: *** [scDHA.so] Error 1 -ERROR: compilation failed for package ‘scDHA’ -* removing ‘/Users/dfalbel/Documents/posit/torch/revdep/checks.noindex/scDHA/new/scDHA.Rcheck/scDHA’ - - -``` -### CRAN - -``` -* installing *source* package ‘scDHA’ ... -** package ‘scDHA’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/old/Rcpp/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/scDHA/RcppArmadillo/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/scDHA/RcppParallel/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/scDHA/RcppAnnoy/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o -clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/old/Rcpp/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/scDHA/RcppArmadillo/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/scDHA/RcppParallel/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/scDHA/RcppAnnoy/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Support.cpp -o Support.o -clang++ -arch arm64 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib -L/opt/R/arm64/lib -o scDHA.so RcppExports.o Support.o -L/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib -lRblas -L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1 -L/opt/R/arm64/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/Versions/4.2-arm64 -framework R -Wl,-framework -Wl,CoreFoundation -ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1' -ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib' -ld: library not found for -lgfortran -clang: error: linker command failed with exit code 1 (use -v to see invocation) -make: *** [scDHA.so] Error 1 -ERROR: compilation failed for package ‘scDHA’ -* removing ‘/Users/dfalbel/Documents/posit/torch/revdep/checks.noindex/scDHA/old/scDHA.Rcheck/scDHA’ - +* R CMD check timed out + -``` -# sits +# torchdatasets
-* Version: 1.4.0 -* GitHub: https://github.com/e-sensing/sits -* Source code: https://github.com/cran/sits -* Date/Publication: 2023-05-17 16:50:02 UTC -* Number of recursive dependencies: 211 +* Version: 0.3.1 +* GitHub: https://github.com/mlverse/torchdatasets +* Source code: https://github.com/cran/torchdatasets +* Date/Publication: 2024-06-20 12:40:01 UTC +* Number of recursive dependencies: 71 -Run `revdepcheck::revdep_details(, "sits")` for more info +Run `revdepcheck::revdep_details(, "torchdatasets")` for more info
## In both -* checking whether package ‘sits’ can be installed ... ERROR - ``` - Installation failed. - See ‘/Users/dfalbel/Documents/posit/torch/revdep/checks.noindex/sits/new/sits.Rcheck/00install.out’ for details. - ``` - -## Installation - -### Devel - -``` -* installing *source* package ‘sits’ ... -** package ‘sits’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/include" -DNDEBUG -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/new/Rcpp/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/sits/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o -clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/include" -DNDEBUG -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/new/Rcpp/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/sits/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c combine_data.cpp -o combine_data.o -clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/include" -DNDEBUG -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/new/Rcpp/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/sits/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c kernel.cpp -o kernel.o -clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/include" -DNDEBUG -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/new/Rcpp/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/sits/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c label_class.cpp -o label_class.o -clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/include" -DNDEBUG -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/new/Rcpp/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/sits/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c linear_interp.cpp -o linear_interp.o -clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/include" -DNDEBUG -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/new/Rcpp/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/sits/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c nnls_solver.cpp -o nnls_solver.o -... -clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/include" -DNDEBUG -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/new/Rcpp/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/sits/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c smooth_whit.cpp -o smooth_whit.o -clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/include" -DNDEBUG -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/new/Rcpp/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/sits/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c uncertainty.cpp -o uncertainty.o -clang++ -arch arm64 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib -L/opt/R/arm64/lib -o sits.so RcppExports.o combine_data.o kernel.o label_class.o linear_interp.o nnls_solver.o normalize_data.o normalize_data_0.o sampling_window.o smooth.o smooth_bayes.o smooth_sgp.o smooth_whit.o uncertainty.o -L/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib -lRblas -L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1 -L/opt/R/arm64/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/Versions/4.2-arm64 -framework R -Wl,-framework -Wl,CoreFoundation -ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1' -ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib' -ld: library not found for -lgfortran -clang: error: linker command failed with exit code 1 (use -v to see invocation) -make: *** [sits.so] Error 1 -ERROR: compilation failed for package ‘sits’ -* removing ‘/Users/dfalbel/Documents/posit/torch/revdep/checks.noindex/sits/new/sits.Rcheck/sits’ - - -``` -### CRAN - -``` -* installing *source* package ‘sits’ ... -** package ‘sits’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/include" -DNDEBUG -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/old/Rcpp/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/sits/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o -clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/include" -DNDEBUG -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/old/Rcpp/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/sits/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c combine_data.cpp -o combine_data.o -clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/include" -DNDEBUG -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/old/Rcpp/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/sits/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c kernel.cpp -o kernel.o -clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/include" -DNDEBUG -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/old/Rcpp/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/sits/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c label_class.cpp -o label_class.o -clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/include" -DNDEBUG -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/old/Rcpp/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/sits/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c linear_interp.cpp -o linear_interp.o -clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/include" -DNDEBUG -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/old/Rcpp/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/sits/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c nnls_solver.cpp -o nnls_solver.o -... -clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/include" -DNDEBUG -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/old/Rcpp/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/sits/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c smooth_whit.cpp -o smooth_whit.o -clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/include" -DNDEBUG -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/old/Rcpp/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/sits/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c uncertainty.cpp -o uncertainty.o -clang++ -arch arm64 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib -L/opt/R/arm64/lib -o sits.so RcppExports.o combine_data.o kernel.o label_class.o linear_interp.o nnls_solver.o normalize_data.o normalize_data_0.o sampling_window.o smooth.o smooth_bayes.o smooth_sgp.o smooth_whit.o uncertainty.o -L/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib -lRblas -L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1 -L/opt/R/arm64/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/Versions/4.2-arm64 -framework R -Wl,-framework -Wl,CoreFoundation -ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1' -ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib' -ld: library not found for -lgfortran -clang: error: linker command failed with exit code 1 (use -v to see invocation) -make: *** [sits.so] Error 1 -ERROR: compilation failed for package ‘sits’ -* removing ‘/Users/dfalbel/Documents/posit/torch/revdep/checks.noindex/sits/old/sits.Rcheck/sits’ - +* R CMD check timed out + -``` -# SPQR +# torchvisionlib
-* Version: 0.1.0 -* GitHub: https://github.com/stevengxu/SPQR -* Source code: https://github.com/cran/SPQR -* Date/Publication: 2022-05-02 20:02:03 UTC -* Number of recursive dependencies: 65 +* Version: 0.5.0 +* GitHub: https://github.com/mlverse/torchvisionlib +* Source code: https://github.com/cran/torchvisionlib +* Date/Publication: 2024-02-15 19:20:02 UTC +* Number of recursive dependencies: 31 -Run `revdepcheck::revdep_details(, "SPQR")` for more info +Run `revdepcheck::revdep_details(, "torchvisionlib")` for more info
-## In both +## Newly broken -* checking whether package ‘SPQR’ can be installed ... ERROR +* checking whether package ‘torchvisionlib’ can be installed ... ERROR ``` Installation failed. - See ‘/Users/dfalbel/Documents/posit/torch/revdep/checks.noindex/SPQR/new/SPQR.Rcheck/00install.out’ for details. + See ‘/Users/dfalbel/Documents/posit/torch/revdep/checks.noindex/torchvisionlib/new/torchvisionlib.Rcheck/00install.out’ for details. ``` ## Installation @@ -264,147 +192,54 @@ Run `revdepcheck::revdep_details(, "SPQR")` for more info ### Devel ``` -* installing *source* package ‘SPQR’ ... -** package ‘SPQR’ successfully unpacked and MD5 sums checked +* installing *source* package ‘torchvisionlib’ ... +** package ‘torchvisionlib’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/include" -DNDEBUG -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/new/Rcpp/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/SPQR/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o -clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/include" -DNDEBUG -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/new/Rcpp/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/SPQR/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c mcmc_export.cpp -o mcmc_export.o -clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib -L/opt/R/arm64/lib -o SPQR.so RcppExports.o mcmc_export.o -L/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib -lRblas -L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1 -L/opt/R/arm64/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/Versions/4.2-arm64 -framework R -Wl,-framework -Wl,CoreFoundation -ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1' -ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib' -ld: library not found for -lgfortran -clang: error: linker command failed with exit code 1 (use -v to see invocation) -make: *** [SPQR.so] Error 1 -ERROR: compilation failed for package ‘SPQR’ -* removing ‘/Users/dfalbel/Documents/posit/torch/revdep/checks.noindex/SPQR/new/SPQR.Rcheck/SPQR’ +using C++ compiler: ‘Apple clang version 16.0.0 (clang-1600.0.26.3)’ +using SDK: ‘MacOSX15.1.sdk’ +clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/include" -DNDEBUG -I../inst/include/ -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/new/Rcpp/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/new/torch/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o +clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/include" -DNDEBUG -I../inst/include/ -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/new/Rcpp/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/new/torch/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c exports.cpp -o exports.o +clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/include" -DNDEBUG -I../inst/include/ -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/new/Rcpp/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/new/torch/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c torchvisionlib.cpp -o torchvisionlib.o +clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/include" -DNDEBUG -I../inst/include/ -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/new/Rcpp/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/new/torch/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c torchvisionlib_types.cpp -o torchvisionlib_types.o +... + .onLoad failed in loadNamespace() for 'torchvisionlib', details: + call: dyn.load(lib_path("torchvision"), local = FALSE) + error: unable to load shared object '/Users/dfalbel/Documents/posit/torch/revdep/checks.noindex/torchvisionlib/new/torchvisionlib.Rcheck/00LOCK-torchvisionlib/00new/torchvisionlib//lib/libtorchvision.dylib': + dlopen(/Users/dfalbel/Documents/posit/torch/revdep/checks.noindex/torchvisionlib/new/torchvisionlib.Rcheck/00LOCK-torchvisionlib/00new/torchvisionlib//lib/libtorchvision.dylib, 0x000A): Symbol not found: __ZN2at4_ops10zeros_like4callERKNS_6TensorEN3c108optionalINS5_10ScalarTypeEEENS6_INS5_6LayoutEEENS6_INS5_6DeviceEEENS6_IbEENS6_INS5_12MemoryFormatEEE + Referenced from: <7770DCC4-8CD6-3A42-8643-D57BF69E720D> /Users/dfalbel/Documents/posit/torch/revdep/checks.noindex/torchvisionlib/new/torchvisionlib.Rcheck/00LOCK-torchvisionlib/00new/torchvisionlib/lib/libtorchvision.dylib + Expected in: <30A54DCC-A845-368C-8B03-ADCDD3639E86> /Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/new/torch/lib/libtorch_cpu.dylib +Error: loading failed +Execution halted +ERROR: loading failed +* removing ‘/Users/dfalbel/Documents/posit/torch/revdep/checks.noindex/torchvisionlib/new/torchvisionlib.Rcheck/torchvisionlib’ ``` ### CRAN ``` -* installing *source* package ‘SPQR’ ... -** package ‘SPQR’ successfully unpacked and MD5 sums checked +* installing *source* package ‘torchvisionlib’ ... +** package ‘torchvisionlib’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/include" -DNDEBUG -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/old/Rcpp/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/SPQR/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o -clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/include" -DNDEBUG -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/old/Rcpp/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/SPQR/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c mcmc_export.cpp -o mcmc_export.o -clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib -L/opt/R/arm64/lib -o SPQR.so RcppExports.o mcmc_export.o -L/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib -lRblas -L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1 -L/opt/R/arm64/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/Versions/4.2-arm64 -framework R -Wl,-framework -Wl,CoreFoundation -ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1' -ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib' -ld: library not found for -lgfortran -clang: error: linker command failed with exit code 1 (use -v to see invocation) -make: *** [SPQR.so] Error 1 -ERROR: compilation failed for package ‘SPQR’ -* removing ‘/Users/dfalbel/Documents/posit/torch/revdep/checks.noindex/SPQR/old/SPQR.Rcheck/SPQR’ - - -``` -# targets - -
- -* Version: 1.1.3 -* GitHub: https://github.com/ropensci/targets -* Source code: https://github.com/cran/targets -* Date/Publication: 2023-05-23 14:10:02 UTC -* Number of recursive dependencies: 177 - -Run `revdepcheck::revdep_details(, "targets")` for more info - -
- -## Newly broken - -* R CMD check timed out - - -# torchdatasets - -
- -* Version: 0.3.0 -* GitHub: https://github.com/mlverse/torchdatasets -* Source code: https://github.com/cran/torchdatasets -* Date/Publication: 2023-02-14 11:00:02 UTC -* Number of recursive dependencies: 70 - -Run `revdepcheck::revdep_details(, "torchdatasets")` for more info - -
- -## In both - -* R CMD check timed out - - -# torchvision - -
- -* Version: 0.5.1 -* GitHub: https://github.com/mlverse/torchvision -* Source code: https://github.com/cran/torchvision -* Date/Publication: 2023-04-14 10:00:02 UTC -* Number of recursive dependencies: 43 - -Run `revdepcheck::revdep_details(, "torchvision")` for more info - -
- -## Newly broken - -* checking examples ...sh: line 1: 12985 Abort trap: 6 LANGUAGE=en _R_CHECK_INTERNALS2_=1 '/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/bin/R' --vanilla > 'torchvision-Ex.Rout' 2>&1 < 'torchvision-Ex.R' - ``` - ERROR - Running examples in ‘torchvision-Ex.R’ failed - The error most likely occurred in: - - > ### Name: draw_bounding_boxes - > ### Title: Draws bounding boxes on image. - > ### Aliases: draw_bounding_boxes - > - > ### ** Examples - > - > if (torch::torch_is_installed()) { - + image <- torch::torch_randint(170, 250, size = c(3, 360, 360))$to(torch::torch_uint8()) - + x <- torch::torch_randint(low = 1, high = 160, size = c(12,1)) - + y <- torch::torch_randint(low = 1, high = 260, size = c(12,1)) - + boxes <- torch::torch_cat(c(x, y, x + 20, y + 10), dim = 2) - + bboxed <- draw_bounding_boxes(image, boxes, colors = "black", fill = TRUE) - + tensor_image_browse(bboxed) - + } - Error : R: UnableToReadFont `helvetica' @ error/annotate.c/RenderFreetype/1396 - ``` - -## Newly fixed - -* checking examples ...sh: line 1: 12283 Abort trap: 6 LANGUAGE=en _R_CHECK_INTERNALS2_=1 '/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/bin/R' --vanilla > 'torchvision-Ex.Rout' 2>&1 < 'torchvision-Ex.R' - ``` - ERROR - Running examples in ‘torchvision-Ex.R’ failed - The error most likely occurred in: - - > ### Name: draw_bounding_boxes - > ### Title: Draws bounding boxes on image. - > ### Aliases: draw_bounding_boxes - > - > ### ** Examples - > - > if (torch::torch_is_installed()) { - + image <- torch::torch_randint(170, 250, size = c(3, 360, 360))$to(torch::torch_uint8()) - + x <- torch::torch_randint(low = 1, high = 160, size = c(12,1)) - + y <- torch::torch_randint(low = 1, high = 260, size = c(12,1)) - + boxes <- torch::torch_cat(c(x, y, x + 20, y + 10), dim = 2) - + bboxed <- draw_bounding_boxes(image, boxes, colors = "black", fill = TRUE) - + tensor_image_browse(bboxed) - + } - Error : R: UnableToReadFont `helvetica' @ error/annotate.c/RenderFreetype/1396 - ``` +using C++ compiler: ‘Apple clang version 16.0.0 (clang-1600.0.26.3)’ +using SDK: ‘MacOSX15.1.sdk’ +clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/include" -DNDEBUG -I../inst/include/ -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/old/Rcpp/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/old/torch/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o +clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/include" -DNDEBUG -I../inst/include/ -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/old/Rcpp/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/old/torch/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c exports.cpp -o exports.o +clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/include" -DNDEBUG -I../inst/include/ -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/old/Rcpp/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/old/torch/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c torchvisionlib.cpp -o torchvisionlib.o +clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/include" -DNDEBUG -I../inst/include/ -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/old/Rcpp/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/old/torch/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c torchvisionlib_types.cpp -o torchvisionlib_types.o +... +** testing if installed package can be loaded from temporary location +trying URL 'https://github.com/mlverse/torchvisionlib/releases/download/v0.5.0/torchvisionlib-0.5.0+cpu+arm64-Darwin.zip' +Content type 'application/octet-stream' length 928798 bytes (907 KB) +================================================== +downloaded 907 KB -## In both +** checking absolute paths in shared objects and dynamic libraries +** testing if installed package can be loaded from final location +** testing if installed package keeps a record of temporary installation path +* DONE (torchvisionlib) -* R CMD check timed out - +``` diff --git a/revdep/problems.md b/revdep/problems.md index 449d239ba6..cfdc27abd0 100644 --- a/revdep/problems.md +++ b/revdep/problems.md @@ -1,100 +1,12 @@ -# targets - -
- -* Version: 1.1.3 -* GitHub: https://github.com/ropensci/targets -* Source code: https://github.com/cran/targets -* Date/Publication: 2023-05-23 14:10:02 UTC -* Number of recursive dependencies: 177 - -Run `revdepcheck::revdep_details(, "targets")` for more info - -
- -## Newly broken - -* R CMD check timed out - - -# torchvision - -
- -* Version: 0.5.1 -* GitHub: https://github.com/mlverse/torchvision -* Source code: https://github.com/cran/torchvision -* Date/Publication: 2023-04-14 10:00:02 UTC -* Number of recursive dependencies: 43 - -Run `revdepcheck::revdep_details(, "torchvision")` for more info - -
- -## Newly broken - -* checking examples ...sh: line 1: 12985 Abort trap: 6 LANGUAGE=en _R_CHECK_INTERNALS2_=1 '/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/bin/R' --vanilla > 'torchvision-Ex.Rout' 2>&1 < 'torchvision-Ex.R' - ``` - ERROR - Running examples in ‘torchvision-Ex.R’ failed - The error most likely occurred in: - - > ### Name: draw_bounding_boxes - > ### Title: Draws bounding boxes on image. - > ### Aliases: draw_bounding_boxes - > - > ### ** Examples - > - > if (torch::torch_is_installed()) { - + image <- torch::torch_randint(170, 250, size = c(3, 360, 360))$to(torch::torch_uint8()) - + x <- torch::torch_randint(low = 1, high = 160, size = c(12,1)) - + y <- torch::torch_randint(low = 1, high = 260, size = c(12,1)) - + boxes <- torch::torch_cat(c(x, y, x + 20, y + 10), dim = 2) - + bboxed <- draw_bounding_boxes(image, boxes, colors = "black", fill = TRUE) - + tensor_image_browse(bboxed) - + } - Error : R: UnableToReadFont `helvetica' @ error/annotate.c/RenderFreetype/1396 - ``` - -## Newly fixed - -* checking examples ...sh: line 1: 12283 Abort trap: 6 LANGUAGE=en _R_CHECK_INTERNALS2_=1 '/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/bin/R' --vanilla > 'torchvision-Ex.Rout' 2>&1 < 'torchvision-Ex.R' - ``` - ERROR - Running examples in ‘torchvision-Ex.R’ failed - The error most likely occurred in: - - > ### Name: draw_bounding_boxes - > ### Title: Draws bounding boxes on image. - > ### Aliases: draw_bounding_boxes - > - > ### ** Examples - > - > if (torch::torch_is_installed()) { - + image <- torch::torch_randint(170, 250, size = c(3, 360, 360))$to(torch::torch_uint8()) - + x <- torch::torch_randint(low = 1, high = 160, size = c(12,1)) - + y <- torch::torch_randint(low = 1, high = 260, size = c(12,1)) - + boxes <- torch::torch_cat(c(x, y, x + 20, y + 10), dim = 2) - + bboxed <- draw_bounding_boxes(image, boxes, colors = "black", fill = TRUE) - + tensor_image_browse(bboxed) - + } - Error : R: UnableToReadFont `helvetica' @ error/annotate.c/RenderFreetype/1396 - ``` - -## In both - -* R CMD check timed out - - # torchvisionlib
-* Version: 0.4.0 -* GitHub: NA +* Version: 0.5.0 +* GitHub: https://github.com/mlverse/torchvisionlib * Source code: https://github.com/cran/torchvisionlib -* Date/Publication: 2023-05-30 13:10:02 UTC -* Number of recursive dependencies: 36 +* Date/Publication: 2024-02-15 19:20:02 UTC +* Number of recursive dependencies: 31 Run `revdepcheck::revdep_details(, "torchvisionlib")` for more info @@ -102,26 +14,65 @@ Run `revdepcheck::revdep_details(, "torchvisionlib")` for more info ## Newly broken -* checking tests ... +* checking whether package ‘torchvisionlib’ can be installed ... ERROR ``` - Running ‘testthat.R’ - ERROR - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - ============================================= - downloaded 68.1 MB - - [ FAIL 1 | WARN 2 | SKIP 0 | PASS 13 ] - - ══ Failed tests ════════════════════════════════════════════════════════════════ - ── Error ('test-vision.R:5:3'): We can load a detection model ────────────────── - Error in `download.file(url, destfile = tmp, mode = "wb")`: download from 'https://storage.googleapis.com/torch-lantern-builds/testing-models/fasterrcnn_mobilenet_v3_large_320_fpn.pt' failed - Backtrace: - ▆ - 1. └─utils::download.file(url, destfile = tmp, mode = "wb") at test-vision.R:5:2 - - [ FAIL 1 | WARN 2 | SKIP 0 | PASS 13 ] - Error: Test failures - Execution halted + Installation failed. + See ‘/Users/dfalbel/Documents/posit/torch/revdep/checks.noindex/torchvisionlib/new/torchvisionlib.Rcheck/00install.out’ for details. ``` +## Installation + +### Devel + +``` +* installing *source* package ‘torchvisionlib’ ... +** package ‘torchvisionlib’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘Apple clang version 16.0.0 (clang-1600.0.26.3)’ +using SDK: ‘MacOSX15.1.sdk’ +clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/include" -DNDEBUG -I../inst/include/ -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/new/Rcpp/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/new/torch/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o +clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/include" -DNDEBUG -I../inst/include/ -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/new/Rcpp/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/new/torch/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c exports.cpp -o exports.o +clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/include" -DNDEBUG -I../inst/include/ -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/new/Rcpp/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/new/torch/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c torchvisionlib.cpp -o torchvisionlib.o +clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/include" -DNDEBUG -I../inst/include/ -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/new/Rcpp/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/new/torch/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c torchvisionlib_types.cpp -o torchvisionlib_types.o +... + .onLoad failed in loadNamespace() for 'torchvisionlib', details: + call: dyn.load(lib_path("torchvision"), local = FALSE) + error: unable to load shared object '/Users/dfalbel/Documents/posit/torch/revdep/checks.noindex/torchvisionlib/new/torchvisionlib.Rcheck/00LOCK-torchvisionlib/00new/torchvisionlib//lib/libtorchvision.dylib': + dlopen(/Users/dfalbel/Documents/posit/torch/revdep/checks.noindex/torchvisionlib/new/torchvisionlib.Rcheck/00LOCK-torchvisionlib/00new/torchvisionlib//lib/libtorchvision.dylib, 0x000A): Symbol not found: __ZN2at4_ops10zeros_like4callERKNS_6TensorEN3c108optionalINS5_10ScalarTypeEEENS6_INS5_6LayoutEEENS6_INS5_6DeviceEEENS6_IbEENS6_INS5_12MemoryFormatEEE + Referenced from: <7770DCC4-8CD6-3A42-8643-D57BF69E720D> /Users/dfalbel/Documents/posit/torch/revdep/checks.noindex/torchvisionlib/new/torchvisionlib.Rcheck/00LOCK-torchvisionlib/00new/torchvisionlib/lib/libtorchvision.dylib + Expected in: <30A54DCC-A845-368C-8B03-ADCDD3639E86> /Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/new/torch/lib/libtorch_cpu.dylib +Error: loading failed +Execution halted +ERROR: loading failed +* removing ‘/Users/dfalbel/Documents/posit/torch/revdep/checks.noindex/torchvisionlib/new/torchvisionlib.Rcheck/torchvisionlib’ + + +``` +### CRAN + +``` +* installing *source* package ‘torchvisionlib’ ... +** package ‘torchvisionlib’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘Apple clang version 16.0.0 (clang-1600.0.26.3)’ +using SDK: ‘MacOSX15.1.sdk’ +clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/include" -DNDEBUG -I../inst/include/ -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/old/Rcpp/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/old/torch/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o +clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/include" -DNDEBUG -I../inst/include/ -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/old/Rcpp/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/old/torch/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c exports.cpp -o exports.o +clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/include" -DNDEBUG -I../inst/include/ -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/old/Rcpp/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/old/torch/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c torchvisionlib.cpp -o torchvisionlib.o +clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/include" -DNDEBUG -I../inst/include/ -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/old/Rcpp/include' -I'/Users/dfalbel/Documents/posit/torch/revdep/library.noindex/torch/old/torch/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c torchvisionlib_types.cpp -o torchvisionlib_types.o +... +** testing if installed package can be loaded from temporary location +trying URL 'https://github.com/mlverse/torchvisionlib/releases/download/v0.5.0/torchvisionlib-0.5.0+cpu+arm64-Darwin.zip' +Content type 'application/octet-stream' length 928798 bytes (907 KB) +================================================== +downloaded 907 KB + +** checking absolute paths in shared objects and dynamic libraries +** testing if installed package can be loaded from final location +** testing if installed package keeps a record of temporary installation path +* DONE (torchvisionlib) + + +```