############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:zitools.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings zitools_0.99.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/zitools.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘zitools/DESCRIPTION’ ... OK * this is package ‘zitools’ version ‘0.99.3’ * 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 hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘zitools’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * 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 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 ... NOTE calcWeights: no visible global function definition for ‘predict’ omit_str_zero: no visible global function definition for ‘predict’ Undefined global functions or variables: predict Consider adding importFrom("stats", "predict") to your NAMESPACE file. * checking Rd files ... 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 ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plus 10.883 0.040 10.943 assays 7.763 0.088 7.867 log2p 6.735 0.111 6.861 boxplot 6.726 0.115 6.853 colMedians 6.568 0.100 6.682 heatmap 6.358 0.076 6.446 otu_table 6.380 0.040 6.431 times 6.314 0.056 6.383 subset_feature 6.321 0.044 6.375 rowSds 6.286 0.064 6.362 sample_data 6.301 0.008 6.321 weights 6.263 0.004 6.279 quantile 6.204 0.036 6.253 log1p 6.108 0.010 6.131 inputdata 5.857 0.021 5.890 colData 5.824 0.044 5.878 zi2deseq2 5.810 0.012 5.832 colMeans2 5.694 0.043 5.747 mean 5.729 0.000 5.737 cor 5.677 0.028 5.715 cov 5.656 0.028 5.694 deinflatedcounts 5.636 0.024 5.670 zi2phyloseq 5.547 0.035 5.594 slash 5.568 0.012 5.590 rowData 5.534 0.016 5.561 rowWeightedMeans 5.502 0.024 5.537 subset_sample 5.512 0.012 5.533 show 5.523 0.000 5.535 model 5.494 0.012 5.513 weighted.mean 5.495 0.004 5.509 weightedVar 5.493 0.000 5.503 tax_table 5.484 0.008 5.502 inputcounts 5.469 0.016 5.495 median 5.476 0.000 5.484 rowVars 5.474 0.000 5.484 ziMain 5.459 0.008 5.478 rowWeightedSds 5.457 0.008 5.475 t 5.449 0.016 5.475 plot 5.451 0.012 5.474 resample_deinflatedcounts 5.428 0.000 5.439 sd 5.416 0.000 5.428 rowQuantiles 5.403 0.008 5.422 var 5.368 0.016 5.398 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/zitools.Rcheck/00check.log’ for details.