##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:metaseqR2.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings metaseqR2_1.4.14.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/metaseqR2.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘metaseqR2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘metaseqR2’ version ‘1.4.14’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘metaseqR2’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... 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 R 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 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘metaseqR2-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: metaseqr2
> ### Title: The main metaseqr2 pipeline
> ### Aliases: metaseqr2
> 
> ### ** Examples
> 
> # An example pipeline with gene counts
> data("mm9GeneData",package="metaseqR2")
> 
> result <- metaseqr2(
+     counts=mm9GeneCounts,
+     sampleList=sampleListMm9,
+     contrast=c("adult_8_weeks_vs_e14.5"),
+     libsizeList=libsizeListMm9,
+     annotation="embedded",
+     org="mm9",
+     countType="gene",
+     normalization="edger",
+     statistics="edger",
+     pcut=0.05,
+     figFormat="png",
+     qcPlots="mds",
+     exportWhat=c("annotation","p_value","adj_p_value","fold_change"),
+     exportScale="natural",
+     exportValues="normalized",
+     exportStats="mean",
+     exportWhere=file.path(tempdir(),"test1"),
+     restrictCores=0.1,
+     geneFilters=list(
+         length=list(
+             length=500
+         ),
+         avgReads=list(
+             averagePerBp=100,
+             quantile=0.25
+         ),
+         expression=list(
+             median=TRUE,
+             mean=FALSE,
+             quantile=NA,
+             known=NA,
+             custom=NA
+         ),
+         biotype=getDefaults("biotypeFilter","mm9")
+     ),
+     outList=TRUE
+ )
Warning: The column that contains the gene biotypes ("embedCols$btCol") is missing with embedded annotation! Biotype filters and certain plots will not be available...

2021-10-14 21:02:26: Data processing started...

Read counts file: imported custom data frame
Conditions: e14.5, adult_8_weeks
Samples to include: e14.5_1, e14.5_2, a8w_1, a8w_2
Samples to exclude: none
Requested contrasts: adult_8_weeks_vs_e14.5
Library sizes: 
  e14.5_1: 3102907
  e14.5_2: 2067905
  a8w_1: 3742059
  a8w_2: 4403954
Annotation: embedded
Organism: mm9
Reference source: ensembl
Count type: gene
Transcriptional level: gene
Exon filters: minActiveExons
  minActiveExons: 
    exonsPerGene: 5
    minExons: 2
    frac: 0.2
Gene filters: length, avgReads, expression
  length: 
    length: 500
  avgReads: 
    averagePerBp: 100
    quantile: 0.25
  expression: 
    median: TRUE
    mean: FALSE
    quantile: NA
    known: NA
    custom: NA
Filter application: postnorm
Normalization algorithm: edger
Normalization arguments: 
  method: TMM
  logratioTrim: 0.3
  sumTrim: 0.05
  doWeighting: TRUE
  Acutoff: -1e+10
  p: 0.75
Statistical algorithm(s): edger
Statistical arguments: 
  edger: classic, 5, 10, movingave, NULL, grid, 11, c(-6, 6), NULL, CoxReid, 10000, NULL, auto, NULL, NULL, NULL, NULL, 0.125, NULL, auto, chisq, TRUE, FALSE, c(0.05, 0.1)
Meta-analysis method: none
Multiple testing correction: BH
p-value threshold: 0.05
Logarithmic transformation offset: 1
Quality control plots: mds
Figure format: png
Output directory: /tmp/RtmpIW4dvj/test1
Output data: annotation, p_value, adj_p_value, fold_change
Output scale(s): natural
Output values: normalized
Loading gene annotation...
Saving gene model to /tmp/RtmpIW4dvj/test1/data/gene_model.RData
Removing genes with zero counts in all samples...
Normalizing with: edger
Applying gene filter length...
  Threshold below which ignored: 500
Applying gene filter avgReads...
  Threshold below which ignored: 0.0659629215631332
Applying gene filter expression...
  Threshold below which ignored: 68
2106 genes filtered out
1681 genes remain after filtering
Running statistical tests with: edger
  Contrast: adult_8_weeks_vs_e14.5
  Contrast adult_8_weeks_vs_e14.5: found 906 genesError in .check_ncores(cores) : 3 simultaneous processes spawned
Calls: metaseqr2 -> cmclapply -> mclapply -> .check_ncores
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/metaseqR2.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL metaseqR2
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘metaseqR2’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c pval.c -o pval.o
pval.c:26:11: warning: unused variable 'esttotalperlength' [-Wunused-variable]
   double esttotalperlength = total/2;
          ^
1 warning generated.
clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o metaseqR2.so pval.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-metaseqR2/00new/metaseqR2/libs
** R
** data
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (metaseqR2)

R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

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("metaseqR2")

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min


Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname


Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians


Attaching package: 'limma'

The following object is masked from 'package:DESeq2':

    plotMA

The following object is masked from 'package:BiocGenerics':

    plotMA

locfit 1.5-9.4 	 2020-03-24

Attaching package: 'metaseqR2'

The following object is masked from 'package:limma':

    readTargets


Downsampling counts...
Estimating initial dispersion population...
Estimating dispersions using log-likelihood...

Running simulations... This procedure requires time... Please wait...Using Ensembl host https://nov2020.archive.ensembl.org

2021-10-14 21:03:02: Data processing started...

Read counts file: imported custom data frame
Conditions: G1, G2
Samples to include: G1_rep1, G1_rep2, G1_rep3, G2_rep1, G2_rep2, G2_rep3
Samples to exclude: none
Requested contrasts: G1_vs_G2
Annotation: embedded
Organism: mm10
Reference source: ensembl
Count type: gene
Analysis preset: all_basic
Transcriptional level: gene
Exon filters: none applied
Gene filters: none applied
Filter application: postnorm
Normalization algorithm: edaseq
Normalization arguments: 
  within.which: loess
  between.which: full
Statistical algorithm(s): edger, limma
Statistical arguments: 
  edger: classic, 5, 10, movingave, NULL, grid, 11, c(-6, 6), NULL, CoxReid, 10000, NULL, auto, NULL, NULL, NULL, NULL, 0.125, NULL, auto, chisq, TRUE, FALSE, c(0.05, 0.1)
  limma: none
Meta-analysis method: simes
Multiple testing correction: BH
Logarithmic transformation offset: 1
Analysis preset: all_basic
Quality control plots: 
Figure format: png
Output directory: /tmp/RtmpDQ8xDV
Output data: annotation, p_value, adj_p_value, meta_p_value, adj_meta_p_value, fold_change
Output scale(s): natural, log2
Output values: normalized
Loading gene annotation...
Saving gene model to /tmp/RtmpDQ8xDV/data/gene_model.RData
Removing genes with zero counts in all samples...
Normalizing with: edaseq
Running statistical tests with: edger
  Contrast: G1_vs_G2
Running statistical tests with: limma
  Contrast: G1_vs_G2
Performing meta-analysis with simes
Building output files...
  Contrast: G1_vs_G2
    Adding non-filtered data...
      binding annotation...
      binding p-values...
      binding FDRs...
      binding meta p-values...
      binding adjusted meta p-values...
      binding natural normalized fold changes...
      binding log2 normalized fold changes...
    Writing output...

2021-10-14 21:03:03: Data processing finished!


Total processing time: 00 seconds


Estimating AUFC weights... Please wait...
Processing edger
Processing limma

Retrieving edger
Retrieving limma

2021-10-14 21:03:04: Data processing started...

Read counts file: imported custom data frame
Conditions: e14.5, adult_8_weeks
Samples to include: e14.5_1, e14.5_2, a8w_1, a8w_2
Samples to exclude: none
Requested contrasts: adult_8_weeks_vs_e14.5
Library sizes: 
  e14.5_1: 3102907
  e14.5_2: 2067905
  a8w_1: 3742059
  a8w_2: 4403954
Annotation: embedded
Organism: mm9
Reference source: ensembl
Count type: gene
Analysis preset: medium_basic
Transcriptional level: gene
Exon filters: minActiveExons
  minActiveExons: 
    exonsPerGene: 5
    minExons: 2
    frac: 0.2
Gene filters: length, avgReads, expression, biotype
  length: 
    length: 500
  avgReads: 
    averagePerBp: 100
    quantile: 0.25
  expression: 
    median: TRUE
    mean: FALSE
    quantile: NA
    known: NA
    custom: NA
  biotype: 
    pseudogene: FALSE
    snRNA: FALSE
    protein_coding: FALSE
    antisense: FALSE
    miRNA: FALSE
    lincRNA: FALSE
    snoRNA: FALSE
    processed_transcript: FALSE
    misc_RNA: FALSE
    rRNA: TRUE
    sense_overlapping: FALSE
    sense_intronic: FALSE
    polymorphic_pseudogene: FALSE
    non_coding: FALSE
    three_prime_overlapping_ncrna: FALSE
    IG_C_gene: FALSE
    IG_J_gene: FALSE
    IG_D_gene: FALSE
    IG_V_gene: FALSE
    ncrna_host: FALSE
Filter application: postnorm
Normalization algorithm: edger
Normalization arguments: 
  method: TMM
  logratioTrim: 0.3
  sumTrim: 0.05
  doWeighting: TRUE
  Acutoff: -1e+10
  p: 0.75
Statistical algorithm(s): edger, limma
Statistical arguments: 
  edger: classic, 5, 10, movingave, NULL, grid, 11, c(-6, 6), NULL, CoxReid, 10000, NULL, auto, NULL, NULL, NULL, NULL, 0.125, NULL, auto, chisq, TRUE, FALSE, c(0.05, 0.1)
  limma: none
Meta-analysis method: simes
Multiple testing correction: BH
p-value threshold: 0.05
Logarithmic transformation offset: 1
Analysis preset: medium_basic
Quality control plots: mds
Figure format: png
Output directory: /tmp/RtmpDQ8xDV
Output data: annotation, p_value, adj_p_value, meta_p_value, adj_meta_p_value, fold_change
Output scale(s): natural, log2
Output values: normalized
Loading gene annotation...
Saving gene model to /tmp/RtmpDQ8xDV/data/gene_model.RData
Removing genes with zero counts in all samples...
Normalizing with: edger
Applying gene filter length...
  Threshold below which ignored: 500
Applying gene filter avgReads...
  Threshold below which ignored: 0.0659629215631332
Applying gene filter expression...
  Threshold below which ignored: 68
Applying gene filter biotype...
  Biotypes ignored: rRNA
2106 genes filtered out
1681 genes remain after filtering
Running statistical tests with: edger
  Contrast: adult_8_weeks_vs_e14.5
  Contrast adult_8_weeks_vs_e14.5: found 906 genes
Running statistical tests with: limma
  Contrast: adult_8_weeks_vs_e14.5
  Contrast adult_8_weeks_vs_e14.5: found 911 genes
Performing meta-analysis with simes
Building output files...
  Contrast: adult_8_weeks_vs_e14.5
    Adding non-filtered data...
      binding annotation...
      binding p-values...
      binding FDRs...
      binding meta p-values...
      binding adjusted meta p-values...
      binding natural normalized fold changes...
      binding log2 normalized fold changes...
    Writing output...
    Adding filtered data...
      binding annotation...
      binding p-values...
      binding FDRs...
      binding meta p-values...
      binding adjusted meta p-values...
      binding natural normalized fold changes...
      binding log2 normalized fold changes...
    Writing output...
    Adding report data...
      binding annotation...
      binding meta p-values...
      binding adjusted meta p-values...
      binding log2 normalized fold changes...
      binding normalized mean counts...
      binding normalized mean counts...
Creating quality control graphs...
Plotting in png format...
  Plotting mds...
  Importing mds...
Writing plot database in /tmp/RtmpDQ8xDV/data/reportdb.js
Creating HTML report...
Compressing figures...  adding: tmp/RtmpDQ8xDV/plots/qc/mds.png (deflated 51%)

Downloading required JavaScript libraries...trying URL 'https://raw.github.com/HubSpot/pace/v1.0.0/pace.min.js'
Content type 'text/plain; charset=utf-8' length 12363 bytes (12 KB)
==================================================
downloaded 12 KB

trying URL 'https://code.highcharts.com/highcharts.js'
downloaded 293 KB

trying URL 'https://code.highcharts.com/highcharts-more.js'
downloaded 95 KB

trying URL 'https://code.highcharts.com/modules/exporting.js'
downloaded 18 KB

trying URL 'https://code.highcharts.com/modules/offline-exporting.js'
downloaded 8380 bytes

trying URL 'https://code.highcharts.com/modules/export-data.js'
downloaded 10 KB

trying URL 'http://jvenn.toulouse.inra.fr/app/js/canvas2svg.js'
Content type 'text/javascript' length 35122 bytes (34 KB)
==================================================
downloaded 34 KB

trying URL 'http://jvenn.toulouse.inra.fr/app/js/jvenn.min.js'
Content type 'text/javascript' length 100524 bytes (98 KB)
==================================================
downloaded 98 KB

trying URL 'https://unpkg.com/dexie@2.0.4/dist/dexie.min.js'
downloaded 55 KB



processing file: metaseqr2_report.Rmd
   inline R code fragments

label: knitr_init (with options) 
List of 2
 $ echo : logi FALSE
 $ cache: logi FALSE

  ordinary text without R code

label: load_js
  ordinary text without R code

label: pace_opts (with options) 
List of 1
 $ engine: chr "js"

  ordinary text without R code

label: decide_dexie
  ordinary text without R code

label: define_getplot_funs (with options) 
List of 1
 $ engine: chr "js"

  ordinary text without R code

label: report_init

Attaching package: 'gplots'

The following object is masked from 'package:IRanges':

    space

The following object is masked from 'package:S4Vectors':

    space

The following object is masked from 'package:stats':

    lowess

Loading required package: plotly
Loading required package: ggplot2

Attaching package: 'plotly'

The following object is masked from 'package:ggplot2':

    last_plot

The following object is masked from 'package:IRanges':

    slice

The following object is masked from 'package:S4Vectors':

    rename

The following object is masked from 'package:stats':

    filter

The following object is masked from 'package:graphics':

    layout

Loading required package: viridis
Loading required package: viridisLite

======================
Welcome to heatmaply version 1.3.0

Type citation('heatmaply') for how to cite the package.
Type ?heatmaply for the main documentation.

The github page is: https://github.com/talgalili/heatmaply/
Please submit your suggestions and bug-reports at: https://github.com/talgalili/heatmaply/issues
You may ask questions at stackoverflow, use the r and heatmaply tags: 
	 https://stackoverflow.com/questions/tagged/heatmaply
======================


Attaching package: 'heatmaply'

The following object is masked from 'package:BiocGenerics':

    normalize


Attaching package: 'pander'

The following object is masked from 'package:htmltools':

    p

  ordinary text without R code

label: summary_analysis_summary
  ordinary text without R code

label: summary_input_options_1
  ordinary text without R code

label: summary_input_options_2
  ordinary text without R code

label: summary_input_options_3
  ordinary text without R code

label: summary_input_options_4
  ordinary text without R code

label: summary_input_options_5
  ordinary text without R code

label: summary_input_options_6
  ordinary text without R code

label: summary_input_options_7
  ordinary text without R code

label: summary_input_options_8
  ordinary text without R code

label: summary_input_options_9
  ordinary text without R code

label: summary_input_options_10
  ordinary text without R code

label: summary_input_options_11
  ordinary text without R code

label: summary_input_options_12
  ordinary text without R code

label: summary_input_options_13
  ordinary text without R code

label: summary_input_options_14
  ordinary text without R code

label: summary_input_options_15
  ordinary text without R code

label: summary_input_options_16
  ordinary text without R code

label: summary_input_options_17
  ordinary text without R code

label: summary_input_options_18
  ordinary text without R code

label: summary_input_options_19
  ordinary text without R code

label: summary_input_options_20
  ordinary text without R code

label: summary_input_options_21
  ordinary text without R code

label: summary_input_options_22
  ordinary text without R code

label: summary_input_options_23
  ordinary text without R code

label: summary_input_options_24
  ordinary text without R code

label: summary_input_options_25
  ordinary text without R code

label: summary_input_options_26
  ordinary text without R code

label: summary_input_options_27
  ordinary text without R code

label: summary_input_options_28
  ordinary text without R code

label: summary_input_options_29
  ordinary text without R code

label: summary_input_options_30
  ordinary text without R code

label: summary_input_options_31
  ordinary text without R code

label: summary_filtered_what_1
  ordinary text without R code

label: summary_filtered_what_2
label: summary_filtered_howmany_1
  ordinary text without R code

label: summary_filtered_howmany_2
  ordinary text without R code

label: summary_filtered_howmany_3
  ordinary text without R code

label: summary_filtered_howmany_4
  ordinary text without R code

label: summary_filtered_howmany_5
  ordinary text without R code

label: summary_de_what_1
  ordinary text without R code

label: summary_de_what_2
  ordinary text without R code

label: fun_call
  ordinary text without R code

label: display_targets
  ordinary text without R code

label: summary_run_log
   inline R code fragments

label: tracks_1
  ordinary text without R code

label: tracks_2
  ordinary text without R code

label: decide_qc
  ordinary text without R code

label: analysis_figures_mds
  ordinary text without R code

label: analysis_figures_biodetection
  ordinary text without R code

label: analysis_figures_countsbio
  ordinary text without R code

label: analysis_figures_saturation
  ordinary text without R code

label: analysis_figures_readsnoise
  ordinary text without R code

label: analysis_figures_correl
  ordinary text without R code

label: analysis_figures_pairwise
  ordinary text without R code

label: analysis_figures_filtered
  ordinary text without R code

label: decide_norm
  ordinary text without R code

label: analysis_figures_boxplot
  ordinary text without R code

label: analysis_figures_gcbias
  ordinary text without R code

label: analysis_figures_lengthbias
  ordinary text without R code

label: analysis_figures_meandiff
  ordinary text without R code

label: analysis_figures_meanvar
  ordinary text without R code

label: analysis_figures_rnacomp
  ordinary text without R code

label: decide_stat
  ordinary text without R code

label: analysis_figures_volcano
  ordinary text without R code

label: analysis_figures_mastat
  ordinary text without R code

label: analysis_figures_deheatmap
  ordinary text without R code

label: deheatmap_render (with options) 
List of 1
 $ engine: chr "js"

  ordinary text without R code

label: analysis_figures_biodist
  ordinary text without R code

label: analysis_figures_deregulogram
  ordinary text without R code

label: analysis_figures_statvenn
label: analysis_figures_foldvenn
  ordinary text without R code

label: results_tables_header
  ordinary text without R code

label: dt_hack (with options) 
List of 1
 $ include: logi FALSE

  ordinary text without R code

label: results_tables
  ordinary text without R code

label: detable_render (with options) 
List of 1
 $ engine: chr "js"

  ordinary text without R code

label: export_links
  ordinary text without R code

label: references
  ordinary text without R code

label: bind_event_changes (with options) 
List of 1
 $ engine: chr "js"

output file: metaseqr2_report.knit.md

/usr/local/bin/pandoc +RTS -K512m -RTS metaseqr2_report.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /private/tmp/RtmpDQ8xDV/index.html --lua-filter /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rmarkdown/rmarkdown/lua/latex-div.lua +RTS -K2048m -RTS --variable 'material:true' --variable 'lightbox:true' --variable 'thumbnails:true' --variable 'gallery:true' --variable 'cards:true' --variable bs3=TRUE --standalone --section-divs --table-of-contents --toc-depth 1 --template /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rmdformats/templates/material/material.html --highlight-style kate --variable theme=bootstrap --include-in-header /tmp/RtmpDQ8xDV/rmarkdown-str13c3d78d4d3e9.html 

Output created: /private/tmp/RtmpDQ8xDV/index.html


2021-10-14 21:03:16: Data processing finished!


Total processing time: 11 seconds



RUNIT TEST PROTOCOL -- Thu Oct 14 21:03:16 2021 
*********************************************** 
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
metaseqR2 RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 
There were 50 or more warnings (use warnings() to see the first 50)
> 
> proc.time()
   user  system elapsed 
 37.473   1.854  46.905