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CHECK report for coMET on merida2

This page was generated on 2019-04-09 13:30:56 -0400 (Tue, 09 Apr 2019).

Package 320/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
coMET 1.15.2
Tiphaine Martin
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/coMET
Branch: master
Last Commit: 73ea7a6
Last Changed Date: 2018-12-24 04:08:42 -0400 (Mon, 24 Dec 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK 

Summary

Package: coMET
Version: 1.15.2
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_1.15.2.tar.gz
StartedAt: 2019-04-09 00:04:16 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 00:12:36 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 499.8 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_1.15.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/coMET.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘1.15.2’
* 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.web            6.238  0.111  57.664
coMET-package        6.060  0.105  17.734
chromatinHMMAll_UCSC 5.310  0.014   5.369
* 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-3.9-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
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/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 Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 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, 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 -- Tue Apr  9 00:12:24 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 
 16.897   0.804  17.756 

Example timings

coMET.Rcheck/coMET-Ex.timings

nameusersystemelapsed
COSMIC_UCSC1.9710.0532.041
ChIPTF_ENCODE1.1640.0401.213
ClinVarCnv_UCSC0.4990.0030.506
ClinVarMain_UCSC0.5420.0060.551
CoreillCNV_UCSC0.4850.0030.489
DNAse_UCSC0.5650.0030.571
DNaseI_FANTOM0.6930.0100.706
DNaseI_RoadMap0.2390.0120.252
GAD_UCSC0.4370.0030.445
GWAScatalog_UCSC0.4410.0030.453
GeneReviews_UCSC0.6530.0040.668
HiCdata2matrix0.0350.0040.039
HistoneAll_UCSC4.7620.0124.820
HistoneOne_UCSC0.4170.0030.424
ISCA_UCSC0.5150.0030.527
TFBS_FANTOM0.3840.0030.395
bindingMotifsBiomart_ENSEMBL0.2610.0060.277
chrUCSC2ENSEMBL0.0000.0010.000
chromHMM_RoadMap0.8150.0070.831
chromatinHMMAll_UCSC5.3100.0145.369
chromatinHMMOne_UCSC0.7020.0040.711
coMET-package 6.060 0.10517.734
comet3.8960.0483.973
comet.list1.4790.0131.506
comet.web 6.238 0.11157.664
cpgIslands_UCSC0.2170.0030.220
dgfootprints_RoadMap1.2120.0301.246
eQTL1.4780.0081.491
eQTL_GTEx1.4930.0061.504
gcContent_UCSC1.4080.0191.431
genesName_ENSEMBL0.0040.0020.005
genes_ENSEMBL1.0390.0131.053
imprintedGenes_GTEx4.3660.0494.783
interestGenes_ENSEMBL0.7420.0150.768
interestTranscript_ENSEMBL0.8420.0100.856
knownGenes_UCSC1.0390.0041.048
metQTL1.2730.0101.295
miRNATargetRegionsBiomart_ENSEMBL0.0900.0020.092
otherRegulatoryRegionsBiomart_ENSEMBL0.1760.0140.191
psiQTL_GTEx1.1700.0061.182
refGenes_UCSC0.9960.0041.022
regulationBiomart_ENSEMBL0.4590.0030.470
regulatoryEvidenceBiomart_ENSEMBL0.2650.0060.272
regulatoryFeaturesBiomart_ENSEMBL0.2920.0060.301
regulatorySegmentsBiomart_ENSEMBL0.2860.0080.296
repeatMasker_UCSC0.7590.0030.764
segmentalDups_UCSC0.5750.0030.581
snpBiomart_ENSEMBL0.5950.0020.598
snpLocations_UCSC1.2180.0041.229
structureBiomart_ENSEMBL0.5800.0030.587
transcript_ENSEMBL2.2210.0152.242
xenorefGenes_UCSC0.8030.0040.811