* using log directory ‘/data/gannet/ripley/R/packages/tests-Suggests/rbiom.Rcheck’ * using R Under development (unstable) (2024-08-23 r87043) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc-14 (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: Fedora Linux 36 (Workstation Edition) * using session charset: UTF-8 * using option ‘--no-stop-on-test-error’ * checking for file ‘rbiom/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘rbiom’ version ‘1.0.3’ * 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 ‘rbiom’ can be installed ... [78s/41s] OK * used C++ compiler: ‘g++-14 (GCC) 14.2.0’ * checking package 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 ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... 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 ... [13s/16s] OK * checking Rd files ... 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 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 examples ... ERROR Running examples in ‘rbiom-Ex.R’ failed The error most likely occurred in: > ### Name: read.biom > ### Title: Extracts counts, metadata, taxonomy, and phylogeny from a biom > ### file. > ### Aliases: read.biom > > ### ** Examples > > library(rbiom) > > infile <- system.file("extdata", "hmp50.bz2", package = "rbiom") > biom <- read.biom(infile) > > summary(biom) Length Class Mode counts 6 simple_triplet_matrix list metadata 6 data.frame list taxonomy 2940 -none- character phylogeny 4 phylo list sequences 490 -none- character info 10 -none- list > > # Taxa Abundances > as.matrix(biom$counts[1:4,1:4]) HMP01 HMP02 HMP03 HMP04 UncO2713 0 0 0 0 UncO4101 1 5 6 18 AnmMass2 0 0 0 0 PreBivi6 0 0 0 0 > > top5 <- names(head(rev(sort(slam::row_sums(biom$counts))), 5)) > biom$taxonomy[top5,c('Family', 'Genus')] Family Genus Unc01yki "__Lactobacillaceae" "__Lactobacillus" Unc53100 "__Streptococcaceae" "__Streptococcus" LtbAci52 "__Lactobacillaceae" "__Lactobacillus" CnbTube3 "__Corynebacteriaceae" "__Corynebacterium_1" Unc02qsf "__Staphylococcaceae" "__Staphylococcus" > as.matrix(biom$counts[top5, 1:6]) HMP01 HMP02 HMP03 HMP04 HMP05 HMP06 Unc01yki 0 0 0 0 0 0 Unc53100 1083 543 301 223 2672 748 LtbAci52 0 0 0 0 0 0 CnbTube3 0 0 0 0 0 0 Unc02qsf 0 0 0 0 0 0 > > # Metadata > table(biom$metadata$Sex, biom$metadata$`Body Site`) Anterior nares Buccal mucosa Mid vagina Saliva Stool Female 5 5 10 5 5 Male 5 5 0 5 5 > sprintf("Mean age: %.1f", mean(biom$metadata$Age)) [1] "Mean age: 27.8" > > # Phylogenetic tree > tree <- biom$phylogeny > top5.tree <- rbiom::subtree(tree, top5) > ape::plot.phylo(top5.tree) Error in loadNamespace(x) : there is no package called ‘ape’ Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > > test_check("rbiom") Loading required package: rbiom [ FAIL 1 | WARN 0 | SKIP 0 | PASS 51 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_subsetting.r:21:3'): Rarefaction ─────────────────────────────── Error in `loadNamespace(x)`: there is no package called 'reshape2' Backtrace: ▆ 1. ├─base::merge(...) at test_subsetting.r:21:3 2. └─base::loadNamespace(x) 3. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL) 4. └─base (local) withOneRestart(expr, restarts[[1L]]) 5. └─base (local) doWithOneRestart(return(expr), restart) [ FAIL 1 | WARN 0 | SKIP 0 | PASS 51 ] Error: Test failures Execution halted * checking PDF version of manual ... [8s/15s] OK * checking HTML version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 2 ERRORs See ‘/data/gannet/ripley/R/packages/tests-Suggests/rbiom.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 2:04.80, 124.04 + 13.49