BioC 3.0: CHECK report for SGSeq on oaxaca

Package: SGSeq

Version: 1.0.6

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch SGSeq_1.0.6.tar.gz

StartedAt: 2015-04-10 03:19:39 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 03:26:09 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 389.7 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 --no-multiarch SGSeq_1.0.6.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/SGSeq.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘1.0.6’
* 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 ... [27s/27s] 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 object imported by a ':::' call: ‘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 ... [100s/100s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
analyzeFeatures    32.368  6.544  40.154
predictTxFeatures  17.214  3.433  21.126
getSGFeatureCounts 11.877  3.451  15.299
* 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

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-3.0-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	0.176	0.006	0.183
SGFeatures	0.051	0.000	0.052
TxFeatures	0.354	0.001	0.355
TxVariantCounts	0.243	0.004	0.248
TxVariants	0.183	0.000	0.188
analyzeFeatures	32.368	6.544	40.154
analyzeVariants	1.930	0.022	2.015
annotate	2.078	0.004	2.087
assays	0.003	0.000	0.003
convertToSGFeatures	2.229	0.008	2.242
convertToTxFeatures	0.606	0.005	0.613
exportFeatures	0.001	0.000	0.000
filterTerminalExons	0.242	0.001	0.243
findTxVariants	1.841	0.002	1.846
getBamInfo	0.148	0.026	0.175
getSGFeatureCounts	11.877	3.451	15.299
getTxVariantCounts	0.059	0.005	0.063
mergeTxFeatures	0.52	0.01	0.53
plotFeatures	0.001	0.000	0.001
plotSpliceGraph	0.001	0.000	0.001
plotVariants	0.001	0.000	0.001
predictTxFeatures	17.214	3.433	21.126
slots	0.004	0.001	0.005