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: 2017-10-17 22:56:02 -0400 (Tue, 17 Oct 2017)

EndedAt: 2017-10-17 23:20:14 -0400 (Tue, 17 Oct 2017)

EllapsedTime: 1452.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: coMET.Rcheck

Warnings: 2

##############################################################################
##############################################################################
###
### Running 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
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/coMET.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* 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     18.05   0.72  383.81
coMET-package  7.27   0.45   32.18
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
comet.web     18.55   0.63  391.73
coMET-package  8.22   0.40   34.62
comet          4.80   0.08    5.36
* 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
** 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_1.8.0.zip
* DONE (coMET)

name	user	system	elapsed
COSMIC_UCSC	2.38	0.06	2.44
ChIPTF_ENCODE	0.45	0.05	0.50
ClinVarCnv_UCSC	0.8	0.0	0.8
ClinVarMain_UCSC	0.34	0.00	0.34
CoreillCNV_UCSC	0.29	0.00	0.28
DNAse_UCSC	1.11	0.00	1.11
DNaseI_FANTOM	0.64	0.00	0.64
DNaseI_RoadMap	0.41	0.00	0.40
GAD_UCSC	0.28	0.00	0.28
GWAScatalog_UCSC	0.26	0.00	0.27
GeneReviews_UCSC	0.55	0.00	0.55
HiCdata2matrix	0.03	0.01	0.04
HistoneAll_UCSC	3.00	0.02	3.01
HistoneOne_UCSC	0.33	0.01	0.35
ISCA_UCSC	0	0	0
TFBS_FANTOM	0.28	0.00	0.28
bindingMotifsBiomart_ENSEMBL	0.22	0.03	0.25
chrUCSC2ENSEMBL	0	0	0
chromHMM_RoadMap	0.81	0.02	0.83
chromatinHMMAll_UCSC	3.67	0.03	3.70
chromatinHMMOne_UCSC	0.63	0.02	0.64
coMET-package	7.27	0.45	32.18
comet	3.40	0.06	3.47
comet.list	0.72	0.00	0.72
comet.web	18.05	0.72	383.81
cpgIslands_UCSC	0.14	0.00	0.15
dgfootprints_RoadMap	0.69	0.06	0.75
eQTL	1	0	1
eQTL_GTEx	0.98	0.00	0.98
gcContent_UCSC	0.36	0.02	0.37
genesName_ENSEMBL	0.00	0.02	0.02
genes_ENSEMBL	0.63	0.01	0.64
imprintedGenes_GTEx	3.11	0.03	3.56
interestGenes_ENSEMBL	0.45	0.02	0.47
interestTranscript_ENSEMBL	0.64	0.01	0.66
knownGenes_UCSC	0.81	0.00	0.81
metQTL	0.74	0.00	0.74
miRNATargetRegionsBiomart_ENSEMBL	0.07	0.00	0.07
otherRegulatoryRegionsBiomart_ENSEMBL	0.13	0.00	0.13
psiQTL_GTEx	0.78	0.02	0.80
refGenes_UCSC	0.70	0.01	0.71
regulationBiomart_ENSEMBL	0.24	0.00	0.24
regulatoryEvidenceBiomart_ENSEMBL	0.2	0.0	0.2
regulatoryFeaturesBiomart_ENSEMBL	0.17	0.02	0.18
regulatorySegmentsBiomart_ENSEMBL	0.19	0.05	0.24
repeatMasker_UCSC	0.43	0.00	0.44
segmentalDups_UCSC	0.30	0.00	0.29
snpBiomart_ENSEMBL	0.33	0.00	0.33
snpLocations_UCSC	0.80	0.01	0.81
structureBiomart_ENSEMBL	0.39	0.02	0.41
transcript_ENSEMBL	1.46	0.01	1.48
xenorefGenes_UCSC	0.43	0.02	0.44

name	user	system	elapsed
COSMIC_UCSC	2.64	0.04	2.67
ChIPTF_ENCODE	0.63	0.01	0.64
ClinVarCnv_UCSC	0.96	0.02	0.97
ClinVarMain_UCSC	0.39	0.01	0.40
CoreillCNV_UCSC	0.33	0.02	0.35
DNAse_UCSC	0.43	0.01	0.45
DNaseI_FANTOM	0.71	0.00	0.70
DNaseI_RoadMap	0.32	0.00	0.33
GAD_UCSC	0.36	0.02	0.38
GWAScatalog_UCSC	0.27	0.00	0.26
GeneReviews_UCSC	0.59	0.00	0.59
HiCdata2matrix	0.05	0.00	0.05
HistoneAll_UCSC	3.36	0.00	3.36
HistoneOne_UCSC	0.34	0.00	0.34
ISCA_UCSC	0.02	0.00	0.02
TFBS_FANTOM	0.28	0.00	0.28
bindingMotifsBiomart_ENSEMBL	0.20	0.02	0.22
chrUCSC2ENSEMBL	0	0	0
chromHMM_RoadMap	0.82	0.00	0.81
chromatinHMMAll_UCSC	3.69	0.01	3.70
chromatinHMMOne_UCSC	0.67	0.02	0.69
coMET-package	8.22	0.40	34.62
comet	4.80	0.08	5.36
comet.list	1.40	0.00	1.41
comet.web	18.55	0.63	391.73
cpgIslands_UCSC	0.25	0.00	0.25
dgfootprints_RoadMap	0.72	0.01	0.74
eQTL	1.06	0.02	1.08
eQTL_GTEx	1.16	0.00	1.15
gcContent_UCSC	0.51	0.00	0.52
genesName_ENSEMBL	0.02	0.00	0.01
genes_ENSEMBL	0.80	0.01	0.82
imprintedGenes_GTEx	3.81	0.05	4.22
interestGenes_ENSEMBL	0.53	0.00	0.53
interestTranscript_ENSEMBL	0.72	0.02	0.73
knownGenes_UCSC	0.86	0.00	0.86
metQTL	0.89	0.01	0.91
miRNATargetRegionsBiomart_ENSEMBL	0.04	0.02	0.06
otherRegulatoryRegionsBiomart_ENSEMBL	0.13	0.01	0.15
psiQTL_GTEx	0.81	0.02	0.82
refGenes_UCSC	0.73	0.01	0.75
regulationBiomart_ENSEMBL	0.25	0.00	0.25
regulatoryEvidenceBiomart_ENSEMBL	0.37	0.02	0.39
regulatoryFeaturesBiomart_ENSEMBL	0.27	0.01	0.28
regulatorySegmentsBiomart_ENSEMBL	0.33	0.04	0.36
repeatMasker_UCSC	0.7	0.0	0.7
segmentalDups_UCSC	0.34	0.01	0.36
snpBiomart_ENSEMBL	0.39	0.00	0.39
snpLocations_UCSC	0.89	0.02	0.91
structureBiomart_ENSEMBL	0.35	0.01	0.36
transcript_ENSEMBL	1.59	0.02	1.61
xenorefGenes_UCSC	0.49	0.00	0.48