* using log directory 'd:/Rcompile/CRANpkg/local/4.4/SPECK.Rcheck' * using R version 4.4.3 Patched (2026-02-12 r89426 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'SPECK/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'SPECK' version '1.0.1' * 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 hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'SPECK' can be installed ... OK * checking installed package size ... OK * checking package directory ... 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 ... [10s] OK * checking whether the package can be loaded with stated dependencies ... [9s] OK * checking whether the package can be unloaded cleanly ... [8s] OK * checking whether the namespace can be loaded with stated dependencies ... [8s] OK * checking whether the namespace can be unloaded cleanly ... [10s] OK * checking loading without being on the library search path ... [11s] 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 ... [20s] OK * checking Rd files ... [1s] OK * checking Rd metadata ... 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 ... [5s] OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking sizes of PDF files under 'inst/doc' ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... [15s] OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [203s] ERROR Error(s) in re-building vignettes: --- re-building 'SPECKVignette.Rmd' using rmarkdown Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| | | | 0% | |== | 3% | |==== | 6% | |====== | 9% | |======== | 12% | |========== | 15% | |============ | 18% | |============== | 21% | |================ | 24% | |=================== | 26% | |===================== | 29% | |======================= | 32% | |========================= | 35% | |=========================== | 38% | |============================= | 41% | |=============================== | 44% | |================================= | 47% | |=================================== | 50% | |===================================== | 53% | |======================================= | 56% | |========================================= | 59% | |=========================================== | 62% | |============================================= | 65% | |=============================================== | 68% | |================================================= | 71% | |=================================================== | 74% | |====================================================== | 76% | |======================================================== | 79% | |========================================================== | 82% | |============================================================ | 85% | |============================================================== | 88% | |================================================================ | 91% | |================================================================== | 94% | |==================================================================== | 97% | |======================================================================| 100% 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Using method 'umap' 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| ! Package pdftex.def Error: File `2ae56ec62e8f1ec782481ec6b6f34f8458a4b317.pdf' not found: using draft setting. Error: processing vignette 'SPECKVignette.Rmd' failed with diagnostics: LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/SPECK.Rcheck/vign_test/SPECK/vignettes/SPECKVignette.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See SPECKVignette.log for more info. --- failed re-building 'SPECKVignette.Rmd' SUMMARY: processing the following file failed: 'SPECKVignette.Rmd' Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... [17s] OK * checking HTML version of manual ... [2s] OK * DONE Status: 1 ERROR