Yuxi (Jennifer) Sun
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/BioTIP |
| git_branch: master |
| git_last_commit: f11d28d |
| git_last_commit_date: 2022-03-15 17:00:31 -0400 (Tue, 15 Mar 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:03 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
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. |
| Package 192/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BioTIP 1.9.1 (landing page) Yuxi (Jennifer) Sun
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: BioTIP |
| Version: 1.9.1 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BioTIP.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings BioTIP_1.9.1.tar.gz |
| StartedAt: 2022-03-17 18:34:49 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 18:36:19 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 89.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: BioTIP.Rcheck |
| Warnings: 5 |
##############################################################################
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BioTIP.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings BioTIP_1.9.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/BioTIP.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* 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 '1.9.1'
* 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
* 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 ... WARNING
'::' or ':::' import not declared from: 'scran'
'library' or 'require' calls not declared from:
'SingleCellExperiment' 'monocle3'
'library' or 'require' calls in package code:
'SingleCellExperiment' 'ggplot2' 'monocle3' 'utils'
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
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
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 binding for global variable 'pb'
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 assayNames axis barplot boxplot cor cutree density
dev.off dist getTopHVGs getTopMCI.gene.maxsiz hclust i is legend
logcounts matplot maxMCIms mtext normalized_counts par pb pdf points
queryHits rainbow readthrough sd 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 ... 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 ... NOTE
Note: found 15 marked UTF-8 strings
* 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 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-3.15-bioc/meat/BioTIP.Rcheck/00check.log'
for details.
BioTIP.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL BioTIP
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* 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
* DONE (BioTIP)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'MOGAMUN' is missing or broken
done
BioTIP.Rcheck/BioTIP-Ex.timings
| name | user | system | elapsed | |
| avg.cor.shrink | 1.98 | 0.79 | 2.77 | |
| cor.shrink | 0.24 | 0.31 | 0.55 | |
| getBiotypes | 0.41 | 0.12 | 0.53 | |
| getCTS | 0 | 0 | 0 | |
| getCluster_methods | 0.04 | 0.00 | 0.05 | |
| getIc | 0.02 | 0.00 | 0.02 | |
| getIc.new | 0.45 | 0.46 | 0.90 | |
| getMCI | 0.02 | 0.00 | 0.02 | |
| getMaxMCImember | 0.04 | 0.01 | 0.06 | |
| getMaxStats | 0.02 | 0.00 | 0.02 | |
| getNetwork | 0.02 | 0.00 | 0.01 | |
| getReadthrough | 2.21 | 0.08 | 2.30 | |
| plotBar_MCI | 0.02 | 0.00 | 0.01 | |
| plotIc | 0 | 0 | 0 | |
| plotMaxMCI | 0.02 | 0.00 | 0.02 | |
| plot_Ic_Simulation | 0 | 0 | 0 | |
| plot_MCI_Simulation | 0 | 0 | 0 | |
| plot_SS_Simulation | 0.01 | 0.00 | 0.02 | |
| sd_selection | 0 | 0 | 0 | |
| simulationMCI | 0.00 | 0.00 | 0.03 | |
| simulation_Ic | 0.00 | 0.00 | 0.04 | |
| simulation_Ic_sample | 0 | 0 | 0 | |