Sorin Draghici
| Snapshot Date: 2024-05-30 18:28:32 -0400 (Thu, 30 May 2024) |
| git_url: https://git.bioconductor.org/packages/ROntoTools |
| git_branch: RELEASE_3_19 |
| git_last_commit: b64b430 |
| git_last_commit_date: 2024-04-30 10:31:13 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-31 17:03:12 -0400 (Fri, 31 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4753 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4464 |
| 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 | ||||
| Package 1809/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ROntoTools 2.32.0 (landing page) Sorin Draghici
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
|
To the developers/maintainers of the ROntoTools package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: ROntoTools |
| Version: 2.32.0 |
| Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ROntoTools.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ROntoTools_2.32.0.tar.gz |
| StartedAt: 2024-05-31 07:36:46 -0400 (Fri, 31 May 2024) |
| EndedAt: 2024-05-31 07:39:45 -0400 (Fri, 31 May 2024) |
| EllapsedTime: 179.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: ROntoTools.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ROntoTools.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ROntoTools_2.32.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/ROntoTools.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘ROntoTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ROntoTools’ version ‘2.32.0’
* 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 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 ... 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 loading without being on the library search path ... 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 ... WARNING
Codoc mismatches from Rd file 'compute.fisher.Rd':
compute.fisher
Code: function(p, eps = 1e-24)
Docs: function(p, eps = 1e-06)
Mismatches in argument default values:
Name: 'eps' Code: 1e-24 Docs: 1e-06
* checking Rd \usage sections ... NOTE
S3 methods shown with full name in Rd file 'summary.pDisRes.Rd':
‘summary.pDisRes’
S3 methods shown with full name in Rd file 'summary.peRes.Rd':
‘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 8.358 0.012 8.370
peNodeRenderInfo 7.200 0.024 7.225
peEdgeRenderInfo 6.705 0.032 6.736
plot.pePathway-methods 6.655 0.032 6.687
pDis 6.169 0.472 6.642
summary.peRes 6.581 0.016 6.598
pe 6.420 0.056 6.476
summary.pDisRes 5.544 0.028 5.572
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 5 NOTEs
See
‘/home/biocbuild/bbs-3.19-bioc/meat/ROntoTools.Rcheck/00check.log’
for details.
ROntoTools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL ROntoTools ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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 version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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, 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 4.320937 secs.
RUNIT TEST PROTOCOL -- Fri May 31 07:39:15 2024
***********************************************
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
11.952 0.331 12.274
ROntoTools.Rcheck/ROntoTools-Ex.timings
| name | user | system | elapsed | |
| alpha1MR | 0.012 | 0.002 | 0.014 | |
| alphaMLG | 0.010 | 0.000 | 0.011 | |
| compute.fisher | 0 | 0 | 0 | |
| compute.normalInv | 0 | 0 | 0 | |
| keggPathwayGraphs | 0.372 | 0.004 | 0.378 | |
| keggPathwayNames | 0.253 | 0.000 | 0.253 | |
| nodeWeights | 0.005 | 0.000 | 0.005 | |
| pDis | 6.169 | 0.472 | 6.642 | |
| pe | 6.420 | 0.056 | 6.476 | |
| peEdgeRenderInfo | 6.705 | 0.032 | 6.736 | |
| peNodeRenderInfo | 7.200 | 0.024 | 7.225 | |
| plot.pePathway-methods | 6.655 | 0.032 | 6.687 | |
| plot.peRes-methods | 8.358 | 0.012 | 8.370 | |
| setEdgeWeights | 1.793 | 0.012 | 1.806 | |
| setNodeWeights | 0.409 | 0.000 | 0.409 | |
| summary.pDisRes | 5.544 | 0.028 | 5.572 | |
| summary.peRes | 6.581 | 0.016 | 6.598 | |