BioC 3.5: CHECK report for SGSeq on oaxaca

Package: SGSeq

Version: 1.9.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SGSeq_1.9.2.tar.gz

StartedAt: 2017-03-04 09:03:02 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 09:11:29 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 506.5 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_1.9.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/SGSeq.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* 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 ‘1.9.2’
* 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 ... 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 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 32.545  0.085  32.739
analyzeFeatures       23.050  0.320  23.378
predictTxFeatures     12.468  0.146  12.622
getSGVariantCounts     7.232  0.118   7.352
getSGFeatureCounts     5.721  0.111   5.835
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-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	1.042	0.004	1.048
SGFeatures	0.128	0.001	0.129
SGVariantCounts	0.401	0.025	0.425
SGVariants	0.184	0.000	0.185
TxFeatures	0.058	0.000	0.059
analyzeFeatures	23.050	0.320	23.378
analyzeVariants	2.331	0.012	2.342
annotate	2.583	0.015	2.600
assays	0.04	0.00	0.04
convertToSGFeatures	1.287	0.008	1.296
convertToTxFeatures	0.475	0.001	0.475
exportFeatures	0.000	0.000	0.001
findSGVariants	2.331	0.005	2.337
getBamInfo	1.017	0.146	1.178
getSGFeatureCounts	5.721	0.111	5.835
getSGVariantCounts	7.232	0.118	7.352
importTranscripts	0.000	0.000	0.001
makeSGFeatureCounts	0.053	0.000	0.053
makeVariantNames	0.009	0.000	0.010
mergeTxFeatures	0.393	0.001	0.394
plotCoverage	0.000	0.000	0.001
plotFeatures	0	0	0
plotSpliceGraph	0.001	0.000	0.001
plotVariants	0.001	0.000	0.001
predictTxFeatures	12.468	0.146	12.622
predictVariantEffects	32.545	0.085	32.739
processTerminalExons	0.442	0.001	0.444
slots	0.005	0.001	0.006