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CHECK report for coMET on malbec1

This page was generated on 2018-04-12 13:13:07 -0400 (Thu, 12 Apr 2018).

Package 278/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
coMET 1.10.2
Tiphaine Martin
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/coMET
Branch: RELEASE_3_6
Last Commit: 0162ac1
Last Changed Date: 2017-11-21 11:08:39 -0400 (Tue, 21 Nov 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: coMET
Version: 1.10.2
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings coMET_1.10.2.tar.gz
StartedAt: 2018-04-11 22:28:25 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 22:36:53 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 508.1 seconds
RetCode: 0
Status:  OK 
CheckDir: coMET.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings coMET_1.10.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/coMET.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.10.2’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘grid’ ‘biomaRt’ ‘Gviz’ ‘psych’ ‘ggbio’ ‘trackViewer’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 28.0Mb
  sub-directories of 1Mb or more:
    data      9.7Mb
    doc       7.1Mb
    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 loading without being on the library search path ... 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
chromHMM_RoadMap: no visible binding for global variable
  'chromosome_stop'
chromHMM_RoadMap: no visible binding for global variable
  'chromosome_start'
chromHMM_RoadMap: no visible binding for global variable
  'chromosome_name'
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 pos_middle_exon pos_snp snp_chrom
  snp_pos
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
comet.web     11.832  0.148  90.657
coMET-package  5.940  0.072  39.367
* 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/coMET.Rcheck/00check.log’
for details.



Installation output

coMET.Rcheck/00install.out

* installing *source* package ‘coMET’ ...
** R
** data
** inst
** preparing 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 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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, cbind, colMeans, colSums, colnames, 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

Loading required package: ggbio
Loading required package: ggplot2

Attaching package: 'ggplot2'

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

    %+%, alpha

Need specific help about ggbio? try mailing 
 the maintainer or visit http://tengfei.github.com/ggbio/

Attaching package: 'ggbio'

The following objects are masked from 'package:ggplot2':

    geom_bar, geom_rect, geom_segment, ggsave, stat_bin, stat_identity,
    xlim

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

    rescale

Loading required package: trackViewer
[1] TRUE
> BiocGenerics:::testPackage("coMET")


RUNIT TEST PROTOCOL -- Wed Apr 11 22:36:48 2018 
*********************************************** 
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 
 13.208   0.244  14.130 

Example timings

coMET.Rcheck/coMET-Ex.timings

nameusersystemelapsed
COSMIC_UCSC1.7720.0041.779
ChIPTF_ENCODE0.4600.0000.461
ClinVarCnv_UCSC0.7880.0000.791
ClinVarMain_UCSC0.3280.0000.330
CoreillCNV_UCSC0.3560.0000.358
DNAse_UCSC0.4280.0000.429
DNaseI_FANTOM0.6240.0040.630
DNaseI_RoadMap0.2840.0000.286
GAD_UCSC0.2960.0000.294
GWAScatalog_UCSC0.2440.0000.243
GeneReviews_UCSC0.5120.0000.513
HiCdata2matrix0.0280.0040.069
HistoneAll_UCSC3.0120.0003.015
HistoneOne_UCSC0.2760.0000.274
ISCA_UCSC0.0000.0000.001
TFBS_FANTOM0.2560.0040.258
bindingMotifsBiomart_ENSEMBL0.1960.0040.201
chrUCSC2ENSEMBL000
chromHMM_RoadMap0.8800.0000.886
chromatinHMMAll_UCSC3.4920.0003.496
chromatinHMMOne_UCSC0.6080.0040.610
coMET-package 5.940 0.07239.367
comet4.0400.0044.046
comet.list0.9160.0000.916
comet.web11.832 0.14890.657
cpgIslands_UCSC0.2080.0000.209
dgfootprints_RoadMap0.5880.0120.601
eQTL0.9760.0000.978
eQTL_GTEx1.0560.0001.057
gcContent_UCSC0.2920.0000.291
genesName_ENSEMBL0.0040.0000.004
genes_ENSEMBL0.660.000.66
imprintedGenes_GTEx3.1440.0123.424
interestGenes_ENSEMBL0.5480.0000.546
interestTranscript_ENSEMBL0.6600.0040.666
knownGenes_UCSC0.7840.0000.784
metQTL0.8960.0040.899
miRNATargetRegionsBiomart_ENSEMBL0.1120.0000.110
otherRegulatoryRegionsBiomart_ENSEMBL0.1320.0000.132
psiQTL_GTEx0.8680.0040.871
refGenes_UCSC0.7640.0000.765
regulationBiomart_ENSEMBL0.2520.0000.254
regulatoryEvidenceBiomart_ENSEMBL0.1920.0000.190
regulatoryFeaturesBiomart_ENSEMBL0.2160.0000.216
regulatorySegmentsBiomart_ENSEMBL0.2480.0040.252
repeatMasker_UCSC0.5320.0000.530
segmentalDups_UCSC0.3760.0000.375
snpBiomart_ENSEMBL0.4160.0000.416
snpLocations_UCSC1.0960.0001.101
structureBiomart_ENSEMBL0.4600.0000.465
transcript_ENSEMBL1.4000.0201.422
xenorefGenes_UCSC0.4840.0040.489