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This page was generated on 2021-09-24 15:05:42 -0400 (Fri, 24 Sep 2021).

CHECK results for coMET on nebbiolo1

To the developers/maintainers of the coMET package:
- Please 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 How and When does the builder pull? When will my changes propagate? here 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 366/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
coMET 1.24.0  (landing page)
Tiphaine Martin
Snapshot Date: 2021-09-23 04:50:12 -0400 (Thu, 23 Sep 2021)
git_url: https://git.bioconductor.org/packages/coMET
git_branch: RELEASE_3_13
git_last_commit: fb8047d
git_last_commit_date: 2021-05-19 12:10:24 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    ERROR  skippedskipped
machv2macOS 10.14.6 Mojave / x86_64  OK    ERROR  skippedskipped

Summary

Package: coMET
Version: 1.24.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:coMET.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings coMET_1.24.0.tar.gz
StartedAt: 2021-09-23 09:19:24 -0400 (Thu, 23 Sep 2021)
EndedAt: 2021-09-23 09:27:05 -0400 (Thu, 23 Sep 2021)
EllapsedTime: 461.4 seconds
RetCode: 0
Status:   OK  
CheckDir: coMET.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:coMET.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings coMET_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/coMET.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘coMET/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘coMET’ version ‘1.24.0’
* 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 ... OK
* checking installed package size ... NOTE
  installed size is 14.8Mb
  sub-directories of 1Mb or more:
    data      8.0Mb
    extdata   6.1Mb
* 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'
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 pos_middle_exon pos_snp
  snp_chrom snp_pos trackList viewTracks
Consider adding
  importFrom("methods", "as")
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 ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
comet.web     9.605  0.337  40.679
coMET-package 5.886  0.192  14.806
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/coMET.Rcheck/00check.log’
for details.



Installation output

coMET.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL coMET
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘coMET’ ...
** using staged installation
** R
** data
** 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 (coMET)

Tests output

coMET.Rcheck/tests/runTests.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-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.

> 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
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, 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: 'S4Vectors'

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:IRanges':

    reflect

[1] TRUE
> BiocGenerics:::testPackage("coMET")


RUNIT TEST PROTOCOL -- Thu Sep 23 09:27:02 2021 
*********************************************** 
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 
 14.223   0.561  14.769 

Example timings

coMET.Rcheck/coMET-Ex.timings

nameusersystemelapsed
COSMIC_UCSC2.1170.1162.233
ChIPTF_ENCODE0.6390.0860.725
ClinVarCnv_UCSC0.4720.0760.548
ClinVarMain_UCSC0.4840.0320.516
CoreillCNV_UCSC0.4570.0000.456
DNAse_UCSC0.5590.0000.558
DNaseI_FANTOM0.5580.0120.569
DNaseI_RoadMap0.2090.0040.213
GAD_UCSC0.4810.0000.481
GWAScatalog_UCSC0.4400.0240.463
GeneReviews_UCSC0.6900.0040.694
HiCdata2matrix0.0320.0040.035
HistoneAll_UCSC4.9290.0044.933
HistoneOne_UCSC0.4250.0000.425
ISCA_UCSC0.5070.0000.507
TFBS_FANTOM0.4160.0000.415
bindingMotifsBiomart_ENSEMBL0.1360.0040.140
chrUCSC2ENSEMBL0.0010.0000.001
chromHMM_RoadMap0.6530.0040.657
chromatinHMMAll_UCSC4.9240.0164.940
chromatinHMMOne_UCSC0.6780.0040.682
coMET-package 5.886 0.19214.806
comet3.2130.0563.269
comet.list0.6650.0000.665
comet.web 9.605 0.33740.679
cpgIslands_UCSC0.1740.0040.178
dgfootprints_RoadMap0.8040.0360.840
eQTL1.5910.0241.615
eQTL_GTEx1.5130.0441.557
gcContent_UCSC1.9420.0842.027
genesName_ENSEMBL0.0040.0000.003
genes_ENSEMBL0.9030.0040.908
imprintedGenes_GTEx4.5460.0764.623
interestGenes_ENSEMBL0.8550.0000.855
interestTranscript_ENSEMBL0.9010.0200.922
knownGenes_UCSC1.1250.0271.151
metQTL1.2960.0241.320
miRNATargetRegionsBiomart_ENSEMBL0.0510.0000.051
otherRegulatoryRegionsBiomart_ENSEMBL0.1000.0120.112
psiQTL_GTEx1.1630.0081.171
refGenes_UCSC1.1350.0231.159
regulationBiomart_ENSEMBL0.4440.0000.444
regulatoryEvidenceBiomart_ENSEMBL0.1650.0040.169
regulatoryFeaturesBiomart_ENSEMBL0.1700.0350.205
regulatorySegmentsBiomart_ENSEMBL0.1580.0030.161
repeatMasker_UCSC0.6720.0010.672
segmentalDups_UCSC0.5130.0000.513
snpBiomart_ENSEMBL0.6150.0240.640
snpLocations_UCSC1.4010.0001.400
structureBiomart_ENSEMBL0.5490.0240.573
transcript_ENSEMBL1.7450.0031.750
xenorefGenes_UCSC0.8450.0360.881