Zhezhen Wang
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/BioTIP |
| Branch: RELEASE_3_11 |
| Last Commit: 8c08cc8 |
| Last Changed Date: 2020-04-27 15:30:56 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:58:08 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE BioTIP PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 184/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| BioTIP 1.2.0 Zhezhen Wang
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| Package: BioTIP |
| Version: 1.2.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BioTIP.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BioTIP_1.2.0.tar.gz |
| StartedAt: 2020-10-16 23:08:14 -0400 (Fri, 16 Oct 2020) |
| EndedAt: 2020-10-16 23:10:38 -0400 (Fri, 16 Oct 2020) |
| EllapsedTime: 144.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: BioTIP.Rcheck |
| Warnings: 3 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BioTIP.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BioTIP_1.2.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/BioTIP.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BioTIP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BioTIP’ version ‘1.2.0’
* 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 ‘BioTIP’ can be installed ... WARNING
Found the following significant warnings:
Warning: /Users/biocbuild/bbs-3.11-bioc/meat/BioTIP/man/optimize.sd_selection.Rd:40: unknown macro '\item'
Warning: /Users/biocbuild/bbs-3.11-bioc/meat/BioTIP/man/optimize.sd_selection.Rd:52: unknown macro '\item'
Warning: /Users/biocbuild/bbs-3.11-bioc/meat/BioTIP/man/optimize.sd_selection.Rd:55: unknown macro '\item'
Warning: /Users/biocbuild/bbs-3.11-bioc/meat/BioTIP/man/optimize.sd_selection.Rd:58: unexpected section header '\value'
Warning: /Users/biocbuild/bbs-3.11-bioc/meat/BioTIP/man/optimize.sd_selection.Rd:63: unexpected section header '\description'
Warning: /Users/biocbuild/bbs-3.11-bioc/meat/BioTIP/man/optimize.sd_selection.Rd:68: unexpected section header '\examples'
Warning: /Users/biocbuild/bbs-3.11-bioc/meat/BioTIP/man/optimize.sd_selection.Rd:78: unexpected section header '\seealso'
Warning: /Users/biocbuild/bbs-3.11-bioc/meat/BioTIP/man/optimize.sd_selection.Rd:81: unexpected section header '\author'
Warning: /Users/biocbuild/bbs-3.11-bioc/meat/BioTIP/man/optimize.sd_selection.Rd:84: unexpected END_OF_INPUT '
Warning: /Users/biocbuild/bbs-3.11-bioc/meat/BioTIP/man/sd_selection.Rd:29: unknown macro '\item'
Warning: /Users/biocbuild/bbs-3.11-bioc/meat/BioTIP/man/sd_selection.Rd:41: unknown macro '\item'
Warning: /Users/biocbuild/bbs-3.11-bioc/meat/BioTIP/man/sd_selection.Rd:44: unknown macro '\item'
Warning: /Users/biocbuild/bbs-3.11-bioc/meat/BioTIP/man/sd_selection.Rd:47: unexpected section header '\value'
Warning: /Users/biocbuild/bbs-3.11-bioc/meat/BioTIP/man/sd_selection.Rd:54: unexpected section header '\description'
Warning: /Users/biocbuild/bbs-3.11-bioc/meat/BioTIP/man/sd_selection.Rd:61: unexpected section header '\examples'
Warning: /Users/biocbuild/bbs-3.11-bioc/meat/BioTIP/man/sd_selection.Rd:71: unexpected section header '\seealso'
Warning: /Users/biocbuild/bbs-3.11-bioc/meat/BioTIP/man/sd_selection.Rd:74: unexpected section header '\author'
Warning: /Users/biocbuild/bbs-3.11-bioc/meat/BioTIP/man/sd_selection.Rd:77: unexpected END_OF_INPUT '
See ‘/Users/biocbuild/bbs-3.11-bioc/meat/BioTIP.Rcheck/00install.out’ for details.
* 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 ... 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’
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: 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 ‘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’
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
is legend matplot mtext par points queryHits rainbow readthrough sd
subjectHits text
Consider adding
importFrom("grDevices", "rainbow")
importFrom("graphics", "abline", "axis", "barplot", "boxplot",
"legend", "matplot", "mtext", "par", "points", "text")
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
prepare_Rd: man/optimize.sd_selection.Rd:40: unknown macro '\item'
prepare_Rd: man/optimize.sd_selection.Rd:52: unknown macro '\item'
prepare_Rd: man/optimize.sd_selection.Rd:55: unknown macro '\item'
prepare_Rd: man/optimize.sd_selection.Rd:58: unexpected section header '\value'
prepare_Rd: man/optimize.sd_selection.Rd:63: unexpected section header '\description'
prepare_Rd: man/optimize.sd_selection.Rd:68: unexpected section header '\examples'
prepare_Rd: man/optimize.sd_selection.Rd:78: unexpected section header '\seealso'
prepare_Rd: man/optimize.sd_selection.Rd:81: unexpected section header '\author'
prepare_Rd: man/optimize.sd_selection.Rd:84: unexpected END_OF_INPUT '
'
checkRd: (5) optimize.sd_selection.Rd:0-85: Must have a \description
prepare_Rd: man/sd_selection.Rd:29: unknown macro '\item'
prepare_Rd: man/sd_selection.Rd:41: unknown macro '\item'
prepare_Rd: man/sd_selection.Rd:44: unknown macro '\item'
prepare_Rd: man/sd_selection.Rd:47: unexpected section header '\value'
prepare_Rd: man/sd_selection.Rd:54: unexpected section header '\description'
prepare_Rd: man/sd_selection.Rd:61: unexpected section header '\examples'
prepare_Rd: man/sd_selection.Rd:71: unexpected section header '\seealso'
prepare_Rd: man/sd_selection.Rd:74: unexpected section header '\author'
prepare_Rd: man/sd_selection.Rd:77: unexpected END_OF_INPUT '
'
checkRd: (5) sd_selection.Rd:0-78: Must have a \description
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘TSdist’
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'optimize.sd_selection'
‘method’ ‘control_df’ ‘control_samplesL’
Undocumented arguments in documentation object 'plot_Ic_Simulation'
‘which2point’
Documented arguments not in \usage in documentation object 'plot_SS_Simulation':
‘which2point’
Undocumented arguments in documentation object 'sd_selection'
‘method’ ‘control_df’ ‘control_samplesL’
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 data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
getReadthrough 5.074 0.127 5.509
* 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: 3 WARNINGs, 4 NOTEs
See
‘/Users/biocbuild/bbs-3.11-bioc/meat/BioTIP.Rcheck/00check.log’
for details.
BioTIP.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL BioTIP ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘BioTIP’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** byte-compile and prepare package for lazy loading ** help Warning: /Users/biocbuild/bbs-3.11-bioc/meat/BioTIP/man/optimize.sd_selection.Rd:40: unknown macro '\item' Warning: /Users/biocbuild/bbs-3.11-bioc/meat/BioTIP/man/optimize.sd_selection.Rd:52: unknown macro '\item' Warning: /Users/biocbuild/bbs-3.11-bioc/meat/BioTIP/man/optimize.sd_selection.Rd:55: unknown macro '\item' Warning: /Users/biocbuild/bbs-3.11-bioc/meat/BioTIP/man/optimize.sd_selection.Rd:58: unexpected section header '\value' Warning: /Users/biocbuild/bbs-3.11-bioc/meat/BioTIP/man/optimize.sd_selection.Rd:63: unexpected section header '\description' Warning: /Users/biocbuild/bbs-3.11-bioc/meat/BioTIP/man/optimize.sd_selection.Rd:68: unexpected section header '\examples' Warning: /Users/biocbuild/bbs-3.11-bioc/meat/BioTIP/man/optimize.sd_selection.Rd:78: unexpected section header '\seealso' Warning: /Users/biocbuild/bbs-3.11-bioc/meat/BioTIP/man/optimize.sd_selection.Rd:81: unexpected section header '\author' Warning: /Users/biocbuild/bbs-3.11-bioc/meat/BioTIP/man/optimize.sd_selection.Rd:84: unexpected END_OF_INPUT ' ' Warning: /Users/biocbuild/bbs-3.11-bioc/meat/BioTIP/man/sd_selection.Rd:29: unknown macro '\item' Warning: /Users/biocbuild/bbs-3.11-bioc/meat/BioTIP/man/sd_selection.Rd:41: unknown macro '\item' Warning: /Users/biocbuild/bbs-3.11-bioc/meat/BioTIP/man/sd_selection.Rd:44: unknown macro '\item' Warning: /Users/biocbuild/bbs-3.11-bioc/meat/BioTIP/man/sd_selection.Rd:47: unexpected section header '\value' Warning: /Users/biocbuild/bbs-3.11-bioc/meat/BioTIP/man/sd_selection.Rd:54: unexpected section header '\description' Warning: /Users/biocbuild/bbs-3.11-bioc/meat/BioTIP/man/sd_selection.Rd:61: unexpected section header '\examples' Warning: /Users/biocbuild/bbs-3.11-bioc/meat/BioTIP/man/sd_selection.Rd:71: unexpected section header '\seealso' Warning: /Users/biocbuild/bbs-3.11-bioc/meat/BioTIP/man/sd_selection.Rd:74: unexpected section header '\author' Warning: /Users/biocbuild/bbs-3.11-bioc/meat/BioTIP/man/sd_selection.Rd:77: unexpected END_OF_INPUT ' ' *** 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)
BioTIP.Rcheck/BioTIP-Ex.timings
| name | user | system | elapsed | |
| avg.cor.shrink | 2.406 | 0.301 | 2.710 | |
| cor.shrink | 0.647 | 0.117 | 0.763 | |
| getBiotypes | 1.056 | 0.136 | 1.362 | |
| getCTS | 0.002 | 0.001 | 0.002 | |
| getCluster_methods | 0.052 | 0.003 | 0.072 | |
| getIc | 0.014 | 0.000 | 0.018 | |
| getIc.new | 0.988 | 0.227 | 1.538 | |
| getMCI | 0.024 | 0.001 | 0.031 | |
| getMaxMCImember | 0.081 | 0.003 | 0.110 | |
| getMaxStats | 0.023 | 0.001 | 0.027 | |
| getNetwork | 0.024 | 0.001 | 0.033 | |
| getReadthrough | 5.074 | 0.127 | 5.509 | |
| plotBar_MCI | 0.049 | 0.001 | 0.051 | |
| plotIc | 0.004 | 0.001 | 0.005 | |
| plotMaxMCI | 0.002 | 0.001 | 0.003 | |
| plot_Ic_Simulation | 0.003 | 0.001 | 0.004 | |
| plot_MCI_Simulation | 0.010 | 0.002 | 0.011 | |
| plot_SS_Simulation | 0.013 | 0.001 | 0.013 | |
| simulationMCI | 0.007 | 0.000 | 0.052 | |
| simulation_Ic | 0.020 | 0.001 | 0.205 | |
| simulation_Ic_sample | 0.009 | 0.000 | 0.010 | |