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CHECK report for coMET on malbec1

This page was generated on 2019-04-16 11:51:02 -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: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:coMET.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings coMET_1.14.0.tar.gz
StartedAt: 2019-04-15 23:05:11 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 23:13:03 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 471.1 seconds
RetCode: 0
Status:  OK 
CheckDir: coMET.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:coMET.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings coMET_1.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/coMET.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.14.0’
* 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 18.9Mb
  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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
comet.web           6.048  0.012  56.826
imprintedGenes_GTEx 4.708  0.008   5.239
coMET-package       4.320  0.020  17.676
* 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-3.8-bioc/meat/coMET.Rcheck/00check.log’
for details.



Installation output

coMET.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL coMET
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/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-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, 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 23:12:57 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 
 15.932   0.440  16.419 

Example timings

coMET.Rcheck/coMET-Ex.timings

nameusersystemelapsed
COSMIC_UCSC2.0360.0522.107
ChIPTF_ENCODE0.9240.0240.957
ClinVarCnv_UCSC0.5360.0080.560
ClinVarMain_UCSC0.5440.0000.542
CoreillCNV_UCSC0.5040.0000.520
DNAse_UCSC0.4320.0040.436
DNaseI_FANTOM0.6520.0040.657
DNaseI_RoadMap0.3040.0000.317
GAD_UCSC0.5200.0000.536
GWAScatalog_UCSC0.3280.0000.327
GeneReviews_UCSC0.8000.0000.801
HiCdata2matrix0.0400.0000.053
HistoneAll_UCSC4.5840.0044.604
HistoneOne_UCSC0.5120.0000.515
ISCA_UCSC0.5720.0000.572
TFBS_FANTOM0.4760.0000.487
bindingMotifsBiomart_ENSEMBL0.2960.0000.297
chrUCSC2ENSEMBL000
chromHMM_RoadMap0.8840.0080.893
chromatinHMMAll_UCSC4.7280.0004.732
chromatinHMMOne_UCSC0.7600.0040.764
coMET-package 4.320 0.02017.676
comet3.2080.0123.233
comet.list1.1280.0041.137
comet.web 6.048 0.01256.826
cpgIslands_UCSC0.2200.0000.225
dgfootprints_RoadMap0.7680.0160.784
eQTL1.2560.0001.259
eQTL_GTEx1.2320.0001.231
gcContent_UCSC1.4160.0001.434
genesName_ENSEMBL0.0040.0000.004
genes_ENSEMBL0.8000.0080.805
imprintedGenes_GTEx4.7080.0085.239
interestGenes_ENSEMBL0.7560.0040.772
interestTranscript_ENSEMBL1.2080.0001.209
knownGenes_UCSC1.0080.0001.007
metQTL1.2840.0001.401
miRNATargetRegionsBiomart_ENSEMBL0.0760.0000.074
otherRegulatoryRegionsBiomart_ENSEMBL0.2080.0000.207
psiQTL_GTEx1.4440.0041.530
refGenes_UCSC0.8600.0040.862
regulationBiomart_ENSEMBL0.4280.0000.449
regulatoryEvidenceBiomart_ENSEMBL0.3120.0080.338
regulatoryFeaturesBiomart_ENSEMBL0.3120.0000.338
regulatorySegmentsBiomart_ENSEMBL0.3240.0040.330
repeatMasker_UCSC0.7720.0000.772
segmentalDups_UCSC0.4080.0000.457
snpBiomart_ENSEMBL0.4080.0000.410
snpLocations_UCSC1.0960.0041.117
structureBiomart_ENSEMBL0.4280.0000.429
transcript_ENSEMBL1.5560.0041.563
xenorefGenes_UCSC0.9120.0000.913