• using R Under development (unstable) (2025-07-10 r88399)
• 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 13 (trixie)
• using session charset: UTF-8
• checking for file ‘FLORAL/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘FLORAL’ version ‘0.4.0’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [1s/1s] OK
• 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 ‘FLORAL’ 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
• 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 ... [7s/9s] OK
• checking whether the package can be loaded with stated dependencies ... [7s/8s] OK
• checking whether the package can be unloaded cleanly ... [7s/8s] OK
• checking whether the namespace can be loaded with stated dependencies ... [7s/8s] OK
• checking whether the namespace can be unloaded cleanly ... [7s/9s] OK
• checking loading without being on the library search path ... [7s/8s] 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 ... [40s/51s] 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 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 ... [13s/16s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [14s/17s] OK   Running ‘spelling.R’ [0s/0s]   Running ‘testthat.R’ [13s/16s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [368s/382s] ERROR Error(s) in re-building vignettes:   ... --- re-building ‘Using-FLORAL-for-Microbiome-Analysis.Rmd’ using rmarkdown 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| --- finished re-building ‘Using-FLORAL-for-Microbiome-Analysis.Rmd’ --- re-building ‘Using-FLORAL-for-survival-models-with-longitudinal-microbiome-data.Rmd’ using rmarkdown --- finished re-building ‘Using-FLORAL-for-survival-models-with-longitudinal-microbiome-data.Rmd’ --- re-building ‘Using-FLORAL-with-phyloseq.Rmd’ using rmarkdown Quitting from Using-FLORAL-with-phyloseq.Rmd:25-41 [unnamed-chunk-1] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `file()`: ! cannot open the connection to 'https://figshare.com/ndownloader/files/33076496' --- Backtrace:     ▆  1. ├─... %>% distinct()  2. ├─dplyr::distinct(.)  3. ├─dplyr::select(., -Pool, -Run, -ShotgunBatchID)  4. ├─dplyr::distinct(.)  5. └─utils::read.csv("https://figshare.com/ndownloader/files/33076496")  6. └─utils::read.table(...)  7. └─base::file(file, "rt") ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'Using-FLORAL-with-phyloseq.Rmd' failed with diagnostics: cannot open the connection to 'https://figshare.com/ndownloader/files/33076496' --- failed re-building ‘Using-FLORAL-with-phyloseq.Rmd’ SUMMARY: processing the following file failed:   ‘Using-FLORAL-with-phyloseq.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [4s/5s] OK
• checking HTML version of manual ... [0s/0s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR