BioC 3.2: CHECK report for SGSeq on oaxaca

Package: SGSeq

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SGSeq_1.4.0.tar.gz

StartedAt: 2015-10-27 07:52:29 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 07:58:58 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 389.2 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_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-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 ‘1.4.0’
* 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 ... [20s/20s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [74s/75s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
predictVariantEffects 17.595  0.040  17.645
analyzeFeatures       17.226  0.259  17.490
predictTxFeatures      9.003  0.108   9.115
getSGVariantCounts     7.437  0.106   7.547
getSGFeatureCounts     5.305  0.097   5.405
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [107s/107s]
 [107s/108s] 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-3.2-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	0.205	0.001	0.206
SGFeatures	0.032	0.000	0.031
SGVariantCounts	0.18	0.00	0.18
SGVariants	0.13	0.00	0.13
TxFeatures	0.049	0.000	0.050
analyzeFeatures	17.226	0.259	17.490
analyzeVariants	1.527	0.003	1.529
annotate	1.560	0.003	1.564
assays	0.002	0.000	0.002
convertToSGFeatures	1.743	0.007	1.751
convertToTxFeatures	0.398	0.001	0.400
exportFeatures	0.001	0.000	0.000
findSGVariants	1.349	0.004	1.354
getBamInfo	0.730	0.058	0.789
getSGFeatureCounts	5.305	0.097	5.405
getSGVariantCounts	7.437	0.106	7.547
importTranscripts	0.001	0.000	0.000
makeSGFeatureCounts	0.059	0.000	0.059
makeVariantNames	0.004	0.000	0.004
mergeTxFeatures	0.331	0.000	0.331
plotCoverage	0	0	0
plotFeatures	0.000	0.000	0.001
plotSpliceGraph	0.001	0.000	0.001
plotVariants	0.001	0.000	0.001
predictTxFeatures	9.003	0.108	9.115
predictVariantEffects	17.595	0.040	17.645
processTerminalExons	0.383	0.020	0.402
slots	0.003	0.000	0.002