BioC 3.1: CHECK report for SGSeq on morelia

Package: SGSeq

Version: 1.2.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SGSeq_1.2.2.tar.gz

StartedAt: 2015-10-09 06:16:04 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 06:20:19 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 255.7 seconds

RetCode: 0

Status:  OK

CheckDir: SGSeq.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SGSeq_1.2.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/SGSeq.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.2.2’
* 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 ... [16s/16s] 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 loading without being on the library search path ... 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 ... OK
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [75s/95s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
analyzeFeatures    14.803  5.646  31.034
predictTxFeatures  11.666  5.546  16.885
getSGVariantCounts  8.961  3.618  13.523
getBamInfo          2.601  2.312   5.188
getSGFeatureCounts  1.585  1.612  13.222
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/SGSeq.Rcheck/00check.log’
for details.

* installing *source* package ‘SGSeq’ ...
** R
** data
*** moving datasets to lazyload DB
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (SGSeq)

name	user	system	elapsed
SGFeatureCounts	0.112	0.008	0.119
SGFeatures	0.034	0.000	0.033
SGVariantCounts	0.125	0.000	0.126
SGVariants	0.121	0.025	0.146
TxFeatures	0.044	0.013	0.056
analyzeFeatures	14.803	5.646	31.034
analyzeVariants	1.503	0.028	1.531
annotate	1.210	0.002	1.211
assays	0.001	0.000	0.002
convertToSGFeatures	1.674	0.191	1.865
convertToTxFeatures	0.418	0.073	0.492
exportFeatures	0.000	0.000	0.001
findSGVariants	1.156	0.002	1.157
getBamInfo	2.601	2.312	5.188
getSGFeatureCounts	1.585	1.612	13.222
getSGVariantCounts	8.961	3.618	13.523
makeSGFeatureCounts	0.058	0.021	0.078
makeVariantNames	0.014	0.005	0.018
mergeTxFeatures	0.491	0.142	0.632
plotFeatures	0.001	0.000	0.001
plotSpliceGraph	0.001	0.000	0.000
plotVariants	0	0	0
predictTxFeatures	11.666	5.546	16.885
processTerminalExons	0.311	0.000	0.311
slots	0.003	0.000	0.002