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BioC 3.5: CHECK report for coMET on malbec2

This page was generated on 2017-10-18 14:16:30 -0400 (Wed, 18 Oct 2017).

Package 263/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
coMET 1.8.0
Tiphaine Martin
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/coMET
Branch: RELEASE_3_5
Last Commit: 04f4c5f
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: coMET
Version: 1.8.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings coMET_1.8.0.tar.gz
StartedAt: 2017-10-17 22:13:59 -0400 (Tue, 17 Oct 2017)
EndedAt: 2017-10-17 22:27:22 -0400 (Tue, 17 Oct 2017)
EllapsedTime: 803.0 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: coMET.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings coMET_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/coMET.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.8.0’
* 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 ... WARNING
Found the following significant warnings:
  WARNING: omitting pointless dependence on 'R' without a version requirement
See ‘/home/biocbuild/bbs-3.5-bioc/meat/coMET.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is 17.3Mb
  sub-directories of 1Mb or more:
    data      9.7Mb
    doc       2.6Mb
    extdata   4.5Mb
* 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 ... WARNING
  Error in if (dep$op != ">=") next : argument is of length zero
  Calls: <Anonymous>
  Execution halted
* 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     17.552  0.200 383.584
coMET-package  4.996  0.028  31.621
* 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: 2 WARNINGs, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/coMET.Rcheck/00check.log’
for details.


coMET.Rcheck/00install.out:

WARNING: omitting pointless dependence on 'R' without a version requirement
* 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)

coMET.Rcheck/coMET-Ex.timings:

nameusersystemelapsed
COSMIC_UCSC2.6520.0362.690
ChIPTF_ENCODE0.640.000.64
ClinVarCnv_UCSC0.8800.0120.889
ClinVarMain_UCSC0.4360.0000.439
CoreillCNV_UCSC0.5040.0000.504
DNAse_UCSC0.6920.0000.707
DNaseI_FANTOM0.8920.0120.907
DNaseI_RoadMap0.5280.0000.529
GAD_UCSC0.460.000.46
GWAScatalog_UCSC0.4080.0000.405
GeneReviews_UCSC0.7400.0040.743
HiCdata2matrix0.0360.0040.048
HistoneAll_UCSC3.8040.0003.806
HistoneOne_UCSC0.2800.0000.281
ISCA_UCSC0.0000.0000.001
TFBS_FANTOM0.2760.0000.275
bindingMotifsBiomart_ENSEMBL0.2400.0040.246
chrUCSC2ENSEMBL000
chromHMM_RoadMap0.8680.0040.876
chromatinHMMAll_UCSC3.4880.0003.490
chromatinHMMOne_UCSC0.5720.0000.572
coMET-package 4.996 0.02831.621
comet4.3560.0084.374
comet.list0.940.000.94
comet.web 17.552 0.200383.584
cpgIslands_UCSC0.1320.0000.131
dgfootprints_RoadMap0.5840.0000.586
eQTL0.8880.0040.894
eQTL_GTEx1.0400.0001.042
gcContent_UCSC0.2800.0000.283
genesName_ENSEMBL0.0000.0040.004
genes_ENSEMBL0.6320.0000.635
imprintedGenes_GTEx3.8080.0084.298
interestGenes_ENSEMBL0.7960.0040.798
interestTranscript_ENSEMBL0.8480.0000.850
knownGenes_UCSC0.8760.0000.879
metQTL1.0120.0041.018
miRNATargetRegionsBiomart_ENSEMBL0.1080.0000.108
otherRegulatoryRegionsBiomart_ENSEMBL0.1800.0000.182
psiQTL_GTEx0.9160.0000.915
refGenes_UCSC0.740.000.74
regulationBiomart_ENSEMBL0.2640.0000.266
regulatoryEvidenceBiomart_ENSEMBL0.2400.0040.242
regulatoryFeaturesBiomart_ENSEMBL0.2000.0000.199
regulatorySegmentsBiomart_ENSEMBL0.2360.0000.237
repeatMasker_UCSC0.4760.0000.474
segmentalDups_UCSC0.2720.0000.271
snpBiomart_ENSEMBL0.3480.0000.350
snpLocations_UCSC0.760.000.76
structureBiomart_ENSEMBL0.3000.0040.305
transcript_ENSEMBL1.5600.0001.563
xenorefGenes_UCSC0.6160.0000.618