| Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-02-08 01:15:26 -0000 (Wed, 08 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
| 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 | ||||
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To the developers/maintainers of the ROntoTools package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ROntoTools.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1705/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ROntoTools 2.27.0 (landing page) Calin Voichita
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: ROntoTools |
| Version: 2.27.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ROntoTools.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings ROntoTools_2.27.0.tar.gz |
| StartedAt: 2023-02-07 13:54:13 -0000 (Tue, 07 Feb 2023) |
| EndedAt: 2023-02-07 13:59:03 -0000 (Tue, 07 Feb 2023) |
| EllapsedTime: 290.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ROntoTools.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ROntoTools.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings ROntoTools_2.27.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/ROntoTools.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 ‘ROntoTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ROntoTools’ version ‘2.27.0’
* 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 ‘ROntoTools’ 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 ... NOTE
Problems with news in ‘NEWS’:
Cannot process chunk/lines:
action between the genes (as edgeWeights) and the relevance of each gene (as
Cannot process chunk/lines:
weights to be used as nodeWeights
* 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 ... NOTE
Warning: no function found corresponding to methods exports from ‘ROntoTools’ for: ‘Summary’
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
‘Rgraphviz’ ‘methods’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
KEGGpathway2Graph: no visible global function definition for ‘is’
KEGGpathway2Graph: no visible global function definition for ‘new’
compute.B: no visible global function definition for ‘as’
compute.B_pDis: no visible global function definition for ‘as’
compute.normalInv: no visible global function definition for ‘pnorm’
compute.normalInv: no visible binding for global variable ‘qnorm’
compute.pORA: no visible global function definition for ‘phyper’
get.totalAccNorm: no visible global function definition for ‘sd’
get.totalPertNorm: no visible global function definition for ‘sd’
get.totalpDisNorm: no visible global function definition for ‘sd’
graph2ftM: no visible global function definition for ‘as’
keggPathwayGraphs: no visible global function definition for
‘txtProgressBar’
keggPathwayGraphs : <anonymous>: no visible global function definition
for ‘new’
keggPathwayGraphs : <anonymous>: no visible global function definition
for ‘setTxtProgressBar’
keggPathwayGraphs : <anonymous>: no visible global function definition
for ‘getTxtProgressBar’
loadKEGGpathwayDataREST: no visible global function definition for
‘txtProgressBar’
loadKEGGpathwayDataREST : <anonymous>: no visible global function
definition for ‘setTxtProgressBar’
loadKEGGpathwayDataREST : <anonymous>: no visible global function
definition for ‘getTxtProgressBar’
pDis.boot: no visible global function definition for ‘new’
pDis.helper: no visible global function definition for ‘txtProgressBar’
pDis.helper : <anonymous>: no visible global function definition for
‘setTxtProgressBar’
pDis.helper : <anonymous>: no visible global function definition for
‘getTxtProgressBar’
pDis.helper: no visible global function definition for ‘new’
pe.boot: no visible global function definition for ‘new’
peEdgeRenderInfo: no visible global function definition for
‘removedEdges’
peNodeRenderInfo: no visible global function definition for ‘slot’
peNodeRenderInfo: no visible global function definition for
‘colorRampPalette’
pf.helper: no visible global function definition for ‘txtProgressBar’
pf.helper : <anonymous>: no visible global function definition for
‘setTxtProgressBar’
pf.helper : <anonymous>: no visible global function definition for
‘getTxtProgressBar’
pf.helper: no visible global function definition for ‘new’
subGraphByNodeType: no visible global function definition for ‘new’
summary.pDisRes : <anonymous>: no visible global function definition
for ‘p.adjust’
summary.peRes : <anonymous>: no visible global function definition for
‘p.adjust’
plot,pePathway-character: no visible global function definition for
‘slot’
plot,pePathway-character: no visible global function definition for
‘abline’
plot,pePathway-character: no visible global function definition for
‘points’
plot,pePathway-character: no visible global function definition for
‘sd’
plot,pePathway-character: no visible global function definition for
‘density’
plot,peRes-character: no visible global function definition for
‘Summary’
plot,peRes-character: no visible global function definition for ‘chull’
plot,peRes-character: no visible global function definition for
‘polygon’
plot,peRes-character: no visible global function definition for
‘points’
plot,peRes-character: no visible global function definition for ‘text’
plot,peRes-character: no visible global function definition for
‘abline’
Undefined global functions or variables:
Summary abline as chull colorRampPalette density getTxtProgressBar is
new p.adjust phyper pnorm points polygon qnorm removedEdges sd
setTxtProgressBar slot text txtProgressBar
Consider adding
importFrom("grDevices", "chull", "colorRampPalette")
importFrom("graphics", "abline", "points", "polygon", "text")
importFrom("methods", "Summary", "as", "is", "new", "slot")
importFrom("stats", "density", "p.adjust", "phyper", "pnorm", "qnorm",
"sd")
importFrom("utils", "getTxtProgressBar", "setTxtProgressBar",
"txtProgressBar")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... NOTE
S3 methods shown with full name in documentation object 'summary.pDisRes':
‘summary.pDisRes’
S3 methods shown with full name in documentation object 'summary.peRes':
‘summary.peRes’
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plot.peRes-methods 12.478 0.012 12.494
peNodeRenderInfo 10.537 0.016 10.555
peEdgeRenderInfo 9.809 0.036 9.860
summary.peRes 9.546 0.032 9.669
plot.pePathway-methods 9.457 0.028 9.787
pe 9.339 0.116 9.709
pDis 9.080 0.064 9.373
summary.pDisRes 8.495 0.028 8.524
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘rontotools.Rnw’... OK
OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 5 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/ROntoTools.Rcheck/00check.log’
for details.
ROntoTools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL ROntoTools ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘ROntoTools’ ... ** using staged installation ** R ** 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 (ROntoTools)
ROntoTools.Rcheck/tests/runTests.Rout
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> BiocGenerics:::testPackage("ROntoTools")
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
Attaching package: 'KEGGgraph'
The following object is masked from 'package:graphics':
plot
The following object is masked from 'package:base':
plot
Using cached pathway data. Database info:
pathway KEGG Pathway Database
path Release 73.0+/01-03, Jan 15
Kanehisa Laboratories
343,170 entries
Default parameters detected. Using pre-parsed data.
Using cached pathway data. Database info:
pathway KEGG Pathway Database
path Release 73.0+/01-03, Jan 15
Kanehisa Laboratories
343,170 entries
Default parameters detected. Using pre-parsed data.
Using cached pathway data. Database info:
pathway KEGG Pathway Database
path Release 73.0+/01-03, Jan 15
Kanehisa Laboratories
343,170 entries
Default parameters detected. Using pre-parsed data.
Performing pathway analysis...
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|======================================================================| 100%Analysis completed in 6.914474 secs.
RUNIT TEST PROTOCOL -- Tue Feb 7 13:57:38 2023
***********************************************
Number of test functions: 6
Number of errors: 0
Number of failures: 0
1 Test Suite :
ROntoTools RUnit Tests - 6 test functions, 0 errors, 0 failures
Number of test functions: 6
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
17.543 0.238 18.204
ROntoTools.Rcheck/ROntoTools-Ex.timings
| name | user | system | elapsed | |
| alpha1MR | 0.016 | 0.000 | 0.022 | |
| alphaMLG | 0.014 | 0.000 | 0.014 | |
| compute.fisher | 0.000 | 0.001 | 0.000 | |
| compute.normalInv | 0.000 | 0.001 | 0.001 | |
| keggPathwayGraphs | 0.519 | 0.018 | 0.540 | |
| keggPathwayNames | 0.375 | 0.008 | 0.383 | |
| nodeWeights | 0.006 | 0.000 | 0.007 | |
| pDis | 9.080 | 0.064 | 9.373 | |
| pe | 9.339 | 0.116 | 9.709 | |
| peEdgeRenderInfo | 9.809 | 0.036 | 9.860 | |
| peNodeRenderInfo | 10.537 | 0.016 | 10.555 | |
| plot.pePathway-methods | 9.457 | 0.028 | 9.787 | |
| plot.peRes-methods | 12.478 | 0.012 | 12.494 | |
| setEdgeWeights | 2.478 | 0.008 | 2.487 | |
| setNodeWeights | 0.568 | 0.000 | 0.568 | |
| summary.pDisRes | 8.495 | 0.028 | 8.524 | |
| summary.peRes | 9.546 | 0.032 | 9.669 | |