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CHECK report for coMET on merida1

This page was generated on 2019-04-16 11:58:15 -0400 (Tue, 16 Apr 2019).

Package 308/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
coMET 1.14.0
Tiphaine Martin
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/coMET
Branch: RELEASE_3_8
Last Commit: 2833a76
Last Changed Date: 2018-10-30 11:41:56 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: coMET
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:coMET.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings coMET_1.14.0.tar.gz
StartedAt: 2019-04-15 23:09:24 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 23:17:49 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 505.0 seconds
RetCode: 0
Status:  OK 
CheckDir: coMET.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:coMET.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings coMET_1.14.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/coMET.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.14.0’
* 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 18.8Mb
  sub-directories of 1Mb or more:
    data      7.5Mb
    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'
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
coMET-package        6.131  0.135  19.144
chromatinHMMAll_UCSC 5.977  0.013   6.023
comet.web            5.856  0.103  57.375
HistoneAll_UCSC      5.499  0.012   5.522
imprintedGenes_GTEx  4.315  0.026   5.136
* 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
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/coMET.Rcheck/00check.log’
for details.



Installation output

coMET.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL coMET
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘coMET’ ...
** 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
* DONE (coMET)

Tests output

coMET.Rcheck/tests/runTests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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("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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min


Attaching package: 'S4Vectors'

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

    expand.grid

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 -- Mon Apr 15 23:17:41 2019 
*********************************************** 
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 
 15.347   0.718  16.179 

Example timings

coMET.Rcheck/coMET-Ex.timings

nameusersystemelapsed
COSMIC_UCSC2.0530.0992.166
ChIPTF_ENCODE1.1860.0761.265
ClinVarCnv_UCSC0.5180.0180.541
ClinVarMain_UCSC0.5260.0030.533
CoreillCNV_UCSC0.5200.0050.525
DNAse_UCSC0.5500.0040.555
DNaseI_FANTOM0.7170.0120.732
DNaseI_RoadMap0.2790.0070.287
GAD_UCSC0.5420.0030.546
GWAScatalog_UCSC0.4620.0020.465
GeneReviews_UCSC0.7810.0050.786
HiCdata2matrix0.0350.0030.038
HistoneAll_UCSC5.4990.0125.522
HistoneOne_UCSC0.4250.0040.429
ISCA_UCSC0.5500.0040.555
TFBS_FANTOM0.4720.0030.477
bindingMotifsBiomart_ENSEMBL0.2910.0070.307
chrUCSC2ENSEMBL000
chromHMM_RoadMap0.7960.0070.805
chromatinHMMAll_UCSC5.9770.0136.023
chromatinHMMOne_UCSC0.7320.0030.740
coMET-package 6.131 0.13519.144
comet3.9660.0644.117
comet.list1.1500.0181.170
comet.web 5.856 0.10357.375
cpgIslands_UCSC0.1730.0030.178
dgfootprints_RoadMap1.0040.0241.039
eQTL1.4680.0101.494
eQTL_GTEx1.4590.0061.477
gcContent_UCSC1.2600.0061.274
genesName_ENSEMBL0.0050.0020.006
genes_ENSEMBL0.9780.0080.994
imprintedGenes_GTEx4.3150.0265.136
interestGenes_ENSEMBL0.7970.0080.808
interestTranscript_ENSEMBL0.9980.0091.014
knownGenes_UCSC1.1610.0181.186
metQTL1.4250.0231.462
miRNATargetRegionsBiomart_ENSEMBL0.0670.0020.070
otherRegulatoryRegionsBiomart_ENSEMBL0.1640.0090.174
psiQTL_GTEx1.1490.0081.161
refGenes_UCSC1.1150.0031.135
regulationBiomart_ENSEMBL0.3520.0020.356
regulatoryEvidenceBiomart_ENSEMBL0.2440.0060.252
regulatoryFeaturesBiomart_ENSEMBL0.2940.0080.304
regulatorySegmentsBiomart_ENSEMBL0.3010.0080.314
repeatMasker_UCSC0.6880.0020.698
segmentalDups_UCSC0.4670.0020.475
snpBiomart_ENSEMBL0.5420.0030.548
snpLocations_UCSC1.1480.0031.170
structureBiomart_ENSEMBL0.5210.0020.532
transcript_ENSEMBL2.1640.0092.198
xenorefGenes_UCSC0.7680.0030.775