Back to Multiple platform build/check report for BioC 3.17:   simplified   long
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This page was generated on 2023-03-28 11:06:41 -0400 (Tue, 28 Mar 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-03-16 r83996) -- "Unsuffered Consequences" 4547
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-03-15 r83984 ucrt) -- "Unsuffered Consequences" 4308
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-03-16 r83985) -- "Unsuffered Consequences" 4301
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

CHECK results for Category on merida1


To the developers/maintainers of the Category package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Category.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.

raw results

Package 268/2195HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Category 2.65.0  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2023-03-27 14:00:21 -0400 (Mon, 27 Mar 2023)
git_url: https://git.bioconductor.org/packages/Category
git_branch: devel
git_last_commit: 6ef74a5
git_last_commit_date: 2022-11-01 10:39:25 -0400 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: Category
Version: 2.65.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Category.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Category_2.65.0.tar.gz
StartedAt: 2023-03-27 23:18:51 -0400 (Mon, 27 Mar 2023)
EndedAt: 2023-03-27 23:27:53 -0400 (Mon, 27 Mar 2023)
EllapsedTime: 542.9 seconds
RetCode: 0
Status:   OK  
CheckDir: Category.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Category.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Category_2.65.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/Category.Rcheck’
* using R Under development (unstable) (2023-03-16 r83985)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* R was compiled by
    Apple clang version 12.0.0 (clang-1200.0.32.29)
    GNU Fortran (GCC) 8.2.0
* running under: macOS Mojave 10.14.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Category/DESCRIPTION’ ... OK
* this is package ‘Category’ version ‘2.65.0’
* 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 ‘Category’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) cb_parse_band_Hs.Rd:23: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) cb_parse_band_Mm.Rd:22: Escaped LaTeX specials: \&
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Unknown package ‘KEGG.db’ in Rd xrefs
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
ChrBandTree-class 7.530  0.289  10.286
MAPAmat           4.482  0.181   6.102
makeChrBandGraph  4.001  0.048   5.166
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc/meat/Category.Rcheck/00check.log’
for details.



Installation output

Category.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Category
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3/Resources/library’
* installing *source* package ‘Category’ ...
** 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 (Category)

Tests output

Category.Rcheck/tests/runTests.Rout


R Under development (unstable) (2023-03-16 r83985) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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.

> require("Category") || stop("unable to load Category")
Loading required package: Category
Loading required package: stats4
Loading required package: BiocGenerics

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

Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: Matrix

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand

[1] TRUE
> BiocGenerics:::testPackage("Category", "UnitTests", ".*_test\\.R$")
Loading required package: org.Hs.eg.db



'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
Loading required package: graph


Attaching package: 'GOstats'

The following object is masked from 'package:AnnotationDbi':

    makeGOGraph



RUNIT TEST PROTOCOL -- Mon Mar 27 23:27:37 2023 
*********************************************** 
Number of test functions: 14 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
Category RUnit Tests - 14 test functions, 0 errors, 0 failures
Number of test functions: 14 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In makeValidParams(.Object) : removing duplicate IDs in geneIds
2: In makeValidParams(.Object) : removing duplicate IDs in universeGeneIds
3: In makeValidParams(.Object) : removing geneIds not in universeGeneIds
4: In makeValidParams(.Object) : removing duplicate IDs in geneIds
5: In makeValidParams(.Object) : removing duplicate IDs in universeGeneIds
6: In makeValidParams(.Object) : removing geneIds not in universeGeneIds
7: In makeValidParams(.Object) :
  converting geneIds from list to atomic vector via unlist
8: In makeValidParams(.Object) :
  converting univ from list to atomic vector via unlist
9: In makeValidParams(.Object) : removing duplicate IDs in universeGeneIds
> 
> proc.time()
   user  system elapsed 
 95.551   9.331 137.991 

Example timings

Category.Rcheck/Category-Ex.timings

nameusersystemelapsed
ChrBandTree-class 7.530 0.28910.286
ChrMapHyperGParams-class0.0020.0000.002
ChrMapHyperGResult-class0.0010.0000.001
ChrMapLinearMParams-class0.0010.0000.001
ChrMapLinearMResult-class0.0010.0010.001
DatPkg-class0.0640.0040.087
HyperGResult-accessors2.1750.0613.004
LinearMResult-class0.0010.0010.002
MAPAmat4.4820.1816.102
applyByCategory0.0050.0000.010
cateGOryMatrix0.4660.0240.647
cb_parse_band_Hs000
cb_parse_band_Mm0.0010.0000.001
findAMstats0.0020.0000.002
getPathNames0.0610.0061.177
gseattperm1.7130.0712.270
hyperg1.1430.0261.523
makeChrBandGraph4.0010.0485.166
makeEBcontr0.3320.0120.444
probes2MAP0.2120.0040.272
probes2Path0.0610.0030.083
ttperm0.0240.0020.029