BioC 3.1: CHECK report for SGSeq on zin2

Package: SGSeq

Version: 1.2.2

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings SGSeq_1.2.2.tar.gz

StartedAt: 2015-10-09 05:28:04 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 05:31:35 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 210.9 seconds

RetCode: 0

Status:  OK

CheckDir: SGSeq.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings SGSeq_1.2.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/SGSeq.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.2.2’
* 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 ... [13s/13s] 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [34s/70s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
getSGVariantCounts 7.852  1.206   9.955
analyzeFeatures    3.635  0.694  22.834
predictTxFeatures  2.328  0.499  11.535
getSGFeatureCounts 1.066  0.558   8.988
* 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-3.1-bioc/meat/SGSeq.Rcheck/00check.log’
for details.

* installing *source* package ‘SGSeq’ ...
** R
** data
*** moving datasets to lazyload DB
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (SGSeq)

name	user	system	elapsed
SGFeatureCounts	0.095	0.000	0.094
SGFeatures	0.03	0.00	0.03
SGVariantCounts	0.140	0.004	0.144
SGVariants	0.09	0.00	0.09
TxFeatures	0.043	0.000	0.043
analyzeFeatures	3.635	0.694	22.834
analyzeVariants	1.334	0.020	1.362
annotate	1.339	0.000	1.340
assays	0.002	0.000	0.002
convertToSGFeatures	1.342	0.000	1.343
convertToTxFeatures	0.358	0.000	0.358
exportFeatures	0	0	0
findSGVariants	1.178	0.000	1.178
getBamInfo	2.145	0.968	3.231
getSGFeatureCounts	1.066	0.558	8.988
getSGVariantCounts	7.852	1.206	9.955
makeSGFeatureCounts	0.041	0.000	0.041
makeVariantNames	0.006	0.000	0.006
mergeTxFeatures	0.303	0.004	0.307
plotFeatures	0.001	0.000	0.001
plotSpliceGraph	0.000	0.000	0.001
plotVariants	0.001	0.000	0.000
predictTxFeatures	2.328	0.499	11.535
processTerminalExons	0.331	0.000	0.330
slots	0.003	0.000	0.003