Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-06-11 14:43 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4522
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4468
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 278/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Category 2.70.0  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/Category
git_branch: RELEASE_3_19
git_last_commit: b4b6161
git_last_commit_date: 2024-04-30 10:14:10 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 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
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for Category on kjohnson3

To the developers/maintainers of the Category package:
- 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 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.

raw results


Summary

Package: Category
Version: 2.70.0
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_2.70.0.tar.gz
StartedAt: 2024-06-10 09:40:02 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 09:45:00 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 298.3 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_2.70.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/Category.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Category/DESCRIPTION’ ... OK
* this is package ‘Category’ version ‘2.70.0’
* 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 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 ... 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) HyperGParams-class.Rd:99: Lost braces
    99 |   \item{code{annotation(object)}}{Accessor for annotation.  If you want
       |             ^
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 5.907  0.194   6.845
* 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 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-3.19-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/4.4-arm64/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 version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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, 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 object is masked from 'package:utils':

    findMatches

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 Jun 10 09:44:45 2024 
*********************************************** 
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 
 56.956  15.652  87.625 

Example timings

Category.Rcheck/Category-Ex.timings

nameusersystemelapsed
ChrBandTree-class5.9070.1946.845
ChrMapHyperGParams-class0.0020.0000.001
ChrMapHyperGResult-class0.0000.0000.001
ChrMapLinearMParams-class0.0000.0000.001
ChrMapLinearMResult-class0.0010.0010.001
DatPkg-class0.0670.0040.070
HyperGResult-accessors1.8670.0552.198
LinearMResult-class0.0010.0010.007
MAPAmat2.5660.1803.350
applyByCategory0.0040.0000.004
cateGOryMatrix0.2600.0200.354
cb_parse_band_Hs0.0000.0000.001
cb_parse_band_Mm000
findAMstats0.0010.0000.002
getPathNames0.0430.0101.788
gseattperm1.0190.0381.344
hyperg0.7810.0360.828
makeChrBandGraph2.1440.0572.396
makeEBcontr0.1420.0060.150
probes2MAP0.1520.0050.156
probes2Path0.0630.0030.067
ttperm0.0090.0020.011