BioC 3.1: CHECK report for SGSeq on petty

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 01:58:02 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 02:06:01 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 478.8 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 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (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 ... [28s/28s] 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 ... [141s/183s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
analyzeFeatures    29.649 10.375  61.739
predictTxFeatures  21.710  8.248  29.987
getSGVariantCounts 18.269  6.291  26.723
getBamInfo          5.108  5.342  10.984
getSGFeatureCounts  3.192  3.184  27.856
* 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	0.177	0.013	0.190
SGFeatures	0.055	0.000	0.055
SGVariantCounts	0.195	0.001	0.196
SGVariants	0.135	0.000	0.135
TxFeatures	0.057	0.000	0.057
analyzeFeatures	29.649	10.375	61.739
analyzeVariants	2.849	0.083	2.935
annotate	2.487	0.003	2.490
assays	0.004	0.000	0.004
convertToSGFeatures	2.588	0.002	2.592
convertToTxFeatures	0.753	0.003	0.757
exportFeatures	0.001	0.000	0.001
findSGVariants	2.361	0.004	2.368
getBamInfo	5.108	5.342	10.984
getSGFeatureCounts	3.192	3.184	27.856
getSGVariantCounts	18.269	6.291	26.723
makeSGFeatureCounts	0.085	0.016	0.101
makeVariantNames	0.027	0.011	0.038
mergeTxFeatures	0.723	0.050	0.774
plotFeatures	0.001	0.000	0.001
plotSpliceGraph	0.001	0.000	0.001
plotVariants	0.001	0.000	0.001
predictTxFeatures	21.710	8.248	29.987
processTerminalExons	0.679	0.001	0.682
slots	0.005	0.001	0.006