BioC 3.4: CHECK report for coMET on moscato1

Package: coMET

Version: 1.5.7

Command: rm -rf coMET.buildbin-libdir coMET.Rcheck && mkdir coMET.buildbin-libdir coMET.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=coMET.buildbin-libdir coMET_1.5.7.tar.gz >coMET.Rcheck\00install.out 2>&1 && cp coMET.Rcheck\00install.out coMET-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=coMET.buildbin-libdir --install="check:coMET-install.out" --force-multiarch --no-vignettes --timings coMET_1.5.7.tar.gz

StartedAt: 2016-09-20 06:16:29 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 06:38:36 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 1326.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: coMET.Rcheck

Warnings: 2

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### Running command:
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###   rm -rf coMET.buildbin-libdir coMET.Rcheck && mkdir coMET.buildbin-libdir coMET.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=coMET.buildbin-libdir coMET_1.5.7.tar.gz >coMET.Rcheck\00install.out 2>&1 && cp coMET.Rcheck\00install.out coMET-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=coMET.buildbin-libdir --install="check:coMET-install.out" --force-multiarch --no-vignettes --timings coMET_1.5.7.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/coMET.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'coMET/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'coMET' version '1.5.7'
* 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 whether package 'coMET' can be installed ... WARNING
Found the following significant warnings:
  WARNING: omitting pointless dependence on 'R' without a version requirement
See 'D:/biocbld/bbs-3.4-bioc/meat/coMET.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is 17.4Mb
  sub-directories of 1Mb or more:
    data      9.8Mb
    doc       2.7Mb
    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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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' ... NOTE
The following directory looks like a leftover from 'knitr':
  'figure'
Please remove from your package.
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
comet.web     13.79   0.22  344.79
coMET-package  5.27   0.15   26.13
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
comet.web     16.58   0.19  340.67
coMET-package 10.56   0.67   32.26
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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, 5 NOTEs
See
  'D:/biocbld/bbs-3.4-bioc/meat/coMET.Rcheck/00check.log'
for details.

install for i386

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

install for x64

WARNING: omitting pointless dependence on 'R' without a version requirement
* installing *source* package 'coMET' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'coMET' as coMET_1.5.7.zip
* DONE (coMET)

name	user	system	elapsed
COSMIC_UCSC	0.70	0.01	0.72
ChIPTF_ENCODE	0.08	0.00	0.08
ClinVarCnv_UCSC	0.65	0.02	0.67
ClinVarMain_UCSC	0.41	0.00	0.40
CoreillCNV_UCSC	0.36	0.00	0.36
DNAse_UCSC	0.40	0.03	0.44
DNaseI_FANTOM	0.83	0.02	0.84
DNaseI_RoadMap	0.36	0.00	0.36
GAD_UCSC	0.35	0.00	0.35
GWAScatalog_UCSC	0.28	0.00	0.28
GeneReviews_UCSC	0.54	0.00	0.54
HiCdata2matrix	0.02	0.01	0.04
HistoneAll_UCSC	3.38	0.00	3.39
HistoneOne_UCSC	0.33	0.03	0.36
ISCA_UCSC	0	0	0
TFBS_FANTOM	0.31	0.00	0.31
bindingMotifsBiomart_ENSEMBL	0.26	0.00	0.27
chrUCSC2ENSEMBL	0	0	0
chromHMM_RoadMap	0.89	0.02	0.90
chromatinHMMAll_UCSC	3.84	0.03	3.95
chromatinHMMOne_UCSC	0.53	0.00	0.53
coMET-package	5.27	0.15	26.13
comet	2.57	0.03	2.60
comet.list	1.10	0.02	1.11
comet.web	13.79	0.22	344.79
cpgIslands_UCSC	0.15	0.00	0.16
dgfootprints_RoadMap	0.83	0.00	0.83
eQTL	1.00	0.01	1.13
eQTL_GTEx	1.22	0.00	1.22
gcContent_UCSC	0.28	0.00	0.28
genesName_ENSEMBL	0.00	0.02	0.02
genes_ENSEMBL	0.89	0.00	0.89
imprintedGenes_GTEx	3.44	0.01	4.15
interestGenes_ENSEMBL	0.58	0.00	0.57
interestTranscript_ENSEMBL	0.75	0.03	0.78
knownGenes_UCSC	1.03	0.02	1.05
metQTL	1.28	0.03	1.31
miRNATargetRegionsBiomart_ENSEMBL	0.08	0.00	0.08
otherRegulatoryRegionsBiomart_ENSEMBL	0.15	0.03	0.18
psiQTL_GTEx	0.94	0.02	0.96
refGenes_UCSC	0.92	0.00	0.92
regulationBiomart_ENSEMBL	0.29	0.01	0.31
regulatoryEvidenceBiomart_ENSEMBL	0.29	0.00	0.28
regulatoryFeaturesBiomart_ENSEMBL	0.25	0.00	0.73
regulatorySegmentsBiomart_ENSEMBL	0.23	0.02	0.25
repeatMasker_UCSC	0.51	0.01	0.53
segmentalDups_UCSC	0.35	0.02	0.36
snpBiomart_ENSEMBL	0.43	0.00	0.44
snpLocations_UCSC	1.03	0.00	1.03
structureBiomart_ENSEMBL	0.39	0.00	0.39
transcript_ENSEMBL	1.94	0.00	1.93
xenorefGenes_UCSC	0.52	0.00	0.51

name	user	system	elapsed
COSMIC_UCSC	0.83	0.01	0.84
ChIPTF_ENCODE	0.56	0.02	0.58
ClinVarCnv_UCSC	0.39	0.02	0.41
ClinVarMain_UCSC	0.45	0.00	0.45
CoreillCNV_UCSC	0.45	0.00	0.70
DNAse_UCSC	0.61	0.00	0.61
DNaseI_FANTOM	1.14	0.00	1.14
DNaseI_RoadMap	0.42	0.01	0.44
GAD_UCSC	0.42	0.02	0.44
GWAScatalog_UCSC	0.34	0.00	0.34
GeneReviews_UCSC	0.66	0.00	0.65
HiCdata2matrix	0.03	0.00	0.03
HistoneAll_UCSC	3.76	0.01	3.78
HistoneOne_UCSC	0.36	0.00	0.36
ISCA_UCSC	0	0	0
TFBS_FANTOM	0.36	0.00	0.36
bindingMotifsBiomart_ENSEMBL	0.28	0.02	0.29
chrUCSC2ENSEMBL	0	0	0
chromHMM_RoadMap	1.06	0.01	1.08
chromatinHMMAll_UCSC	4.62	0.05	4.66
chromatinHMMOne_UCSC	0.7	0.0	0.7
coMET-package	10.56	0.67	32.26
comet	3.34	0.03	3.37
comet.list	1.33	0.00	1.33
comet.web	16.58	0.19	340.67
cpgIslands_UCSC	0.19	0.00	0.19
dgfootprints_RoadMap	0.92	0.03	0.95
eQTL	1.54	0.02	1.56
eQTL_GTEx	2.29	0.03	2.33
gcContent_UCSC	0.32	0.03	0.34
genesName_ENSEMBL	0.01	0.00	0.02
genes_ENSEMBL	1.03	0.00	1.03
imprintedGenes_GTEx	4.43	0.03	4.93
interestGenes_ENSEMBL	0.7	0.0	0.7
interestTranscript_ENSEMBL	1	0	1
knownGenes_UCSC	1.25	0.02	1.27
metQTL	1.27	0.01	1.29
miRNATargetRegionsBiomart_ENSEMBL	0.10	0.02	0.11
otherRegulatoryRegionsBiomart_ENSEMBL	0.20	0.01	0.22
psiQTL_GTEx	1.23	0.00	1.23
refGenes_UCSC	1.25	0.00	1.25
regulationBiomart_ENSEMBL	0.36	0.00	0.36
regulatoryEvidenceBiomart_ENSEMBL	0.28	0.02	0.30
regulatoryFeaturesBiomart_ENSEMBL	0.32	0.01	0.34
regulatorySegmentsBiomart_ENSEMBL	0.33	0.00	0.33
repeatMasker_UCSC	0.67	0.00	0.67
segmentalDups_UCSC	0.47	0.00	0.47
snpBiomart_ENSEMBL	0.55	0.00	0.54
snpLocations_UCSC	1.34	0.02	1.36
structureBiomart_ENSEMBL	0.5	0.0	0.5
transcript_ENSEMBL	2.35	0.02	2.37
xenorefGenes_UCSC	0.7	0.0	0.7