############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:sparseDOSSA.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings sparseDOSSA_1.28.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/sparseDOSSA.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘sparseDOSSA/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘sparseDOSSA’ version ‘1.28.0’ * 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 ‘sparseDOSSA’ 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 whether startup messages can be suppressed ... 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 ... OK * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed sparseDOSSA 6.505 0.019 6.526 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘RunTests.R’ ERROR Running the tests in ‘tests/RunTests.R’ failed. Complete output: > BiocGenerics:::testPackage("sparseDOSSA") Error in library("RUnit", quietly = TRUE) : there is no package called 'RUnit' Calls: -> library In addition: Warning message: In fun(libname, pkgname) : Package 'sparseDOSSA' is deprecated and will be removed from Bioconductor version 3.20 Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: --- re-building ‘sparsedossa-vignette.Rmd’ using rmarkdown sparseDOSSA package:sparseDOSSA R Documentation _S_p_a_r_s_e _D_a_t_a _O_b_s_e_r_v_a_t_i_o_n_s _f_o_r _S_i_m_u_l_a_t_i_n_g _S_y_n_t_h_e_t_i_c _A_b_u_n_d_a_n_c_e _D_e_s_c_r_i_p_t_i_o_n: Sparse Data Observations for Simulating Synthetic Abundance _U_s_a_g_e: sparseDOSSA( strNormalizedFileName = "SyntheticMicrobiome.pcl", strCountFileName = "SyntheticMicrobiome-Counts.pcl", parameter_filename = "SyntheticMicrobiomeParameterFile.txt", bugs_to_spike = 0, spikeFile = NA, calibrate = NA, datasetCount = 1, read_depth = 8030, number_features = 300, bugBugCorr = "0.5", spikeCount = "1", lefse_file = NULL, percent_spiked = 0.03, minLevelPercent = 0.1, number_samples = 50, max_percent_outliers = 0.05, number_metadata = 5, spikeStrength = "1.0", seed = NA, percent_outlier_spikins = 0.05, minOccurence = 0, verbose = TRUE, minSample = 0, scalePercentZeros = 1, association_type = "linear", noZeroInflate = FALSE, noRunMetadata = FALSE, runBugBug = FALSE ) _A_r_g_u_m_e_n_t_s: strNormalizedFileName: This output file records the synthetic microbiome data for null community (no spike-in and outliers), outlier-added community without spike-in and final spiked data. We put samples in columns and features in rows. The first chunk of the file is metadata, with row names Metadata_. The second chunk is for null community, with row names Feature_Lognormal_. The third chunk is for outlier-introduced community, with row names Feature_Outlier_*. The last chunk is for spiked data, with row names Feature_spike. This file records relative abundance data. strCountFileName: This output file has the same organization as the file strNormalizedFileName but records raw counts data. parameter_filename: This output file records diagnostic information and values of model parameters as well as the spike-in assignment. The most part of this file is used only for debugging. Users can focus on lines after Minimum Spiked-in Samples. Those lines record which metadata are correlated with which feature. The format is all metadata that are correlated with a specific features are listed under the name of the feature. bugs_to_spike: Number of bugs to correlate with others. A non-negative integer value is expected. spikeFile: The name of the file where the correlation values are stored. Should have fields `Domain`, `Range`, and `Correlation`. calibrate: Calibration file for generating the random log normal data. TSV file (column = feature). datasetCount: The number of bug-bug spiked datasets to generate. A positive integer value is expected. read_depth: Simulated read depth for counts. A positive integer value is expected. number_features: The number of features per sample to create. A positive integer value is expected. bugBugCorr: A vector of string separated values for the correlation values of the pairwise bug-bug associations. This is the correlation of the log-counts. Values are comma-separated; for example: 0.7,0.5. Default is 0.5. spikeCount: Counts of spiked metadata used in the spike-in dataset - These values should be comma delimited values, in the order of the spikeStrength values (if given), Can be one value, in this case the value will be repeated to pair with the spikeCount values (if multiple are present). For example 1,2,3. lefse_file: Folder containing lefSe inputs. percent_spiked: The percent of features spiked-in. A real number between 0 and 1 is expected. minLevelPercent: Minimum percent of measurements out of the total a level can have in a discontinuous metadata (rounded up to the nearest count). A real number between 0 and 1 is expected. number_samples: The number of samples to generate. A positive integer greater than 0 is expected. max_percent_outliers: The maximum percent of outliers to spike into a sample. A real number between 0 and 1 is expected. number_metadata: Indicates how many metadata are created, number_metadata*2 = number continuous metadata, number_metadata = number binary metadata, number_metadata = number quaternary metadata, A positive integer greater than 0 is expected. spikeStrength: Strength of the metadata association with the spiked-in feature, These values should be comma delimited and in the order of the spikeCount values (if given),Can be one value, in this case the value will be repeated to pair with the spikeStrength values (if multiple are present). For example 0.2,0.3,0.4. seed: A seed to freeze the random generation of counts/relative abundance,If left as default (NA), generation is random - If seeded, data generation will be random within a run but identical if ran again under the same settings,an integer is expected. percent_outlier_spikins: The percent of samples to spike in outliers. A real number between 0 to 1 is expected. minOccurence: Minimum counts a bug can have for the occurrence quality control filter used when creating bugs (filtering minimum number of counts in a minimum number of samples). A positive integer is expected. verbose: If True logging and plotting is made by the underlying methodology. This is a flag, it is either included or not included in the command line, no value needed. minSample: Minimum samples a bug can be in for the occurrence quality control filter used when creating bugs (filtering minimum number of counts in a minimum number of samples). A positive integer is expected. scalePercentZeros: A scale used to multiply the percent zeros of all features across the sample after it is derived from the relationships with it and the feature abundance or calibration file. Requires a number greater than 0. A number greater than 1 increases sparsity, a number less than 1 decreases sparsity, O removes sparsity, 1 (default) does not change the value and the value. association_type: The type of association to generate. Options are 'linear' or 'rounded_linear'. noZeroInflate: If given, zero inflation is not used when generating a feature. This is a flag, it is either included or not included in the command line, no value needed. noRunMetadata: If given, no metadata files are generated, This is a flag, it is either included or not included in the command line, no value needed. runBugBug: If given, bug-bug interaction files are generated in addition to any metadata files. This is a flag, it is either included or not included in the command line, no value needed. _V_a_l_u_e: A list contains the names of the output files. _A_u_t_h_o_r(_s): Boyu Ren, Emma Schwager, Timothy Tickle, Curtis Huttenhower _E_x_a_m_p_l_e_s: sparseDOSSA(strNormalizedFileName = "SyntheticMicrobiome.pcl", strCountFileName = "SyntheticMicrobiome-Counts.pcl", parameter_filename = "SyntheticMicrobiomeParameterFile.txt", bugs_to_spike = 0, calibrate = NA, datasetCount = 1, read_depth = 8030, number_features = 300, spikeCount = "1", lefse_file = NA, percent_spiked = 0.03, minLevelPercent = 0.1, number_samples = 50, max_percent_outliers = 0.05, number_metadata = 5, spikeStrength = "1.0", seed = 1, percent_outlier_spikins = 0.05, minOccurence = 0, verbose = TRUE, minSample = 0, association_type = "linear", noZeroInflate = FALSE, noRunMetadata = FALSE, runBugBug = FALSE) Quitting from lines 134-136 [bugbug] (sparsedossa-vignette.Rmd) Error: processing vignette 'sparsedossa-vignette.Rmd' failed with diagnostics: funcSample:: Can not sample from length of 0 vector. --- failed re-building ‘sparsedossa-vignette.Rmd’ SUMMARY: processing the following file failed: ‘sparsedossa-vignette.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 2 ERRORs, 1 NOTE See ‘/home/biocbuild/bbs-3.19-bioc/meat/sparseDOSSA.Rcheck/00check.log’ for details.