BioC 3.6: CHECK report for coMET on tokay1

Package: coMET

Version: 1.9.0

Command: rm -rf coMET.buildbin-libdir coMET.Rcheck && mkdir coMET.buildbin-libdir coMET.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=coMET.buildbin-libdir coMET_1.9.0.tar.gz >coMET.Rcheck\00install.out 2>&1 && cp coMET.Rcheck\00install.out coMET-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=coMET.buildbin-libdir --install="check:coMET-install.out" --force-multiarch --no-vignettes --timings coMET_1.9.0.tar.gz

StartedAt: 2017-08-15 22:36:43 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 22:59:36 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 1373.1 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 && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=coMET.buildbin-libdir coMET_1.9.0.tar.gz >coMET.Rcheck\00install.out 2>&1 && cp coMET.Rcheck\00install.out coMET-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=coMET.buildbin-libdir --install="check:coMET-install.out" --force-multiarch --no-vignettes --timings coMET_1.9.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/coMET.Rcheck'
* using R version 3.4.1 (2017-06-30)
* 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 '1.9.0'
* 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 whether package 'coMET' can be installed ... WARNING
Found the following significant warnings:
  WARNING: omitting pointless dependence on 'R' without a version requirement
See 'C:/Users/biocbuild/bbs-3.6-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' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
comet.web     17.64   0.55  350.06
coMET-package 11.47   1.17   36.20
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
comet.web     16.93   0.22  349.33
coMET-package 12.87   1.35   37.18
comet          5.39   0.07    5.47
* 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, 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-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
No methods found in "RSQLite" for requests: dbGetQuery
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "RSQLite" for requests: dbGetQuery

install for x64

WARNING: omitting pointless dependence on 'R' without a version requirement
* installing *source* package 'coMET' ...
** testing if installed package can be loaded
No methods found in "RSQLite" for requests: dbGetQuery
* MD5 sums
packaged installation of 'coMET' as coMET_1.9.0.zip
* DONE (coMET)

name	user	system	elapsed
COSMIC_UCSC	2.28	0.13	2.40
ChIPTF_ENCODE	0.44	0.03	0.47
ClinVarCnv_UCSC	0.78	0.01	0.80
ClinVarMain_UCSC	0.30	0.02	0.31
CoreillCNV_UCSC	0.31	0.01	0.33
DNAse_UCSC	0.58	0.00	0.58
DNaseI_FANTOM	1.08	0.04	1.11
DNaseI_RoadMap	0.35	0.00	0.36
GAD_UCSC	0.35	0.00	0.34
GWAScatalog_UCSC	0.41	0.00	0.40
GeneReviews_UCSC	0.88	0.00	0.88
HiCdata2matrix	0.05	0.01	0.06
HistoneAll_UCSC	3.58	0.03	3.61
HistoneOne_UCSC	0.28	0.02	0.30
ISCA_UCSC	0	0	0
TFBS_FANTOM	0.30	0.00	0.29
bindingMotifsBiomart_ENSEMBL	0.20	0.01	0.22
chrUCSC2ENSEMBL	0	0	0
chromHMM_RoadMap	0.86	0.04	0.89
chromatinHMMAll_UCSC	4.47	0.01	4.49
chromatinHMMOne_UCSC	0.58	0.00	0.58
coMET-package	11.47	1.17	36.20
comet	4.29	0.03	4.33
comet.list	0.75	0.00	0.75
comet.web	17.64	0.55	350.06
cpgIslands_UCSC	0.14	0.00	0.15
dgfootprints_RoadMap	0.63	0.00	0.62
eQTL	0.78	0.02	0.80
eQTL_GTEx	0.89	0.00	0.89
gcContent_UCSC	0.34	0.01	0.36
genesName_ENSEMBL	0	0	0
genes_ENSEMBL	0.63	0.02	0.64
imprintedGenes_GTEx	3.14	0.01	3.48
interestGenes_ENSEMBL	0.54	0.02	0.56
interestTranscript_ENSEMBL	0.57	0.00	0.57
knownGenes_UCSC	0.72	0.00	0.72
metQTL	0.79	0.01	0.81
miRNATargetRegionsBiomart_ENSEMBL	0.11	0.00	0.11
otherRegulatoryRegionsBiomart_ENSEMBL	0.14	0.00	0.14
psiQTL_GTEx	0.88	0.00	0.87
refGenes_UCSC	0.72	0.00	0.72
regulationBiomart_ENSEMBL	0.23	0.00	0.23
regulatoryEvidenceBiomart_ENSEMBL	0.19	0.02	0.21
regulatoryFeaturesBiomart_ENSEMBL	0.2	0.0	0.2
regulatorySegmentsBiomart_ENSEMBL	0.20	0.00	0.21
repeatMasker_UCSC	0.41	0.00	0.40
segmentalDups_UCSC	0.29	0.00	0.30
snpBiomart_ENSEMBL	0.36	0.00	0.36
snpLocations_UCSC	0.8	0.0	0.8
structureBiomart_ENSEMBL	0.30	0.00	0.29
transcript_ENSEMBL	1.43	0.01	1.46
xenorefGenes_UCSC	0.43	0.02	0.43

name	user	system	elapsed
COSMIC_UCSC	3.61	0.06	3.67
ChIPTF_ENCODE	0.61	0.00	0.61
ClinVarCnv_UCSC	1.05	0.00	1.05
ClinVarMain_UCSC	0.60	0.00	0.59
CoreillCNV_UCSC	0.59	0.00	0.61
DNAse_UCSC	0.78	0.02	0.80
DNaseI_FANTOM	0.92	0.08	1.00
DNaseI_RoadMap	0.36	0.00	0.36
GAD_UCSC	0.61	0.01	0.62
GWAScatalog_UCSC	0.47	0.02	0.49
GeneReviews_UCSC	0.8	0.0	0.8
HiCdata2matrix	0.04	0.00	0.04
HistoneAll_UCSC	4.33	0.00	4.33
HistoneOne_UCSC	0.31	0.00	0.31
ISCA_UCSC	0	0	0
TFBS_FANTOM	0.32	0.01	0.33
bindingMotifsBiomart_ENSEMBL	0.20	0.02	0.22
chrUCSC2ENSEMBL	0	0	0
chromHMM_RoadMap	0.89	0.02	0.91
chromatinHMMAll_UCSC	4.02	0.00	4.03
chromatinHMMOne_UCSC	0.56	0.01	0.58
coMET-package	12.87	1.35	37.18
comet	5.39	0.07	5.47
comet.list	1.11	0.02	1.12
comet.web	16.93	0.22	349.33
cpgIslands_UCSC	0.15	0.00	0.15
dgfootprints_RoadMap	0.6	0.0	0.6
eQTL	0.89	0.03	0.92
eQTL_GTEx	1.09	0.01	1.11
gcContent_UCSC	0.42	0.00	0.42
genesName_ENSEMBL	0	0	0
genes_ENSEMBL	0.74	0.02	0.75
imprintedGenes_GTEx	3.83	0.00	4.20
interestGenes_ENSEMBL	0.57	0.00	0.58
interestTranscript_ENSEMBL	0.91	0.00	0.91
knownGenes_UCSC	1.11	0.02	1.12
metQTL	1.19	0.01	1.20
miRNATargetRegionsBiomart_ENSEMBL	0.08	0.00	0.08
otherRegulatoryRegionsBiomart_ENSEMBL	0.13	0.02	0.14
psiQTL_GTEx	0.98	0.00	0.98
refGenes_UCSC	0.86	0.01	0.88
regulationBiomart_ENSEMBL	0.28	0.02	0.30
regulatoryEvidenceBiomart_ENSEMBL	0.22	0.01	0.23
regulatoryFeaturesBiomart_ENSEMBL	0.23	0.02	0.25
regulatorySegmentsBiomart_ENSEMBL	0.24	0.00	0.23
repeatMasker_UCSC	0.48	0.00	0.49
segmentalDups_UCSC	0.41	0.00	0.40
snpBiomart_ENSEMBL	0.37	0.00	0.38
snpLocations_UCSC	0.91	0.02	0.92
structureBiomart_ENSEMBL	0.53	0.00	0.53
transcript_ENSEMBL	1.59	0.01	1.61
xenorefGenes_UCSC	0.52	0.00	0.51