BioC 3.6: CHECK report for SGSeq on veracruz1

Package: SGSeq

Version: 1.11.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SGSeq_1.11.2.tar.gz

StartedAt: 2017-08-16 08:28:27 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 08:36:15 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 468.3 seconds

RetCode: 0

Status:  OK

CheckDir: SGSeq.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SGSeq_1.11.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/SGSeq.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SGSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SGSeq’ version ‘1.11.2’
* 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 ‘SGSeq’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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:
  ‘GenomicRanges:::extraColumnSlotNames’
  ‘GenomicRanges:::extraColumnSlotsAsDF’
  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
plotFeatures: no visible global function definition for ‘frame’
plotVariants: no visible global function definition for ‘frame’
Undefined global functions or variables:
  frame
Consider adding
  importFrom("graphics", "frame")
to your NAMESPACE file.
* 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 ... 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
predictVariantEffects 27.695  0.078  28.534
analyzeFeatures       19.162  0.254  20.051
predictTxFeatures     10.329  0.111  10.739
getSGVariantCounts     6.304  0.090   6.588
getSGFeatureCounts     5.060  0.087   5.296
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/SGSeq.Rcheck/00check.log’
for details.

* installing *source* package ‘SGSeq’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (SGSeq)

name	user	system	elapsed
SGFeatureCounts	0.805	0.002	0.834
SGFeatures	0.079	0.002	0.081
SGVariantCounts	0.316	0.023	0.351
SGVariants	0.148	0.000	0.157
TxFeatures	0.054	0.001	0.054
analyzeFeatures	19.162	0.254	20.051
analyzeVariants	2.135	0.011	2.204
annotate	2.845	0.006	2.922
assays	0.036	0.001	0.040
convertToSGFeatures	1.436	0.010	1.500
convertToTxFeatures	0.496	0.001	0.513
exportFeatures	0	0	0
findSGVariants	1.937	0.003	1.996
getBamInfo	1.045	0.143	1.231
getSGFeatureCounts	5.060	0.087	5.296
getSGVariantCounts	6.304	0.090	6.588
importTranscripts	0	0	0
makeSGFeatureCounts	0.042	0.000	0.041
makeVariantNames	0.007	0.000	0.012
mergeTxFeatures	0.290	0.001	0.298
plotCoverage	0.001	0.000	0.001
plotFeatures	0.001	0.000	0.001
plotSpliceGraph	0.001	0.001	0.000
plotVariants	0.001	0.000	0.000
predictTxFeatures	10.329	0.111	10.739
predictVariantEffects	27.695	0.078	28.534
processTerminalExons	0.289	0.001	0.293
slots	0.003	0.000	0.003