BioC 3.5: CHECK report for customProDB on malbec2

Package: customProDB

Version: 1.16.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings customProDB_1.16.0.tar.gz

StartedAt: 2017-10-17 22:26:57 -0400 (Tue, 17 Oct 2017)

EndedAt: 2017-10-17 22:33:40 -0400 (Tue, 17 Oct 2017)

EllapsedTime: 402.8 seconds

RetCode: 0

Status:  OK

CheckDir: customProDB.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings customProDB_1.16.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/customProDB.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.16.0’
* 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 ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
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
Bed2Range: no visible binding for global variable ‘V5’
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’
Varlocation: no visible binding for global variable ‘pro_name’
Undefined global functions or variables:
  V5 aapos aaref aavar alleleCount alleles cds_end cds_start chrom
  ensembl_gene_id genename 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 ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
PrepareAnnotationRefseq  21.688  0.256 167.999
PrepareAnnotationEnsembl  4.992  0.036  23.780
* 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-3.5-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	0.112	0.004	0.116
InputVcf	0.94	0.02	0.96
JunctionType	1.892	0.000	1.893
Multiple_VCF	0.448	0.028	0.480
OutputNovelJun	1.900	0.012	1.916
OutputVarprocodingseq	0.552	0.008	0.563
OutputVarproseq	0.572	0.012	0.583
OutputVarproseq_single	0.444	0.000	0.444
Outputaberrant	0.200	0.008	0.209
Outputproseq	0.684	0.000	0.685
OutputsharedPro	1.408	0.004	1.414
Positionincoding	0.264	0.008	0.271
PrepareAnnotationEnsembl	4.992	0.036	23.780
PrepareAnnotationRefseq	21.688	0.256	167.999
SharedJunc	0.616	0.004	0.619
Varlocation	0.000	0.000	0.001
aaVariation	0.792	0.004	0.793
calculateRPKM	0.552	0.012	0.564
easyRun	1.464	0.008	1.471
easyRun_mul	3.184	0.028	3.214