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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:BioTIP.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BioTIP_1.23.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BioTIP.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BioTIP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BioTIP’ version ‘1.23.0’
* 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 ... NOTE
Found the following hidden files and directories:
  examples/code/gastrulationE8.25_Pijuan-Sala2019/.RData
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... NOTE
Found the following non-portable file paths:
  BioTIP/examples/code/gastrulationE8.25_Pijuan-Sala2019/2.2_E8.25_mesoderm_runBioTP_different.clustering.R
  BioTIP/examples/code/gastrulationE8.25_Pijuan-Sala2019/3_E8.25_mesoderm_runBioTIP_stability_1360cell.R

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BioTIP’ 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 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 ... WARNING
'library' or 'require' calls not declared from:
  ‘doParallel’ ‘foreach’
'library' or 'require' calls in package code:
  ‘doParallel’ ‘foreach’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘foreach’ ‘grDevices’ ‘graphics’ ‘methods’ ‘stats’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
BioTIP.wrap: warning in getMaxMCImember(membersL[["members"]],
  membersL[["MCI"]], min = getTopMCI.gene.minsize, n =
  n.getMaxMCImember): partial argument match of 'min' to 'minsize'
getCluster: warning in cluster_walktrap(igraphL[[i]], weight =
  abs(E(igraphL[[i]])$weight), steps = steps[i]): partial argument
  match of 'weight' to 'weights'
BioTIP.wrap: no visible global function definition for ‘assayNames’
BioTIP.wrap : myplotIc: no visible global function definition for ‘pdf’
BioTIP.wrap : myplotIc: no visible global function definition for ‘par’
BioTIP.wrap : myplotIc: no visible global function definition for
  ‘text’
BioTIP.wrap : myplotIc: no visible global function definition for
  ‘dev.off’
BioTIP.wrap: no visible global function definition for ‘getTopHVGs’
BioTIP.wrap: no visible global function definition for
  ‘normalized_counts’
BioTIP.wrap: no visible global function definition for ‘logcounts’
BioTIP.wrap: no visible global function definition for ‘pdf’
BioTIP.wrap: no visible global function definition for ‘abline’
BioTIP.wrap: no visible global function definition for ‘dev.off’
BioTIP.wrap: no visible global function definition for ‘par’
BioTIP.wrap: no visible binding for global variable
  ‘getTopMCI.gene.maxsiz’
cor.shrink: no visible binding for global variable ‘sd’
getBiotypes: no visible global function definition for ‘is’
getBiotypes: no visible global function definition for ‘queryHits’
getBiotypes: no visible global function definition for ‘subjectHits’
getBiotypes: no visible global function definition for ‘aggregate’
getCluster_methods : <anonymous>: no visible global function definition
  for ‘hclust’
getCluster_methods : <anonymous>: no visible global function definition
  for ‘dist’
getCluster_methods: no visible global function definition for ‘par’
getCluster_methods : <anonymous>: no visible global function definition
  for ‘cutree’
getIc : <anonymous>: no visible global function definition for ‘cor’
getMCI : <anonymous>: no visible global function definition for ‘cor’
getMCI : <anonymous>: no visible binding for global variable ‘sd’
getMCI_inner : <anonymous>: no visible global function definition for
  ‘cor’
getMCI_inner : <anonymous>: no visible binding for global variable ‘sd’
getNextMaxStats: no visible binding for global variable ‘maxMCIms’
getReadthrough: no visible global function definition for ‘subjectHits’
getReadthrough: no visible binding for global variable ‘readthrough’
getReadthrough : <anonymous>: no visible global function definition for
  ‘queryHits’
getReadthrough : <anonymous>: no visible global function definition for
  ‘subjectHits’
optimize.sd_selection: no visible global function definition for
  ‘detectCores’
optimize.sd_selection : <anonymous> : <anonymous>: no visible global
  function definition for ‘sd’
optimize.sd_selection : <anonymous>: no visible binding for global
  variable ‘sd’
optimize.sd_selection: no visible global function definition for
  ‘makeCluster’
optimize.sd_selection: no visible global function definition for
  ‘registerDoParallel’
optimize.sd_selection: no visible global function definition for
  ‘%dopar%’
optimize.sd_selection: no visible global function definition for
  ‘foreach’
optimize.sd_selection: no visible global function definition for
  ‘stopCluster’
plotBar_MCI: no visible global function definition for ‘par’
plotBar_MCI: no visible global function definition for ‘barplot’
plotBar_MCI: no visible global function definition for ‘rainbow’
plotBar_MCI: no visible global function definition for ‘title’
plotBar_MCI: no visible global function definition for ‘text’
plotIc: no visible global function definition for ‘matplot’
plotIc: no visible global function definition for ‘axis’
plotIcSignificance: no visible global function definition for ‘pdf’
plotIcSignificance: no visible global function definition for ‘par’
plotIcSignificance: no visible global function definition for ‘dev.off’
plotMaxMCI: no visible global function definition for ‘is’
plotMaxMCI: no visible global function definition for ‘matplot’
plotMaxMCI: no visible global function definition for ‘text’
plotMaxMCI: no visible global function definition for ‘axis’
plot_Ic_Simulation: no visible global function definition for ‘matplot’
plot_Ic_Simulation: no visible global function definition for ‘boxplot’
plot_Ic_Simulation: no visible global function definition for ‘points’
plot_Ic_Simulation: no visible global function definition for ‘mtext’
plot_Ic_Simulation: no visible global function definition for ‘axis’
plot_Ic_Simulation: no visible global function definition for ‘abline’
plot_MCI_Simulation: no visible global function definition for
  ‘boxplot’
plot_MCI_Simulation: no visible global function definition for ‘axis’
plot_MCI_Simulation: no visible global function definition for ‘points’
plot_MCI_Simulation: no visible global function definition for ‘abline’
plot_SS_Simulation: no visible global function definition for ‘density’
plot_SS_Simulation: no visible global function definition for ‘abline’
plot_SS_Simulation: no visible global function definition for ‘legend’
sd_selection : <anonymous>: no visible binding for global variable ‘sd’
sd_selection: no visible binding for global variable ‘sd’
sd_selection: no visible binding for global variable ‘i’
simulation_Ic: no visible global function definition for ‘detectCores’
simulation_Ic: no visible global function definition for ‘makeCluster’
simulation_Ic: no visible global function definition for
  ‘registerDoParallel’
simulation_Ic: no visible global function definition for ‘%dopar%’
simulation_Ic: no visible global function definition for ‘foreach’
simulation_Ic: no visible global function definition for ‘stopCluster’
simulation_Ic_sample: no visible global function definition for
  ‘density’
simulation_Ic_sample: no visible global function definition for
  ‘abline’
simulation_Ic_sample: no visible global function definition for ‘text’
Undefined global functions or variables:
  %dopar% abline aggregate assayNames axis barplot boxplot cor cutree
  density detectCores dev.off dist foreach getTopHVGs
  getTopMCI.gene.maxsiz hclust i is legend logcounts makeCluster
  matplot maxMCIms mtext normalized_counts par pdf points queryHits
  rainbow readthrough registerDoParallel sd stopCluster subjectHits
  text title
Consider adding
  importFrom("grDevices", "dev.off", "pdf", "rainbow")
  importFrom("graphics", "abline", "axis", "barplot", "boxplot",
             "legend", "matplot", "mtext", "par", "points", "text",
             "title")
  importFrom("methods", "is")
  importFrom("stats", "aggregate", "cor", "cutree", "density", "dist",
             "hclust", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
checkRd: (-1) cod.Rd:11: Lost braces
    11 | \item{ranges}{ranges}{chromosome ranges on the genome (10906201-11029719)}
       |                      ^
checkRd: (-1) plotIc.Rd:24: Lost braces; missing escapes or markup?
    24 | \item{las}{Numeric in {0, 1, 2, 3}; the style of axis labels.
       |                       ^
checkRd: (-1) plotMaxMCI.Rd:18: Lost braces; missing escapes or markup?
    18 | \item{las}{Numeric in {0, 1, 2, 3}; the style of axis labels. Default is 0, meaning labels are parallel.
       |                       ^
checkRd: (-1) plot_Ic_Simulation.Rd:26: Lost braces; missing escapes or markup?
    26 | \item{las}{Numeric in {0, 1, 2, 3}; the style of axis labels.
       |                       ^
checkRd: (-1) plot_MCI_Simulation.Rd:23: Lost braces; missing escapes or markup?
    23 | \item{las}{Numeric in {0, 1, 2, 3}; the style of axis labels. Default is 0, meaning labels are parallel.
       |                       ^
checkRd: (-1) plot_SS_Simulation.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{las}{Numeric in {0, 1, 2, 3}; the style of axis labels.
       |                       ^
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  getMCI.Rd: igraph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package unavailable to check Rd xrefs: ‘TSdist’
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘getNextMaxStats’ ‘getTopMCI’ ‘membersL’ ‘subcounts’
Undocumented data sets:
  ‘membersL’ ‘subcounts’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from Rd file 'avg.cor.shrink.Rd':
avg.cor.shrink
  Code: function(X, Y = NULL, MARGIN = c(1, 2), shrink = TRUE, abs =
                 FALSE, target = 0)
  Docs: function(X, Y = NULL, MARGIN = c(1, 2), shrink = TRUE, abs =
                 FALSE, target = c("zero", "average", "half"))
  Mismatches in argument default values:
    Name: 'target' Code: 0 Docs: c("zero", "average", "half")

Codoc mismatches from Rd file 'cor.shrink.Rd':
cor.shrink
  Code: function(X, Y = NULL, MARGIN = c(1, 2), shrink = TRUE, target =
                 0)
  Docs: function(X, Y = NULL, MARGIN = c(1, 2), shrink = TRUE, target =
                 c("zero", "average", "half"))
  Mismatches in argument default values:
    Name: 'target' Code: 0 Docs: c("zero", "average", "half")

Codoc mismatches from Rd file 'getIc.Rd':
getIc
  Code: function(counts, sampleL, genes, output = c("Ic", "PCCg",
                 "PCCs"), fun = c("cor", "BioTIP"), shrink = TRUE, use
                 = c("everything", "all.obs", "complete.obs",
                 "na.or.complete", "pairwise.complete.obs"),
                 PCC_sample.target = 1)
  Docs: function(counts, sampleL, genes, output = c("Ic", "PCCg",
                 "PCCs"), fun = c("cor", "BioTIP"), shrink = TRUE, use
                 = c("everything", "all.obs", "complete.obs",
                 "na.or.complete", "pairwise.complete.obs"))
  Argument names in code not in docs:
    PCC_sample.target

Codoc mismatches from Rd file 'getIc.new.Rd':
getIc.new
  Code: function(X, method = c("BioTIP", "Ic"), PCC_sample.target = 1,
                 output = c("Ic", "PCCg", "PCCs"))
  Docs: function(X, method = c("BioTIP", "Ic"), PCC_sample.target =
                 c("average", "zero", "half"), output = c("IndexScore",
                 "PCCg", "PCCs"))
  Mismatches in argument default values:
    Name: 'PCC_sample.target' Code: 1 Docs: c("average", "zero", "half")
    Name: 'output' Code: c("Ic", "PCCg", "PCCs") Docs: c("IndexScore", "PCCg", "PCCs")

Codoc mismatches from Rd file 'getMaxMCImember.Rd':
getMaxMCImember
  Code: function(membersL, MCIl, minsize = 1, n = 1)
  Docs: function(membersL, MCIl, minsize = 1)
  Argument names in code not in docs:
    n

Codoc mismatches from Rd file 'optimize.sd_selection.Rd':
optimize.sd_selection
  Code: function(df, samplesL, B = 100, percent = 0.8, times = 0.8,
                 cutoff = 0.01, method = c("other", "reference",
                 "previous", "itself", "longitudinal reference"),
                 control_df = NULL, control_samplesL = NULL, n_cores =
                 3, doParallel = TRUE)
  Docs: function(df, samplesL, B = 100, percent = 0.8, times = 0.8,
                 cutoff = 0.01, method = c("other", "reference",
                 "previous", "itself", "longitudinal reference"),
                 control_df = NULL, control_samplesL = NULL)
  Argument names in code not in docs:
    n_cores doParallel

Codoc mismatches from Rd file 'plotBar_MCI.Rd':
plotBar_MCI
  Code: function(MCIl, ylim = NULL, nr = 1, nc = NULL, order = NULL,
                 minsize = 3, states = NULL, title.size = 30)
  Docs: function(MCIl, ylim = NULL, nr = 1, nc = NULL, order = NULL,
                 minsize = 3, states = NULL)
  Argument names in code not in docs:
    title.size

Codoc mismatches from Rd file 'plotIc.Rd':
plotIc
  Code: function(Ic, las = 0, order = NULL, ylab = "Ic.shrink", col =
                 "black", main = NULL, add = FALSE, ylim = NULL, lty =
                 1:5, lwd = 1)
  Docs: function(Ic, las = 0, order = NULL, ylab = "Ic", col = "black",
                 main = NULL, add = FALSE, ylim = NULL, lty = 1:5, lwd
                 = 1)
  Mismatches in argument default values:
    Name: 'ylab' Code: "Ic.shrink" Docs: "Ic"

Codoc mismatches from Rd file 'plot_Ic_Simulation.Rd':
plot_Ic_Simulation
  Code: function(Ic, simulation, las = 0, ylim = NULL, order = NULL,
                 main = NULL, ylab = "Ic.shrink", fun = c("matplot",
                 "boxplot"), which2point = NULL)
  Docs: function(Ic, simulation, las = 0, ylim = NULL, order = NULL,
                 main = NULL, ylab = "Ic", fun = c("matplot",
                 "boxplot"), which2point = NULL)
  Mismatches in argument default values:
    Name: 'ylab' Code: "Ic.shrink" Docs: "Ic"

Codoc mismatches from Rd file 'plot_SS_Simulation.Rd':
plot_SS_Simulation
  Code: function(Ic, simulation, las = 0, xlim = NULL, ylim = NULL,
                 order = NULL, main = "1st max - 2nd max", ylab =
                 "Density", na.rm = TRUE)
  Docs: function(Ic, simulation, las = 0, xlim = NULL, ylim = NULL,
                 order = NULL, main = "1st max - 2nd max", ylab = "1st
                 max - 2nd max")
  Argument names in code not in docs:
    na.rm
  Mismatches in argument default values:
    Name: 'ylab' Code: "Density" Docs: "1st max - 2nd max"

Codoc mismatches from Rd file 'simulationMCI.Rd':
simulationMCI
  Code: function(len, samplesL, df, adjust.size = FALSE, B = 1000, fun
                 = c("cor", "BioTIP"), M = NULL)
  Docs: function(len, samplesL, df, adjust.size = FALSE, B = 1000, fun
                 = c("cor", "BioTIP"))
  Argument names in code not in docs:
    M

Codoc mismatches from Rd file 'simulation_Ic.Rd':
simulation_Ic
  Code: function(obs.x, sampleL, counts, B = 1000, fun = c("cor",
                 "BioTIP"), shrink = TRUE, use = c("everything",
                 "all.obs", "complete.obs", "na.or.complete",
                 "pairwise.complete.obs"), output = c("Ic", "PCCg",
                 "PCCs"), PCC_sample.target = 1, n_cores = 3,
                 doParallel = TRUE)
  Docs: function(obs.x, sampleL, counts, B = 1000, fun = c("cor",
                 "BioTIP"), shrink = TRUE, use = c("everything",
                 "all.obs", "complete.obs", "na.or.complete",
                 "pairwise.complete.obs"), output = c("Ic", "PCCg",
                 "PCCs"))
  Argument names in code not in docs:
    PCC_sample.target n_cores doParallel

Codoc mismatches from Rd file 'simulation_Ic_sample.Rd':
simulation_Ic_sample
  Code: function(counts, sampleNo, Ic = NULL, genes, B = 1000, ylim =
                 NULL, main = "simulation of samples", fun = c("cor",
                 "BioTIP"), shrink = TRUE, use = c("everything",
                 "all.obs", "complete.obs", "na.or.complete",
                 "pairwise.complete.obs"), output = c("Ic", "PCCg",
                 "PCCs"), plot = FALSE, PCC_sample.target = 1)
  Docs: function(counts, sampleNo, Ic = NULL, genes, B = 1000, ylim =
                 NULL, main = "simulation of samples", fun = c("cor",
                 "BioTIP"), shrink = TRUE, use = c("everything",
                 "all.obs", "complete.obs", "na.or.complete",
                 "pairwise.complete.obs"), output = c("Ic", "PCCg",
                 "PCCs"), plot = FALSE)
  Argument names in code not in docs:
    PCC_sample.target

* 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 ... 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: 3 WARNINGs, 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/BioTIP.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL BioTIP
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘BioTIP’ ...
** this is package ‘BioTIP’ version ‘1.23.0’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (BioTIP)