* using log directory ‘/srv/hornik/tmp/CRAN_pretest/BigDataStatMeth.Rcheck’ * using R Under development (unstable) (2025-11-25 r89063) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 21.1.5 (1) Debian flang version 21.1.5 (1) * running under: Debian GNU/Linux forky/sid * using session charset: UTF-8 * checking for file ‘BigDataStatMeth/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘BigDataStatMeth’ version ‘1.0.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [4s/5s] NOTE Maintainer: ‘Dolors Pelegri-Siso ’ New submission Package was archived on CRAN Possibly misspelled words in DESCRIPTION: HDF (3:57, 20:24, 26:38) Scalable (3:48) omics (27:56) scalable (19:30) CRAN repository db overrides: X-CRAN-Comment: Archived on 2022-04-19 for policy violation. Using many threads, using far too much total CPU time. * 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 ‘BigDataStatMeth’ can be installed ... [13m/13m] OK * used C++ compiler: ‘Debian clang version 21.1.5 (1)’ * checking C++ specification ... OK * checking package directory ... OK * checking for future file timestamps ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... NOTE Non-standard file/directory found at top level: ‘cran-comments.md’ * 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 ... [0s/0s] OK * checking whether the package can be loaded with stated dependencies ... [0s/0s] OK * checking whether the package can be unloaded cleanly ... [0s/0s] OK * checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK * checking whether the namespace can be unloaded cleanly ... [0s/0s] OK * checking loading without being on the library search path ... [0s/0s] 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 ... [3s/3s] OK * checking Rd files ... [0s/0s] 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 ... [0s/0s] 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 ... [11s/11s] NOTE Examples with CPU (user + system) or elapsed time > 5s user system elapsed bdblockmult_hdf5 7.399 0.254 7.658 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [29s/29s] OK * checking PDF version of manual ... [7s/7s] WARNING LaTeX errors when creating PDF version. This typically indicates Rd problems. LaTeX errors found: ! LaTeX Error: Unicode character ≠ (U+2260) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character λ (U+03BB) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character ⁺ (U+207A) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character Σ (U+03A3) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character ⁺ (U+207A) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character Σ (U+03A3) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character ⁺ (U+207A) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character Σ (U+03A3) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character ⁺ (U+207A) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character ⁺ (U+207A) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character ⁺ (U+207A) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character ⁺ (U+207A) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character ⁺ (U+207A) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character ⁺ (U+207A) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character ⁺ (U+207A) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character ⁺ (U+207A) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character ⁺ (U+207A) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. * checking PDF version of manual without index ... ERROR * checking HTML version of manual ... [3s/3s] NOTE Found the following HTML validation problems: bdQR_hdf5.html:127:9 (bdQR_hdf5.Rd:49): Error: is not recognized! bdQR_hdf5.html:127:9 (bdQR_hdf5.Rd:49): Warning: discarding unexpected bdQR_hdf5.html:131:9 (bdQR_hdf5.Rd:52): Error: is not recognized! bdQR_hdf5.html:131:9 (bdQR_hdf5.Rd:52): Warning: discarding unexpected bdSplit_matrix_hdf5.html:156:10 (bdSplit_matrix_hdf5.Rd:50): Error: is not recognized! bdSplit_matrix_hdf5.html:156:10 (bdSplit_matrix_hdf5.Rd:50): Warning: discarding unexpected bdSplit_matrix_hdf5.html:156:38 (bdSplit_matrix_hdf5.Rd:50): Error: is not recognized! bdSplit_matrix_hdf5.html:156:38 (bdSplit_matrix_hdf5.Rd:50): Warning: discarding unexpected bdWrite_hdf5_dimnames.html:80:18 (bdWrite_hdf5_dimnames.Rd:28): Error: is not recognized! bdWrite_hdf5_dimnames.html:80:18 (bdWrite_hdf5_dimnames.Rd:28): Warning: discarding unexpected bdWrite_hdf5_dimnames.html:83:25 (bdWrite_hdf5_dimnames.Rd:30): Error: is not recognized! bdWrite_hdf5_dimnames.html:83:25 (bdWrite_hdf5_dimnames.Rd:30): Warning: discarding unexpected BigDataStatMeth.html:4257:9 (bdQR_hdf5.Rd:49): Error: is not recognized! BigDataStatMeth.html:4257:9 (bdQR_hdf5.Rd:49): Warning: discarding unexpected BigDataStatMeth.html:4261:9 (bdQR_hdf5.Rd:52): Error: is not recognized! BigDataStatMeth.html:4261:9 (bdQR_hdf5.Rd:52): Warning: discarding unexpected BigDataStatMeth.html:6046:10 (bdSplit_matrix_hdf5.Rd:50): Error: is not recognized! BigDataStatMeth.html:6046:10 (bdSplit_matrix_hdf5.Rd:50): Warning: discarding unexpected BigDataStatMeth.html:6046:38 (bdSplit_matrix_hdf5.Rd:50): Error: is not recognized! BigDataStatMeth.html:6046:38 (bdSplit_matrix_hdf5.Rd:50): Warning: discarding unexpected BigDataStatMeth.html:6500:18 (bdWrite_hdf5_dimnames.Rd:28): Error: is not recognized! BigDataStatMeth.html:6500:18 (bdWrite_hdf5_dimnames.Rd:28): Warning: discarding unexpected * checking for non-standard things in the check directory ... NOTE Found the following files/directories: ‘BigDataStatMeth-manual.tex’ * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 1 WARNING, 5 NOTEs