BioC 3.2: CHECK report for myvariant on linux1.bioconductor.org

Package: myvariant

Version: 1.0.1

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings myvariant_1.0.1.tar.gz

StartedAt: 2015-10-27 06:09:57 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 06:13:13 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 196.5 seconds

RetCode: 0

Status:  OK

CheckDir: myvariant.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings myvariant_1.0.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/myvariant.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘myvariant/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘myvariant’ version ‘1.0.1’
* 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 ‘myvariant’ can be installed ... [21s/21s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
package 'methods' is used but not declared
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.getIndels: no visible binding for global variable ‘REF’
.getIndels: no visible binding for global variable ‘ALT’
formatHgvs: no visible global function definition for
  ‘seqlevelsStyle<-’
* 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 ... [9s/11s] 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/myvariant.Rcheck/00check.log’
for details.

* installing *source* package ‘myvariant’ ...
** R
** inst
** preparing package for lazy loading
Note: the specification for S3 class “AsIs” in package ‘jsonlite’ seems equivalent to one from package ‘BiocGenerics’: not turning on duplicate class definitions for this class.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Note: the specification for S3 class “AsIs” in package ‘jsonlite’ seems equivalent to one from package ‘BiocGenerics’: not turning on duplicate class definitions for this class.
* DONE (myvariant)

name	user	system	elapsed
MyVariant-class	0.001	0.000	0.001
MyVariant	0.002	0.000	0.002
formatHgvs	0.490	0.011	0.503
formatSingleHgvs	0.000	0.000	0.001
getVariant	0.057	0.004	0.360
getVariants	0.026	0.000	0.197
metadata	0.015	0.000	0.090
queryVariant	0.339	0.004	1.714
queryVariants	0.001	0.000	0.000