BioC 3.5: CHECK report for coMET on toluca2

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: 2017-04-23 02:11:17 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 02:25:57 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 880.7 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 r72187)
* 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       2.6Mb
    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 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            19.613  0.469 353.152
coMET-package         6.587  0.096  29.181
comet                 6.257  0.054   6.399
chromatinHMMAll_UCSC  5.063  0.013   5.168
imprintedGenes_GTEx   4.748  0.034   7.384
* 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	3.448	0.068	3.532
ChIPTF_ENCODE	0.803	0.006	0.813
ClinVarCnv_UCSC	1.282	0.005	1.288
ClinVarMain_UCSC	0.473	0.002	0.477
CoreillCNV_UCSC	0.443	0.004	0.464
DNAse_UCSC	0.606	0.003	0.612
DNaseI_FANTOM	0.951	0.014	0.975
DNaseI_RoadMap	0.407	0.009	0.422
GAD_UCSC	0.449	0.003	0.459
GWAScatalog_UCSC	0.369	0.002	0.377
GeneReviews_UCSC	0.825	0.004	0.844
HiCdata2matrix	0.031	0.003	0.034
HistoneAll_UCSC	4.765	0.019	4.815
HistoneOne_UCSC	0.371	0.003	0.376
ISCA_UCSC	0.001	0.000	0.001
TFBS_FANTOM	0.385	0.003	0.389
bindingMotifsBiomart_ENSEMBL	0.242	0.005	0.251
chrUCSC2ENSEMBL	0.000	0.000	0.001
chromHMM_RoadMap	1.046	0.007	1.063
chromatinHMMAll_UCSC	5.063	0.013	5.168
chromatinHMMOne_UCSC	0.813	0.004	0.832
coMET-package	6.587	0.096	29.181
comet	6.257	0.054	6.399
comet.list	1.461	0.011	1.483
comet.web	19.613	0.469	353.152
cpgIslands_UCSC	0.174	0.003	0.182
dgfootprints_RoadMap	0.703	0.022	0.728
eQTL	1.258	0.009	1.284
eQTL_GTEx	1.520	0.006	1.540
gcContent_UCSC	0.628	0.005	0.638
genesName_ENSEMBL	0.005	0.001	0.006
genes_ENSEMBL	0.971	0.009	0.994
imprintedGenes_GTEx	4.748	0.034	7.384
interestGenes_ENSEMBL	0.698	0.008	0.710
interestTranscript_ENSEMBL	0.894	0.010	0.907
knownGenes_UCSC	1.161	0.005	1.184
metQTL	1.207	0.007	1.241
miRNATargetRegionsBiomart_ENSEMBL	0.091	0.002	0.093
otherRegulatoryRegionsBiomart_ENSEMBL	0.179	0.009	0.194
psiQTL_GTEx	1.162	0.005	1.187
refGenes_UCSC	1.046	0.003	1.050
regulationBiomart_ENSEMBL	0.338	0.003	0.341
regulatoryEvidenceBiomart_ENSEMBL	0.294	0.005	0.302
regulatoryFeaturesBiomart_ENSEMBL	0.252	0.006	0.261
regulatorySegmentsBiomart_ENSEMBL	0.243	0.005	0.252
repeatMasker_UCSC	0.572	0.003	0.575
segmentalDups_UCSC	0.412	0.002	0.418
snpBiomart_ENSEMBL	0.490	0.003	0.495
snpLocations_UCSC	1.055	0.005	1.062
structureBiomart_ENSEMBL	0.427	0.002	0.430
transcript_ENSEMBL	2.284	0.013	2.306
xenorefGenes_UCSC	0.669	0.003	0.682