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###
### 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
###
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* 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: <Anonymous> -> 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<bor158@mail.harvard.edu>, Emma
     Schwager<eschwager@hsph.harvard.edu>, Timothy
     Tickle<ttickle@hsph.harvard.edu>, Curtis Huttenhower
     <chuttenh@hsph.harvard.edu>

_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.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL sparseDOSSA
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘sparseDOSSA’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in fun(libname, pkgname) :
  Package 'sparseDOSSA' is deprecated and will be removed from
  Bioconductor version 3.20
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'sparseDOSSA' is deprecated and will be removed from
  Bioconductor version 3.20
** testing if installed package keeps a record of temporary installation path
* DONE (sparseDOSSA)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("sparseDOSSA")
Error in library("RUnit", quietly = TRUE) : 
  there is no package called 'RUnit'
Calls: <Anonymous> -> library
In addition: Warning message:
In fun(libname, pkgname) :
  Package 'sparseDOSSA' is deprecated and will be removed from
  Bioconductor version 3.20
Execution halted