BioC 3.5: CHECK report for coMET on tokay2

Package: coMET

Version: 1.8.0

Command: rm -rf coMET.buildbin-libdir coMET.Rcheck && mkdir coMET.buildbin-libdir coMET.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=coMET.buildbin-libdir coMET_1.8.0.tar.gz >coMET.Rcheck\00install.out 2>&1 && cp coMET.Rcheck\00install.out coMET-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=coMET.buildbin-libdir --install="check:coMET-install.out" --force-multiarch --no-vignettes --timings coMET_1.8.0.tar.gz

StartedAt: 2017-08-15 22:52:51 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 23:16:19 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 1408.6 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-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=coMET.buildbin-libdir coMET_1.8.0.tar.gz >coMET.Rcheck\00install.out 2>&1 && cp coMET.Rcheck\00install.out coMET-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=coMET.buildbin-libdir --install="check:coMET-install.out" --force-multiarch --no-vignettes --timings coMET_1.8.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.5-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 '1.8.0'
* 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 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-3.5-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            19.21   0.59  353.97
coMET-package        11.55   1.06   36.25
chromatinHMMAll_UCSC  5.07   0.04    5.11
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
comet.web            19.54   0.48  354.11
coMET-package         8.89   0.31   33.26
chromatinHMMAll_UCSC  5.80   0.03    5.83
* 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-3.5-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_1.8.0.zip
* DONE (coMET)

name	user	system	elapsed
COSMIC_UCSC	3.05	0.14	3.19
ChIPTF_ENCODE	0.64	0.00	0.65
ClinVarCnv_UCSC	0.78	0.00	0.78
ClinVarMain_UCSC	0.33	0.01	0.35
CoreillCNV_UCSC	0.36	0.00	0.36
DNAse_UCSC	0.44	0.00	0.43
DNaseI_FANTOM	0.66	0.04	0.69
DNaseI_RoadMap	0.34	0.01	0.36
GAD_UCSC	0.31	0.00	0.31
GWAScatalog_UCSC	0.25	0.00	0.25
GeneReviews_UCSC	0.83	0.02	0.85
HiCdata2matrix	0.05	0.01	0.06
HistoneAll_UCSC	4.23	0.02	4.25
HistoneOne_UCSC	0.44	0.01	0.45
ISCA_UCSC	0	0	0
TFBS_FANTOM	0.39	0.00	0.39
bindingMotifsBiomart_ENSEMBL	0.30	0.03	0.33
chrUCSC2ENSEMBL	0	0	0
chromHMM_RoadMap	1.13	0.00	1.12
chromatinHMMAll_UCSC	5.07	0.04	5.11
chromatinHMMOne_UCSC	0.55	0.01	0.56
coMET-package	11.55	1.06	36.25
comet	4.51	0.05	4.57
comet.list	1.25	0.00	1.25
comet.web	19.21	0.59	353.97
cpgIslands_UCSC	0.22	0.00	0.21
dgfootprints_RoadMap	1.03	0.02	1.05
eQTL	1.26	0.00	1.27
eQTL_GTEx	1.52	0.00	1.51
gcContent_UCSC	0.42	0.05	0.47
genesName_ENSEMBL	0.00	0.01	0.02
genes_ENSEMBL	0.73	0.02	0.75
imprintedGenes_GTEx	4.16	0.03	4.50
interestGenes_ENSEMBL	0.53	0.02	0.54
interestTranscript_ENSEMBL	0.66	0.01	0.68
knownGenes_UCSC	0.83	0.00	0.83
metQTL	0.89	0.03	0.92
miRNATargetRegionsBiomart_ENSEMBL	0.10	0.02	0.11
otherRegulatoryRegionsBiomart_ENSEMBL	0.2	0.0	0.2
psiQTL_GTEx	1.06	0.01	1.08
refGenes_UCSC	0.85	0.00	0.85
regulationBiomart_ENSEMBL	0.4	0.0	0.4
regulatoryEvidenceBiomart_ENSEMBL	0.31	0.02	0.33
regulatoryFeaturesBiomart_ENSEMBL	0.32	0.01	0.33
regulatorySegmentsBiomart_ENSEMBL	0.33	0.02	0.34
repeatMasker_UCSC	0.59	0.00	0.60
segmentalDups_UCSC	0.39	0.00	0.39
snpBiomart_ENSEMBL	0.47	0.02	0.48
snpLocations_UCSC	1.15	0.01	1.17
structureBiomart_ENSEMBL	0.32	0.02	0.33
transcript_ENSEMBL	1.72	0.00	1.72
xenorefGenes_UCSC	0.71	0.01	0.73

name	user	system	elapsed
COSMIC_UCSC	3.20	0.08	3.30
ChIPTF_ENCODE	0.53	0.02	0.54
ClinVarCnv_UCSC	0.98	0.00	0.98
ClinVarMain_UCSC	0.33	0.00	0.33
CoreillCNV_UCSC	0.34	0.01	0.36
DNAse_UCSC	0.53	0.02	0.54
DNaseI_FANTOM	0.95	0.02	0.97
DNaseI_RoadMap	0.47	0.01	0.49
GAD_UCSC	0.38	0.02	0.39
GWAScatalog_UCSC	0.33	0.00	0.32
GeneReviews_UCSC	0.65	0.00	0.66
HiCdata2matrix	0.05	0.00	0.05
HistoneAll_UCSC	4.83	0.01	4.84
HistoneOne_UCSC	0.40	0.02	0.42
ISCA_UCSC	0	0	0
TFBS_FANTOM	0.3	0.0	0.3
bindingMotifsBiomart_ENSEMBL	0.23	0.01	0.25
chrUCSC2ENSEMBL	0	0	0
chromHMM_RoadMap	1.08	0.02	1.09
chromatinHMMAll_UCSC	5.80	0.03	5.83
chromatinHMMOne_UCSC	0.84	0.02	0.86
coMET-package	8.89	0.31	33.26
comet	4.64	0.08	4.72
comet.list	0.91	0.00	0.91
comet.web	19.54	0.48	354.11
cpgIslands_UCSC	0.19	0.02	0.20
dgfootprints_RoadMap	0.97	0.01	0.98
eQTL	1.21	0.00	1.22
eQTL_GTEx	1.33	0.02	1.34
gcContent_UCSC	0.41	0.03	0.44
genesName_ENSEMBL	0.00	0.01	0.02
genes_ENSEMBL	0.75	0.02	0.76
imprintedGenes_GTEx	4.08	0.03	4.47
interestGenes_ENSEMBL	0.54	0.00	0.55
interestTranscript_ENSEMBL	1.07	0.00	1.06
knownGenes_UCSC	1.48	0.02	1.50
metQTL	1.30	0.03	1.33
miRNATargetRegionsBiomart_ENSEMBL	0.08	0.00	0.08
otherRegulatoryRegionsBiomart_ENSEMBL	0.15	0.00	0.15
psiQTL_GTEx	0.89	0.03	0.92
refGenes_UCSC	0.96	0.02	0.97
regulationBiomart_ENSEMBL	0.34	0.00	0.35
regulatoryEvidenceBiomart_ENSEMBL	0.25	0.04	0.29
regulatoryFeaturesBiomart_ENSEMBL	0.26	0.00	0.27
regulatorySegmentsBiomart_ENSEMBL	0.21	0.03	0.23
repeatMasker_UCSC	0.56	0.00	0.57
segmentalDups_UCSC	0.36	0.00	0.36
snpBiomart_ENSEMBL	0.56	0.02	0.57
snpLocations_UCSC	1.27	0.01	1.28
structureBiomart_ENSEMBL	0.41	0.00	0.41
transcript_ENSEMBL	1.86	0.00	1.86
xenorefGenes_UCSC	0.58	0.00	0.57