BioC 3.3: CHECK report for customProDB on linux2.bioconductor.org

Package: customProDB

Version: 1.11.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings customProDB_1.11.0.tar.gz

StartedAt: 2015-10-27 03:07:04 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 03:16:09 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 544.6 seconds

RetCode: 0

Status:  OK

CheckDir: customProDB.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings customProDB_1.11.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/customProDB.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘customProDB/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘customProDB’ version ‘1.11.0’
* 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 ‘customProDB’ can be installed ... [15s/15s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘IRanges’ ‘biomaRt’ ‘AnnotationDbi’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* 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 dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘biomaRt:::martBM’ ‘biomaRt:::martDataset’ ‘biomaRt:::martHost’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.parseBMMartParams: no visible global function definition for
  ‘isSingleString’
Bed2Range: no visible binding for global variable ‘V5’
InputVcf: no visible global function definition for ‘DataFrame’
InputVcf: no visible binding for global variable ‘DataFrame’
InputVcf : <anonymous>: no visible global function definition for
  ‘DataFrame’
OutputNovelJun: no visible binding for global variable ‘jun_type’
OutputVarproseq: no visible binding for global variable ‘genename’
OutputVarproseq: no visible binding for global variable ‘txname’
OutputVarproseq: no visible binding for global variable ‘proname’
OutputVarproseq: no visible binding for global variable ‘aaref’
OutputVarproseq: no visible binding for global variable ‘aapos’
OutputVarproseq: no visible binding for global variable ‘aavar’
OutputVarproseq: no visible binding for global variable ‘rsid’
OutputVarproseq_single: no visible binding for global variable
  ‘genename’
OutputVarproseq_single: no visible binding for global variable ‘txname’
OutputVarproseq_single: no visible binding for global variable
  ‘proname’
OutputVarproseq_single: no visible binding for global variable ‘aaref’
OutputVarproseq_single: no visible binding for global variable ‘aapos’
OutputVarproseq_single: no visible binding for global variable ‘aavar’
OutputVarproseq_single: no visible binding for global variable ‘rsid’
Outputaberrant: no visible binding for global variable ‘pro_name’
Positionincoding: no visible binding for global variable ‘cds_start’
Positionincoding: no visible binding for global variable ‘cds_end’
PrepareAnnotationEnsembl: no visible binding for global variable
  ‘ensembl_gene_id’
PrepareAnnotationEnsembl: no visible binding for global variable
  ‘pro_name’
PrepareAnnotationEnsembl: no visible global function definition for
  ‘saveDb’
PrepareAnnotationEnsembl: no visible binding for global variable
  ‘chrom’
PrepareAnnotationEnsembl: no visible binding for global variable ‘name’
PrepareAnnotationEnsembl: no visible binding for global variable
  ‘alleleCount’
PrepareAnnotationEnsembl: no visible binding for global variable
  ‘alleles’
PrepareAnnotationRefseq: no visible global function definition for
  ‘saveDb’
PrepareAnnotationRefseq: no visible binding for global variable
  ‘mrnaAcc’
PrepareAnnotationRefseq: no visible binding for global variable ‘name’
PrepareAnnotationRefseq: no visible binding for global variable
  ‘protAcc’
PrepareAnnotationRefseq: no visible binding for global variable
  ‘transcript’
PrepareAnnotationRefseq: no visible binding for global variable ‘chrom’
PrepareAnnotationRefseq: no visible binding for global variable
  ‘alleleCount’
PrepareAnnotationRefseq: no visible binding for global variable
  ‘alleles’
SharedJunc: no visible binding for global variable ‘allsample’
Varlocation: no visible binding for global variable ‘pro_name’
joinDataFrameWithName2Val: no visible global function definition for
  ‘isSingleString’
setDataFrameColClass: no visible global function definition for
  ‘isTRUEorFALSE’
Undefined global functions or variables:
  DataFrame V5 aapos aaref aavar alleleCount alleles allsample cds_end
  cds_start chrom ensembl_gene_id genename isSingleString isTRUEorFALSE
  jun_type mrnaAcc name pro_name proname protAcc rsid saveDb transcript
  txname
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [49s/404s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
PrepareAnnotationRefseq  24.841  0.353 367.913
PrepareAnnotationEnsembl  1.649  0.032  13.494
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.3-bioc/meat/customProDB.Rcheck/00check.log’
for details.

* installing *source* package ‘customProDB’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (customProDB)

name	user	system	elapsed
Bed2Range	0.341	0.000	0.341
InputVcf	0.279	0.040	0.320
JunctionType	0.413	0.000	0.412
Multiple_VCF	0.362	0.040	0.404
OutputNovelJun	0.977	0.000	0.978
OutputVarproseq	0.498	0.016	0.515
OutputVarproseq_single	0.585	0.024	0.609
Outputaberrant	0.322	0.012	0.335
Outputproseq	0.918	0.000	0.919
OutputsharedPro	2.527	0.008	2.536
Positionincoding	0.373	0.008	0.380
PrepareAnnotationEnsembl	1.649	0.032	13.494
PrepareAnnotationRefseq	24.841	0.353	367.913
SharedJunc	0.507	0.012	0.528
Varlocation	0.001	0.000	0.001
aaVariation	0.727	0.008	0.752
calculateRPKM	0.888	0.004	0.900
easyRun	1.723	0.012	1.737
easyRun_mul	3.648	0.024	3.707