Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-10-23 14:06:20 -0400 (Sat, 23 Oct 2021).

CHECK results for BioTIP on riesling1

To the developers/maintainers of the BioTIP package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BioTIP.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 194/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioTIP 1.7.0  (landing page)
Yuxi (Jennifer) Sun , Zhezhen Wang , and X Holly Yang
Snapshot Date: 2021-10-22 14:50:11 -0400 (Fri, 22 Oct 2021)
git_url: https://git.bioconductor.org/packages/BioTIP
git_branch: master
git_last_commit: ebad957
git_last_commit_date: 2021-05-19 12:46:34 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: BioTIP
Version: 1.7.0
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BioTIP.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings BioTIP_1.7.0.tar.gz
StartedAt: 2021-10-23 05:10:57 -0400 (Sat, 23 Oct 2021)
EndedAt: 2021-10-23 05:14:22 -0400 (Sat, 23 Oct 2021)
EllapsedTime: 205.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: BioTIP.Rcheck
Warnings: 5

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BioTIP.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings BioTIP_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/BioTIP.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BioTIP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BioTIP' version '1.7.0'
* 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 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
Namespace in Imports field not imported from: 'Hmisc'
  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
getCluster: warning in cluster_walktrap(igraphL[[i]], weight =
  abs(E(igraphL[[i]])$weight), steps = steps[i]): partial argument
  match of 'weight' to 'weights'
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 : <anonymous>: no visible binding for global
  variable 'sd'
optimize.sd_selection : <anonymous> : <anonymous>: no visible global
  function definition for 'sd'
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'
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_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:
  abline aggregate axis barplot boxplot cor cutree density dist hclust
  i is legend matplot maxMCIms mtext par points queryHits rainbow
  readthrough sd subjectHits text title
Consider adding
  importFrom("grDevices", "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 ... WARNING
prepare_Rd: gencode.Rd:19-21: Dropping empty section \description
checkRd: (5) gencode.Rd:0-23: Must have a \description
prepare_Rd: getIc.new.Rd:67-69: Dropping empty section \references
prepare_Rd: getMCI_inner.Rd:40-42: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
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 documentation object 'avg.cor.shrink':
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 documentation object 'cor.shrink':
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 documentation object 'getIc':
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 documentation object 'getIc.new':
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 documentation object 'getMaxMCImember':
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 documentation object 'plotBar_MCI':
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 documentation object 'plot_SS_Simulation':
plot_SS_Simulation
  Code: function(Ic, simulation, las = 0, xlim = NULL, ylim = NULL,
                 order = NULL, main = "1st max - 2nd max", ylab =
                 "Density")
  Docs: function(Ic, simulation, las = 0, xlim = NULL, ylim = NULL,
                 order = NULL, main = "1st max - 2nd max", ylab = "1st
                 max - 2nd max")
  Mismatches in argument default values:
    Name: 'ylab' Code: "Density" Docs: "1st max - 2nd max"

Codoc mismatches from documentation object 'simulationMCI':
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 documentation object 'simulation_Ic':
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)
  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

Codoc mismatches from documentation object 'simulation_Ic_sample':
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 ... WARNING
Undocumented arguments in documentation object 'plot_Ic_Simulation'
  'which2point'

Documented arguments not in \usage in documentation object 'plot_SS_Simulation':
  'which2point'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... WARNING
  Warning: found non-ASCII strings
  'flow-cytometry: B220+, CD5<e2><80><93>, CD19+, CD25<e2><80><93>, CD69<e2><80><93>, B7-1<e2><80><93>, B7-2<e2><80><93>, IgD+, sIgM+; clinical-signs: none' in object 'GSE6136_cli'
  'flow-cytometry: B220+, CD5<e2><80><93>, CD19+, CD25+, CD69+, B7-1+, B7-2+, IgDlo, sIgMlo; clinical-signs: none' in object 'GSE6136_cli'
  'flow-cytometry: B220+, CD5+, CD9+, CD19+, CD23lo, CD25<e2><80><93>, CD69<e2><80><93>, sIgM+, B7-1+, B7-2+; clinical-signs: end-stage' in object 'GSE6136_cli'
  'flow-cytometry: B220+, CD5<e2><80><93>, CD19+, CD25<e2><80><93>, CD69<e2><80><93>, B7-1<e2><80><93>, B7-2<e2><80><93>, IgD+, sIgM+; clinical-signs: conjunctivitis' in object 'GSE6136_cli'
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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: 5 WARNINGs, 3 NOTEs
See
  'D:/biocbuild/bbs-3.14-bioc/meat/BioTIP.Rcheck/00check.log'
for details.



Installation output

BioTIP.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/BioTIP_1.7.0.tar.gz && rm -rf BioTIP.buildbin-libdir && mkdir BioTIP.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BioTIP.buildbin-libdir BioTIP_1.7.0.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL BioTIP_1.7.0.zip && rm BioTIP_1.7.0.tar.gz BioTIP_1.7.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 16 6112k   16 1017k    0     0  2281k      0  0:00:02 --:--:--  0:00:02 2276k
 86 6112k   86 5277k    0     0  3667k      0  0:00:01  0:00:01 --:--:-- 3667k
100 6112k  100 6112k    0     0  3834k      0  0:00:01  0:00:01 --:--:-- 3834k

install for i386

* installing *source* package 'BioTIP' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BioTIP'
    finding HTML links ... done
    BioTIP-package                          html  
    GSE6136_cli                             html  
    GSE6136_matrix                          html  
    ILEF                                    html  
    avg.cor.shrink                          html  
    cod                                     html  
    cor.shrink                              html  
    gencode                                 html  
    getBiotypes                             html  
    getCTS                                  html  
    getCluster_methods                      html  
    getIc                                   html  
    getIc.new                               html  
    getMCI                                  html  
    finding level-2 HTML links ... done

    getMCI_inner                            html  
    getMaxMCImember                         html  
    getMaxStats                             html  
    getNetwork                              html  
    getReadthrough                          html  
    intron                                  html  
    optimize.sd_selection                   html  
    plotBar_MCI                             html  
    plotIc                                  html  
    plotMaxMCI                              html  
    plot_Ic_Simulation                      html  
    plot_MCI_Simulation                     html  
    plot_SS_Simulation                      html  
    sd_selection                            html  
    simulationMCI                           html  
    simulation_Ic                           html  
    simulation_Ic_sample                    html  
** 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

install for x64

* installing *source* package 'BioTIP' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BioTIP' as BioTIP_1.7.0.zip
* DONE (BioTIP)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'BioTIP' successfully unpacked and MD5 sums checked

Tests output


Example timings

BioTIP.Rcheck/examples_i386/BioTIP-Ex.timings

nameusersystemelapsed
avg.cor.shrink1.570.121.70
cor.shrink0.180.070.24
getBiotypes0.410.030.44
getCTS000
getCluster_methods0.010.010.03
getIc000
getIc.new0.380.100.47
getMCI000
getMaxMCImember0.030.000.03
getMaxStats0.020.000.02
getNetwork000
getReadthrough1.820.001.83
optimize.sd_selection000
plotBar_MCI0.020.000.01
plotIc000
plotMaxMCI000
plot_Ic_Simulation000
plot_MCI_Simulation0.010.000.02
plot_SS_Simulation0.000.000.01
sd_selection000
simulationMCI0.000.000.05
simulation_Ic0.000.000.05
simulation_Ic_sample000

BioTIP.Rcheck/examples_x64/BioTIP-Ex.timings

nameusersystemelapsed
avg.cor.shrink1.810.202.02
cor.shrink0.250.050.29
getBiotypes0.320.120.45
getCTS000
getCluster_methods0.000.020.01
getIc0.000.010.02
getIc.new0.440.080.52
getMCI0.010.000.01
getMaxMCImember0.030.000.03
getMaxStats000
getNetwork000
getReadthrough1.960.031.98
optimize.sd_selection0.010.000.02
plotBar_MCI0.020.000.01
plotIc000
plotMaxMCI000
plot_Ic_Simulation000
plot_MCI_Simulation0.010.000.02
plot_SS_Simulation000
sd_selection000
simulationMCI0.000.000.05
simulation_Ic0.000.000.04
simulation_Ic_sample000