BioC 3.2: CHECK report for coMET on oaxaca

Package: coMET

Version: 1.2.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings coMET_1.2.1.tar.gz

StartedAt: 2016-04-22 23:03:04 -0700 (Fri, 22 Apr 2016)

EndedAt: 2016-04-22 23:18:56 -0700 (Fri, 22 Apr 2016)

EllapsedTime: 952.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: coMET.Rcheck

Warnings: 1

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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_1.2.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/coMET.Rcheck’
* using R version 3.2.4 (2016-03-10)
* 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 ‘1.2.1’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ... [35s/41s] OK
* checking installed package size ... NOTE
  installed size is 118.5Mb
  sub-directories of 1Mb or more:
    data     16.0Mb
    doc      41.3Mb
    extdata  60.7Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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’
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’
* 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
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                                        old_size new_size compress
  DNaseI_RoadMapSingle.rda                 240Kb    154Kb       xz
  OtherRegulatoryRegionsAll.rda             12Kb      8Kb       xz
  PancreasIG.rda                            99Kb     76Kb       xz
  PancreasIGtrack.rda                       99Kb     76Kb       xz
  RegulatoryEvidenceBiomartAll.rda          19Kb     13Kb       xz
  RegulatoryEvidenceBiomartMultiple.rda     10Kb      9Kb    bzip2
  allIG.rda                                 99Kb     76Kb       xz
  allIGtrack.rda                            99Kb     76Kb       xz
  allimprintedIG.rda                        99Kb     76Kb       xz
  allimprintedIGtrack.rda                   99Kb     76Kb       xz
  dgfootprints_RoadMapSingle.rda           1.2Mb    110Kb       xz
  dyaRM.rda                                213Kb    132Kb       xz
  enhFANTOMtrack.rda                       567Kb    355Kb       xz
  enhRM.rda                                2.2Mb    1.2Mb       xz
  enhRMtrack.rda                           2.2Mb    1.2Mb       xz
  gcContent.rda                             11Kb      6Kb    bzip2
  gctrack.rda                               11Kb      7Kb    bzip2
  geneENSEMBLtrack.rda                     104Kb     79Kb       xz
  genesENSEMBL.rda                         112Kb     85Kb       xz
  genesGencodetrack.rda                    3.4Mb    2.2Mb       xz
  genetrack4RM.rda                         100Kb     76Kb       xz
  genetrack4psiGTEX.rda                    100Kb     76Kb       xz
  grtrack4eGTex.rda                        3.4Mb    2.2Mb       xz
  imprintedGenesGTEx.rda                    12Kb      9Kb       xz
  interestGenesENSEMBL.rda                 112Kb     85Kb       xz
  interestTranscriptENSEMBL.rda            114Kb     86Kb       xz
  interestgenesENSMBLtrack.rda              98Kb     75Kb       xz
  interesttransENSMBLtrack.rda              98Kb     75Kb       xz
  otherRegulatoryRegionsTrackAll.rda        12Kb      8Kb       xz
  promRMtrack.rda                          312Kb    196Kb       xz
  promRMtrackE063.rda                      240Kb    154Kb       xz
  transENSMBLtrack.rda                     113Kb     84Kb       xz
* checking sizes of PDF files under ‘inst/doc’ ... OK
* 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 ... [94s/436s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
comet.web            16.908  0.380 338.605
chromatinHMMAll_UCSC  6.344  0.016   6.388
coMET-package         5.560  0.101  24.424
HistoneAll_UCSC       5.162  0.015   5.190
imprintedGenes_GTEx   4.560  0.015   6.149
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [16s/16s]
 [16s/16s] 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: 1 WARNING, 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/coMET.Rcheck/00check.log’
for details.

* installing *source* package ‘coMET’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘ggplot2::Position’ by ‘BiocGenerics::Position’ when loading ‘ggbio’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘ggplot2::Position’ by ‘BiocGenerics::Position’ when loading ‘ggbio’
* DONE (coMET)

name	user	system	elapsed
COSMIC_UCSC	0.981	0.010	0.993
ChIPTF_ENCODE	0.129	0.002	0.131
ClinVarCnv_UCSC	0.544	0.002	0.552
ClinVarMain_UCSC	0.636	0.004	0.658
CoreillCNV_UCSC	0.597	0.003	0.602
DNAse_UCSC	1.287	0.004	1.294
DNaseI_FANTOM	0.547	0.016	0.564
DNaseI_RoadMap	0.512	0.041	0.558
GAD_UCSC	0.572	0.004	0.582
GWAScatalog_UCSC	0.487	0.004	0.516
GeneReviews_UCSC	0.935	0.004	1.059
HiCdata2matrix	0.043	0.004	0.046
HistoneAll_UCSC	5.162	0.015	5.190
HistoneOne_UCSC	0.488	0.003	0.521
ISCA_UCSC	0.001	0.000	0.001
TFBS_FANTOM	0.463	0.003	0.586
bindingMotifsBiomart_ENSEMBL	0.318	0.006	0.330
chrUCSC2ENSEMBL	0.001	0.000	0.001
chromHMM_RoadMap	1.364	0.008	1.376
chromatinHMMAll_UCSC	6.344	0.016	6.388
chromatinHMMOne_UCSC	0.977	0.005	0.984
coMET-package	5.560	0.101	24.424
comet	3.959	0.040	4.015
comet.list	1.603	0.016	1.622
comet.web	16.908	0.380	338.605
cpgIslands_UCSC	0.191	0.003	0.194
dgfootprints_RoadMap	0.933	0.019	0.953
eQTL	1.882	0.012	1.897
eQTL_GTEx	1.687	0.006	1.697
gcContent_UCSC	0.298	0.002	0.301
genesName_ENSEMBL	0.006	0.001	0.007
genes_ENSEMBL	0.944	0.004	0.948
imprintedGenes_GTEx	4.560	0.015	6.149
interestGenes_ENSEMBL	0.769	0.003	0.776
interestTranscript_ENSEMBL	0.777	0.004	0.873
knownGenes_UCSC	1.292	0.004	1.303
metQTL	1.264	0.006	1.272
miRNATargetRegionsBiomart_ENSEMBL	0.109	0.002	0.112
otherRegulatoryRegionsBiomart_ENSEMBL	0.227	0.004	0.231
psiQTL_GTEx	1.512	0.017	1.531
refGenes_UCSC	1.305	0.005	1.310
regulationBiomart_ENSEMBL	0.391	0.002	0.395
regulatoryEvidenceBiomart_ENSEMBL	0.278	0.004	0.296
regulatoryFeaturesBiomart_ENSEMBL	0.334	0.006	0.342
regulatorySegmentsBiomart_ENSEMBL	0.336	0.005	0.345
repeatMasker_UCSC	0.758	0.002	0.775
segmentalDups_UCSC	0.555	0.002	0.561
snpBiomart_ENSEMBL	0.587	0.003	0.590
snpLocations_UCSC	1.380	0.002	1.384
structureBiomart_ENSEMBL	0.468	0.002	0.497
transcript_ENSEMBL	2.453	0.009	2.611
xenorefGenes_UCSC	0.729	0.004	0.733