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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ILoReg.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings ILoReg_1.9.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/ILoReg.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘ILoReg/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ILoReg’ version ‘1.9.0’
* 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 ‘ILoReg’ 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 ... WARNING
Codoc mismatches from documentation object 'FindAllGeneMarkers':
FindAllGeneMarkers.SingleCellExperiment
  Code: function(object, clustering.type, test, log2fc.threshold,
                 min.pct, min.diff.pct, min.cells.group,
                 max.cells.per.cluster, return.thresh, only.pos)
  Docs: function(object, clustering.type, test, log2fc.threshold,
                 min.pct, min.diff.pct, min.cells.group,
                 max.cells.per.cluster, pseudocount.use, return.thresh,
                 only.pos)
  Argument names in docs not in code:
    pseudocount.use
  Mismatches in argument names:
    Position: 9 Code: return.thresh Docs: pseudocount.use
    Position: 10 Code: only.pos Docs: return.thresh
\S4method{FindAllGeneMarkers}{SingleCellExperiment}
  Code: function(object, clustering.type = "manual", test = "wilcox",
                 log2fc.threshold = 0.25, min.pct = 0.1, min.diff.pct =
                 NULL, min.cells.group = 3, max.cells.per.cluster =
                 NULL, return.thresh = 0.01, only.pos = FALSE)
  Docs: function(object, clustering.type = "manual", test = "wilcox",
                 log2fc.threshold = 0.25, min.pct = 0.1, min.diff.pct =
                 NULL, min.cells.group = 3, max.cells.per.cluster =
                 NULL, pseudocount.use = 1, return.thresh = 0.01,
                 only.pos = FALSE)
  Argument names in docs not in code:
    pseudocount.use
  Mismatches in argument names:
    Position: 9 Code: return.thresh Docs: pseudocount.use
    Position: 10 Code: only.pos Docs: return.thresh

Codoc mismatches from documentation object 'FindGeneMarkers':
FindGeneMarkers.SingleCellExperiment
  Code: function(object, clusters.1, clusters.2, clustering.type, test,
                 logfc.threshold, min.pct, min.diff.pct,
                 min.cells.group, max.cells.per.cluster, return.thresh,
                 only.pos)
  Docs: function(object, clusters.1, clusters.2, clustering.type, test,
                 logfc.threshold, min.pct, min.diff.pct,
                 min.cells.group, max.cells.per.cluster,
                 pseudocount.use, return.thresh, only.pos)
  Argument names in docs not in code:
    pseudocount.use
  Mismatches in argument names:
    Position: 11 Code: return.thresh Docs: pseudocount.use
    Position: 12 Code: only.pos Docs: return.thresh
\S4method{FindGeneMarkers}{SingleCellExperiment}
  Code: function(object, clusters.1 = NULL, clusters.2 = NULL,
                 clustering.type = "", test = "wilcox", logfc.threshold
                 = 0.25, min.pct = 0.1, min.diff.pct = NULL,
                 min.cells.group = 3, max.cells.per.cluster = NULL,
                 return.thresh = 0.01, only.pos = FALSE)
  Docs: function(object, clusters.1 = NULL, clusters.2 = NULL,
                 clustering.type = "", test = "wilcox", logfc.threshold
                 = 0.25, min.pct = 0.1, min.diff.pct = NULL,
                 min.cells.group = 3, max.cells.per.cluster = NULL,
                 pseudocount.use = 1, return.thresh = 0.01, only.pos =
                 FALSE)
  Argument names in docs not in code:
    pseudocount.use
  Mismatches in argument names:
    Position: 11 Code: return.thresh Docs: pseudocount.use
    Position: 12 Code: only.pos Docs: return.thresh

Codoc mismatches from documentation object 'RunICP':
RunICP
  Code: function(normalized.data = NULL, k = 15, d = 0.3, r = 5, C = 5,
                 reg.type = "L1", max.iter = 200, icp.batch.size = Inf)
  Docs: function(normalized.data = NULL, k = 15, d = 0.3, r = 5, C = 5,
                 reg.type = "L1", max.iter = 200)
  Argument names in code not in docs:
    icp.batch.size

Codoc mismatches from documentation object 'RunParallelICP':
RunParallelICP.SingleCellExperiment
  Code: function(object, k, d, L, r, C, reg.type, max.iter, threads,
                 icp.batch.size)
  Docs: function(object, k, d, L, r, C, reg.type, max.iter, threads)
  Argument names in code not in docs:
    icp.batch.size
\S4method{RunParallelICP}{SingleCellExperiment}
  Code: function(object, k = 15, d = 0.3, L = 200, r = 5, C = 0.3,
                 reg.type = "L1", max.iter = 200, threads = 0,
                 icp.batch.size = Inf)
  Docs: function(object, k = 15, d = 0.3, L = 200, r = 5, C = 0.3,
                 reg.type = "L1", max.iter = 200, threads = 0)
  Argument names in code not in docs:
    icp.batch.size

* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘ILoReg-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MergeClusters
> ### Title: Merge clusters
> ### Aliases: MergeClusters MergeClusters.SingleCellExperiment
> ###   MergeClusters,SingleCellExperiment-method
> ### Keywords: clusters merge
> 
> ### ** Examples
> 
> library(SingleCellExperiment)
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

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

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

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, aperm, 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

Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:base’:

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
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

> sce <- SingleCellExperiment(assays = list(logcounts = pbmc3k_500))
> sce <- PrepareILoReg(sce)
Data in `logcounts` slot already of `dgCMatrix` class...
13865/13865 genes remain after filtering genes with only zero values.
> ## These settings are just to accelerate the example, use the defaults.
> sce <- RunParallelICP(sce,L=2,threads=1,C=0.1,k=5,r=1)
Parallelism disabled, because threads = 1
ICP run: 1
probability matrix dimensions = 500 5
EPOCH: 1
current clustering = 105 95 90 102 108
projected clustering = 86 134 104 102 74
ARI=0.0404351245368042
probability matrix dimensions = 500 5
EPOCH: 2
current clustering = 86 134 104 102 74
projected clustering = 117 143 22 130 88
ARI=0.268800805638721
probability matrix dimensions = 500 5
EPOCH: 3
current clustering = 117 143 22 130 88
projected clustering = 133 99 52 125 91
ARI=0.606803019367055
probability matrix dimensions = 500 5
EPOCH: 4
current clustering = 133 99 52 125 91
projected clustering = 107 99 77 125 92
ARI=0.703858233886247
probability matrix dimensions = 500 5
EPOCH: 5
current clustering = 107 99 77 125 92
projected clustering = 73 105 96 126 100
ARI=0.724800059025053
probability matrix dimensions = 500 5
EPOCH: 6
current clustering = 73 105 96 126 100
projected clustering = 72 112 91 125 100
ARI=0.837187412690967
probability matrix dimensions = 500 5
EPOCH: 7
current clustering = 72 112 91 125 100
projected clustering = 73 84 119 125 99
ICP run: 2
probability matrix dimensions = 500 5
EPOCH: 1
current clustering = 103 106 111 95 85
projected clustering = 80 96 147 65 112
ARI=0.0443816245637571
probability matrix dimensions = 500 5
EPOCH: 2
current clustering = 80 96 147 65 112
projected clustering = 75 99 141 72 113
ARI=0.282817209367664
probability matrix dimensions = 500 5
EPOCH: 3
current clustering = 75 99 141 72 113
projected clustering = 95 54 142 77 132
ARI=0.361774472317257
probability matrix dimensions = 500 5
EPOCH: 4
current clustering = 95 54 142 77 132
projected clustering = 109 52 141 85 113
ARI=0.577691012423983
probability matrix dimensions = 500 5
EPOCH: 5
current clustering = 109 52 141 85 113
projected clustering = 113 69 166 86 66
ARI=0.666679369785714
probability matrix dimensions = 500 5
EPOCH: 6
current clustering = 113 69 166 86 66
projected clustering = 112 77 149 80 82
ARI=0.819134272608316
probability matrix dimensions = 500 5
EPOCH: 7
current clustering = 112 77 149 80 82
projected clustering = 107 90 158 74 71
ARI=0.880327482285581
probability matrix dimensions = 500 5
EPOCH: 8
current clustering = 107 90 158 74 71
projected clustering = 108 95 153 74 70
ARI=0.885574572197308
probability matrix dimensions = 500 5
EPOCH: 9
current clustering = 108 95 153 74 70
projected clustering = 110 110 153 72 55
ARI=0.88870438897285
probability matrix dimensions = 500 5
EPOCH: 10
current clustering = 110 110 153 72 55
projected clustering = 109 121 145 71 54
ARI=0.902084833011907
Killed
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘ILoReg.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘ILoReg.Rmd’ using rmarkdown
Quitting from lines 86-94 (ILoReg.Rmd) 
Error: processing vignette 'ILoReg.Rmd' failed with diagnostics:
error reading from connection
--- failed re-building ‘ILoReg.Rmd’

SUMMARY: processing the following file failed:
  ‘ILoReg.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 WARNING
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/ILoReg.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL ILoReg
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘ILoReg’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ILoReg)