BioC 3.3: CHECK report for SGSeq on zin2

Package: SGSeq

Version: 1.6.12

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings SGSeq_1.6.12.tar.gz

StartedAt: 2016-10-13 06:45:40 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 06:51:38 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 357.7 seconds

RetCode: 0

Status:  OK

CheckDir: SGSeq.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings SGSeq_1.6.12.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/SGSeq.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (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 ‘1.6.12’
* 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 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 ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
predictVariantEffects 23.608  0.028  23.634
analyzeFeatures       16.121  0.091  16.258
predictTxFeatures      9.443  0.024   9.496
getSGVariantCounts     5.320  0.036   5.352
getSGFeatureCounts     4.981  0.048   5.025
* 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
  ‘/home/biocbuild/bbs-3.3-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	0.138	0.008	0.146
SGFeatures	0.026	0.000	0.025
SGVariantCounts	0.149	0.000	0.149
SGVariants	0.097	0.000	0.097
TxFeatures	0.042	0.000	0.041
analyzeFeatures	16.121	0.091	16.258
analyzeVariants	1.273	0.000	1.272
annotate	1.712	0.000	1.712
assays	0.008	0.000	0.007
convertToSGFeatures	1.091	0.000	1.089
convertToTxFeatures	0.307	0.000	0.307
exportFeatures	0	0	0
findSGVariants	1.083	0.000	1.082
getBamInfo	1.122	0.100	1.222
getSGFeatureCounts	4.981	0.048	5.025
getSGVariantCounts	5.320	0.036	5.352
importTranscripts	0.001	0.000	0.000
makeSGFeatureCounts	0.038	0.000	0.038
makeVariantNames	0.005	0.000	0.004
mergeTxFeatures	0.225	0.000	0.225
plotCoverage	0.000	0.000	0.001
plotFeatures	0.001	0.000	0.000
plotSpliceGraph	0.000	0.000	0.001
plotVariants	0.001	0.000	0.000
predictTxFeatures	9.443	0.024	9.496
predictVariantEffects	23.608	0.028	23.634
processTerminalExons	0.288	0.000	0.287
slots	0.004	0.000	0.003