BioC 3.4: CHECK report for SGSeq on zin1

Package: SGSeq

Version: 1.7.12

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings SGSeq_1.7.12.tar.gz

StartedAt: 2016-09-20 12:31:43 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 12:37:31 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 347.9 seconds

RetCode: 0

Status:  OK

CheckDir: SGSeq.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings SGSeq_1.7.12.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-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 ‘1.7.12’
* 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 21.864  0.032  21.917
analyzeFeatures       15.344  0.100  15.442
predictTxFeatures      9.276  0.044   9.450
getSGVariantCounts     5.292  0.032   5.329
* 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-3.4-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	0.132	0.000	0.133
SGFeatures	0.028	0.000	0.026
SGVariantCounts	0.196	0.000	0.198
SGVariants	0.408	0.000	0.409
TxFeatures	0.040	0.000	0.039
analyzeFeatures	15.344	0.100	15.442
analyzeVariants	1.352	0.000	1.351
annotate	1.692	0.000	1.694
assays	0.004	0.000	0.007
convertToSGFeatures	1.056	0.000	1.057
convertToTxFeatures	0.340	0.000	0.339
exportFeatures	0	0	0
findSGVariants	1.164	0.000	1.161
getBamInfo	1.372	0.096	1.467
getSGFeatureCounts	4.600	0.036	4.636
getSGVariantCounts	5.292	0.032	5.329
importTranscripts	0.000	0.000	0.001
makeSGFeatureCounts	0.032	0.000	0.031
makeVariantNames	0.004	0.000	0.004
mergeTxFeatures	0.244	0.000	0.243
plotCoverage	0.004	0.000	0.001
plotFeatures	0	0	0
plotSpliceGraph	0.000	0.000	0.001
plotVariants	0	0	0
predictTxFeatures	9.276	0.044	9.450
predictVariantEffects	21.864	0.032	21.917
processTerminalExons	0.276	0.000	0.278
slots	0.004	0.000	0.003