Check results for 'RcppPlanc'

using R version 4.4.3 (2025-02-28)
using platform: x86_64-pc-linux-gnu
R was compiled by gcc-14 (Debian 14.2.0-19) 14.2.0 GNU Fortran (Debian 14.2.0-19) 14.2.0
running under: Debian GNU/Linux trixie/sid
using session charset: UTF-8
checking for file ‘RcppPlanc/DESCRIPTION’ ... OK
checking extension type ... Package
this is package ‘RcppPlanc’ version ‘2.0.0’
package encoding: UTF-8
checking package namespace information ... OK
checking package dependencies ... OK
checking if this is a source package ... OK
checking if there is a namespace ... OK
checking for executable files ... OK
checking for hidden files and directories ... OK
checking for portable file names ... OK
checking for sufficient/correct file permissions ... OK
checking whether package ‘RcppPlanc’ can be installed ... OK See the install log for details.
used C++ compiler: ‘g++-14 (Debian 14.2.0-19) 14.2.0’
checking C++ specification ... OK Not all R platforms support C++17
checking package directory ... OK
checking for future file timestamps ... OK
checking ‘build’ directory ... OK
checking DESCRIPTION meta-information ... OK
checking top-level files ... OK
checking for left-over files ... OK
checking index information ... OK
checking package subdirectories ... OK
checking code files for non-ASCII characters ... OK
checking R files for syntax errors ... OK
checking whether the package can be loaded ... [2s/2s] OK
checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
checking whether the package can be unloaded cleanly ... [2s/2s] OK
checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
checking loading without being on the library search path ... [2s/2s] OK
checking whether startup messages can be suppressed ... [2s/2s] OK
checking use of S3 registration ... OK
checking dependencies in R code ... OK
checking S3 generic/method consistency ... OK
checking replacement functions ... OK
checking foreign function calls ... OK
checking R code for possible problems ... [10s/14s] OK
checking Rd files ... [0s/1s] OK
checking Rd metadata ... OK
checking Rd line widths ... OK
checking Rd cross-references ... OK
checking for missing documentation entries ... OK
checking for code/documentation mismatches ... OK
checking Rd \usage sections ... OK
checking Rd contents ... OK
checking for unstated dependencies in examples ... OK
checking contents of ‘data’ directory ... OK
checking data for non-ASCII characters ... [2s/2s] OK
checking LazyData ... OK
checking data for ASCII and uncompressed saves ... OK
checking line endings in shell scripts ... OK
checking line endings in C/C++/Fortran sources/headers ... OK
checking line endings in Makefiles ... OK
checking compilation flags in Makevars ... OK
checking for GNU extensions in Makefiles ... OK
checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
checking use of PKG_*FLAGS in Makefiles ... OK
checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
checking pragmas in C/C++ headers and code ... OK
checking compilation flags used ... OK
checking compiled code ... OK
checking installed files from ‘inst/doc’ ... OK
checking files in ‘vignettes’ ... OK
checking examples ... [6s/8s] ERROR Running examples in ‘RcppPlanc-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: onlineINMF > ### Title: Perform Integrative Non-negative Matrix Factorization Using > ### Online Learning > ### Aliases: onlineINMF > > ### ** Examples > > library(Matrix) > > # Scenario 1 with sparse matrices > set.seed(1) > res1 <- onlineINMF(list(ctrl.sparse, stim.sparse), + minibatchSize = 50, k = 10, verbose = FALSE) > > # Scenario 2 with H5 dense matrices > h5dense1 <- H5Mat(filename = system.file("extdata", "ctrl_dense.h5", + package = "RcppPlanc", mustWork = TRUE), + dataPath = "scaleData") > h5dense2 <- H5Mat(filename = system.file("extdata", "stim_dense.h5", + package = "RcppPlanc", mustWork = TRUE), + dataPath = "scaleData") > res2 <- onlineINMF(list(ctrl = h5dense1), minibatchSize = 50, k = 10, verbose = FALSE) ==H5Mat constructed== H5File: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppPlanc/extdata/ctrl_dense.h5 Mat path: scaleData Dimension: 173 x 300 > res3 <- onlineINMF(list(ctrl = h5dense1), + newDatasets = list(stim = h5dense2), + Hinit = res2$H, Vinit = res2$V, Winit = res2$W, + Ainit = res2$A, Binit = res2$B, + minibatchSize = 50, k = 10, verbose = FALSE) ==H5Mat constructed== H5File: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppPlanc/extdata/ctrl_dense.h5 Mat path: scaleData Dimension: 173 x 300 ==H5Mat constructed== H5File: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppPlanc/extdata/stim_dense.h5 Mat path: scaleData Dimension: 173 x 300 > > # Scenario 3 with H5 sparse matrices > h5sparse1 <- H5SpMat(filename = system.file("extdata", "ctrl_sparse.h5", + package = "RcppPlanc", mustWork = TRUE), + valuePath = "scaleDataSparse/data", + rowindPath = "scaleDataSparse/indices", + colptrPath = "scaleDataSparse/indptr", + nrow = nrow(ctrl.sparse), + ncol = ncol(ctrl.sparse)) > h5sparse2 <- H5SpMat(filename = system.file("extdata", "stim_sparse.h5", + package = "RcppPlanc", mustWork = TRUE), + valuePath = "scaleDataSparse/data", + rowindPath = "scaleDataSparse/indices", + colptrPath = "scaleDataSparse/indptr", + nrow = nrow(stim.sparse), + ncol = nrow(stim.sparse)) > res4 <- onlineINMF(list(ctrl = h5sparse1), minibatchSize = 50, k = 10, verbose = FALSE) Error in .onlineINMF_h5sparse(sapply(objectList, function(x) x$filename), : HDF5-API Errors: error #000: ../../../src/H5F.c in H5Fopen(): line 827: unable to synchronously open file class: HDF5 major: File accessibility minor: Unable to open file error #001: ../../../src/H5F.c in H5F__open_api_common(): line 788: unable to open file class: HDF5 major: File accessibility minor: Unable to open file error #002: ../../../src/H5VLcallback.c in H5VL_file_open(): line 3680: open failed class: HDF5 major: Virtual Object Layer minor: Can't open object error #003: ../../../src/H5VLcallback.c in H5VL__file_open(): line 3514: open failed class: HDF5 major: Virtual Object Layer minor: Can't open object error #004: ../../../src/H5VLnative_file.c in H5VL__native_file_open(): line 128: unable to open file class: HDF5 major: File accessibility minor: Unable to open file error #005: ../../../src/H5Fint.c in H5F_open(): lin Calls: onlineINMF -> .onlineINMF_h5sparse Execution halted
checking for unstated dependencies in ‘tests’ ... OK
checking tests ...