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This page was generated on 2024-02-28 11:38:44 -0500 (Wed, 28 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4671
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4411
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4438
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4414
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 409/2251HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
coMET 1.35.0  (landing page)
Tiphaine Martin
Snapshot Date: 2024-02-26 14:39:26 -0500 (Mon, 26 Feb 2024)
git_url: https://git.bioconductor.org/packages/coMET
git_branch: devel
git_last_commit: cfaf67e
git_last_commit_date: 2023-10-24 11:45:22 -0500 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  

CHECK results for coMET on merida1


To the developers/maintainers of the coMET package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/coMET.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: coMET
Version: 1.35.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:coMET.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings coMET_1.35.0.tar.gz
StartedAt: 2024-02-27 03:51:36 -0500 (Tue, 27 Feb 2024)
EndedAt: 2024-02-27 04:10:19 -0500 (Tue, 27 Feb 2024)
EllapsedTime: 1122.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: coMET.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:coMET.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings coMET_1.35.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/coMET.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-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 Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘coMET/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘coMET’ version ‘1.35.0’
* 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 ‘coMET’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'utils::findMatches' by 'S4Vectors::findMatches' when loading 'coMET'
See ‘/Users/biocbuild/bbs-3.19-bioc/meat/coMET.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is 18.9Mb
  sub-directories of 1Mb or more:
    data      7.6Mb
    extdata  10.7Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... NOTE
draw.plot.annotation : <anonymous>: no visible global function
  definition for 'ggplotGrob'
draw.plot.annotation: no visible global function definition for
  'viewTracks'
draw.plot.annotation: no visible global function definition for
  'trackList'
eQTL: no visible binding for global variable 'chromosome_stop'
eQTL: no visible binding for global variable 'chromosome_start'
eQTL: no visible binding for global variable 'chromosome_name'
eQTL_GTEx: no visible binding for global variable 'snp_pos'
eQTL_GTEx: no visible binding for global variable 'snp_chrom'
eQTL_GTEx: no visible binding for global variable 'gene_start'
eQTL_GTEx: no visible binding for global variable 'gene_stop'
eQTL_GTEx: no visible binding for global variable 'gene_chr'
geneExpression_GTEx: no visible global function definition for 'as'
metQTL: no visible binding for global variable 'chromosome_stop'
metQTL: no visible binding for global variable 'chromosome_start'
metQTL: no visible binding for global variable 'chromosome_name'
pizza: no visible global function definition for 'par'
pizza: no visible global function definition for 'plot.new'
pizza: no visible global function definition for 'plot.window'
pizza: no visible global function definition for 'polygon'
pizza: no visible global function definition for 'lines'
pizza: no visible global function definition for 'text'
psiQTL_GTEx: no visible binding for global variable 'pos_snp'
psiQTL_GTEx: no visible binding for global variable 'chr_snp'
psiQTL_GTEx: no visible binding for global variable 'pos_middle_exon'
psiQTL_GTEx: no visible binding for global variable 'chr_exon'
Undefined global functions or variables:
  as chr_exon chr_snp chromosome_name chromosome_start chromosome_stop
  gene_chr gene_start gene_stop ggplotGrob lines par plot.new
  plot.window polygon pos_middle_exon pos_snp snp_chrom snp_pos text
  trackList viewTracks
Consider adding
  importFrom("graphics", "lines", "par", "plot.new", "plot.window",
             "polygon", "text")
  importFrom("methods", "as")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
checkRd: (-1) ChIPTF_ENCODE.Rd:36: Escaped LaTeX specials: \#
* 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
Objects in \usage without \alias in Rd file 'check.configVar.cometlist.Rd':
  ‘check.configVar.cometlist’

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 ... OK
* checking data for ASCII and uncompressed saves ... 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
comet.web            13.524  0.436  30.442
coMET-package        12.437  0.391  18.514
chromatinHMMAll_UCSC 10.504  0.091  12.269
HistoneAll_UCSC      10.215  0.099  12.031
imprintedGenes_GTEx   8.882  0.113  10.771
comet                 8.129  0.116   9.492
eQTL_GTEx             4.438  0.042   5.342
* 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: 1 WARNING, 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/coMET.Rcheck/00check.log’
for details.



Installation output

coMET.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘coMET’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'utils::findMatches' by 'S4Vectors::findMatches' when loading 'coMET'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'utils::findMatches' by 'S4Vectors::findMatches' when loading 'coMET'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'utils::findMatches' by 'S4Vectors::findMatches' when loading 'coMET'
** testing if installed package keeps a record of temporary installation path
* DONE (coMET)

Tests output

coMET.Rcheck/tests/runTests.Rout


R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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("coMET") || stop("unable to load Package:coMET")
Loading required package: coMET
Loading required package: grid
Loading required package: biomaRt
Loading required package: Gviz
Loading required package: S4Vectors
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


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: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: psych

Attaching package: 'psych'

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

    distance

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

    distance, reflect

[1] TRUE
Warning message:
replacing previous import 'utils::findMatches' by 'S4Vectors::findMatches' when loading 'coMET' 
> BiocGenerics:::testPackage("coMET")


RUNIT TEST PROTOCOL -- Tue Feb 27 04:09:56 2024 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
coMET RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 30.071   1.619  38.429 

Example timings

coMET.Rcheck/coMET-Ex.timings

nameusersystemelapsed
COSMIC_UCSC3.3520.2144.493
ChIPTF_ENCODE1.8270.0582.178
ClinVarCnv_UCSC0.9930.0371.201
ClinVarMain_UCSC1.0100.0141.189
CoreillCNV_UCSC1.0430.0181.227
DNAse_UCSC0.0000.0010.001
DNaseI_FANTOM1.4380.0271.733
DNaseI_RoadMap0.4190.0170.497
GAD_UCSC1.0610.0211.258
GWAScatalog_UCSC0.8310.0120.986
GeneReviews_UCSC1.3370.0181.560
HiCdata2matrix0.0460.0090.060
HistoneAll_UCSC10.215 0.09912.031
HistoneOne_UCSC0.8670.0141.005
ISCA_UCSC1.0320.0141.206
TFBS_FANTOM1.0570.0141.231
bindingMotifsBiomart_ENSEMBL0.3280.0190.440
chrUCSC2ENSEMBL0.0000.0000.001
chromHMM_RoadMap1.6000.0271.878
chromatinHMMAll_UCSC10.504 0.09112.269
chromatinHMMOne_UCSC1.0520.0181.242
coMET-package12.437 0.39118.514
col2HSV0.0010.0010.001
comet8.1290.1169.492
comet.list1.8990.0272.202
comet.web13.524 0.43630.442
complementary0.0470.0030.057
cpgIslands_UCSC0.3340.0080.418
dgfootprints_RoadMap2.0450.0372.593
eQTL3.4500.0454.156
eQTL_GTEx4.4380.0425.342
gcContent_UCSC1.6740.0282.064
genesName_ENSEMBL0.0040.0050.011
genes_ENSEMBL1.9800.0202.394
imprintedGenes_GTEx 8.882 0.11310.771
interestGenes_ENSEMBL1.7290.0192.082
interestTranscript_ENSEMBL1.9600.0202.412
knownGenes_UCSC2.2580.0202.692
metQTL3.0810.0373.732
miRNATargetRegionsBiomart_ENSEMBL0.1150.0060.143
otherRegulatoryRegionsBiomart_ENSEMBL0.2230.0130.282
pizza0.0450.0030.060
psiQTL_GTEx2.6020.0263.116
refGenes_UCSC2.1580.0182.571
regulationBiomart_ENSEMBL0.8560.0101.032
regulatoryEvidenceBiomart_ENSEMBL0.3240.0180.418
regulatoryFeaturesBiomart_ENSEMBL0.3240.0160.406
regulatorySegmentsBiomart_ENSEMBL0.3280.0180.415
repeatMasker_UCSC1.2620.0141.506
segmentalDups_UCSC1.0060.0131.273
setColors0.0010.0010.002
snpBiomart_ENSEMBL1.0970.0161.325
snpLocations_UCSC2.7740.0223.208
structureBiomart_ENSEMBL1.0010.0121.156
transcript_ENSEMBL3.2420.0293.868
xenorefGenes_UCSC1.5500.0161.888