BioC 3.5: CHECK report for coMET on oaxaca

Package: coMET

Version: 1.7.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings coMET_1.7.0.tar.gz

StartedAt: 2017-03-04 01:02:11 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 01:18:08 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 956.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: coMET.Rcheck

Warnings: 2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings coMET_1.7.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/coMET.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.7.0’
* 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 ‘/Users/biocbuild/bbs-3.5-bioc/meat/coMET.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is 17.2Mb
  sub-directories of 1Mb or more:
    data      9.7Mb
    doc       2.5Mb
    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 sizes of PDF files under ‘inst/doc’ ... 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     16.265  0.622 445.545
coMET-package  5.801  0.118  43.757
comet          5.391  0.033   5.427
* 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
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/coMET.Rcheck/00check.log’
for details.

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)

name	user	system	elapsed
COSMIC_UCSC	2.994	0.056	3.052
ChIPTF_ENCODE	0.639	0.004	0.642
ClinVarCnv_UCSC	1.014	0.003	1.019
ClinVarMain_UCSC	0.426	0.003	0.433
CoreillCNV_UCSC	0.397	0.002	0.400
DNAse_UCSC	0.562	0.003	0.573
DNaseI_FANTOM	0.898	0.011	0.912
DNaseI_RoadMap	0.437	0.007	0.444
GAD_UCSC	0.317	0.002	0.321
GWAScatalog_UCSC	0.320	0.002	0.323
GeneReviews_UCSC	0.637	0.004	0.641
HiCdata2matrix	0.031	0.004	0.041
HistoneAll_UCSC	4.594	0.012	4.610
HistoneOne_UCSC	0.326	0.003	0.330
ISCA_UCSC	0.001	0.000	0.001
TFBS_FANTOM	0.335	0.002	0.336
bindingMotifsBiomart_ENSEMBL	0.255	0.005	0.260
chrUCSC2ENSEMBL	0.000	0.000	0.001
chromHMM_RoadMap	0.972	0.005	0.979
chromatinHMMAll_UCSC	4.488	0.010	4.498
chromatinHMMOne_UCSC	0.776	0.004	0.781
coMET-package	5.801	0.118	43.757
comet	5.391	0.033	5.427
comet.list	1.424	0.007	1.431
comet.web	16.265	0.622	445.545
cpgIslands_UCSC	0.190	0.002	0.196
dgfootprints_RoadMap	0.668	0.016	0.729
eQTL	1.257	0.012	1.270
eQTL_GTEx	1.356	0.005	1.361
gcContent_UCSC	0.480	0.004	0.485
genesName_ENSEMBL	0.006	0.002	0.007
genes_ENSEMBL	0.850	0.009	0.858
imprintedGenes_GTEx	4.248	0.030	4.752
interestGenes_ENSEMBL	0.655	0.008	0.664
interestTranscript_ENSEMBL	0.737	0.010	0.746
knownGenes_UCSC	0.956	0.002	0.960
metQTL	1.098	0.007	1.106
miRNATargetRegionsBiomart_ENSEMBL	0.096	0.002	0.098
otherRegulatoryRegionsBiomart_ENSEMBL	0.168	0.009	0.178
psiQTL_GTEx	1.034	0.004	1.038
refGenes_UCSC	0.876	0.002	0.879
regulationBiomart_ENSEMBL	0.250	0.001	0.257
regulatoryEvidenceBiomart_ENSEMBL	0.240	0.004	0.245
regulatoryFeaturesBiomart_ENSEMBL	0.228	0.005	0.234
regulatorySegmentsBiomart_ENSEMBL	0.290	0.006	0.296
repeatMasker_UCSC	0.572	0.003	0.575
segmentalDups_UCSC	0.443	0.002	0.446
snpBiomart_ENSEMBL	0.517	0.002	0.525
snpLocations_UCSC	1.114	0.003	1.118
structureBiomart_ENSEMBL	0.425	0.001	0.427
transcript_ENSEMBL	1.693	0.008	1.701
xenorefGenes_UCSC	0.538	0.002	0.540