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BioC 2.14: CHECK report for customProDB on morelia

This page was generated on 2014-10-08 09:06:29 -0700 (Wed, 08 Oct 2014).

Package 204/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
customProDB 1.4.1
xiaojing wang
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/customProDB
Last Changed Rev: 94296 / Revision: 95116
Last Changed Date: 2014-09-19 09:53:15 -0700 (Fri, 19 Sep 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 

Summary

Package: customProDB
Version: 1.4.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch customProDB_1.4.1.tar.gz
StartedAt: 2014-10-07 22:17:11 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 22:24:09 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 417.5 seconds
RetCode: 0
Status:  OK 
CheckDir: customProDB.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch customProDB_1.4.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/customProDB.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (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 ‘1.4.1’
* 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 ‘customProDB’ can be installed ... [24s/24s] 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 loading without being on the library search path ... 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.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 binding for global variable
  ‘tx_name’
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 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’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [87s/183s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
PrepareAnnotationRefseq  23.904  0.733  93.472
OutputNovelJun           13.182  1.203  14.638
easyRun_mul              10.227  0.117  10.372
PrepareAnnotationEnsembl  1.998  0.102  28.657
* 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

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/customProDB.Rcheck/00check.log’
for details.

customProDB.Rcheck/00install.out:

* 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)

customProDB.Rcheck/customProDB-Ex.timings:

nameusersystemelapsed
Bed2Range0.1050.0050.111
InputVcf0.8950.0330.927
JunctionType2.2880.0222.312
Multiple_VCF1.2850.0251.312
OutputNovelJun13.182 1.20314.638
OutputVarproseq1.0110.0471.059
OutputVarproseq_single1.0720.0141.086
Outputaberrant0.4690.0130.482
Outputproseq1.6460.0441.692
OutputsharedPro4.7350.1054.842
Positionincoding0.8200.0170.838
PrepareAnnotationEnsembl 1.998 0.10228.657
PrepareAnnotationRefseq23.904 0.73393.472
SharedJunc1.1080.0031.114
Varlocation0.0010.0000.002
aaVariation1.2210.0161.241
calculateRPKM2.1720.0232.197
easyRun4.0990.0394.151
easyRun_mul10.227 0.11710.372