BioC 3.5: CHECK report for ASpli on toluca2

Package: ASpli

Version: 1.1.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ASpli_1.1.0.tar.gz

StartedAt: 2017-04-23 00:31:38 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 00:50:34 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 1136.2 seconds

RetCode: 0

Status:  OK

CheckDir: ASpli.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ASpli_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/ASpli.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ASpli/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ASpli’ version ‘1.1.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘GenomicRanges’ ‘GenomicFeatures’ ‘edgeR’ ‘BiocGenerics’ ‘IRanges’
  ‘GenomicAlignments’ ‘DESeq2’ ‘DEXSeq’ ‘Gviz’ ‘S4Vectors’
  ‘AnnotationDbi’ ‘parallel’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘ASpli’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
readCounts,ASpliFeatures: no visible binding for global variable
  'targets'
Undefined global functions or variables:
  targets
* 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 sizes of PDF files under ‘inst/doc’ ... 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
DUreport_DEXSeq    125.583  6.598 133.597
ASpli-package       92.170  6.571  98.863
acc_AS              79.632  9.071  89.546
AsDiscover-methods  77.475  7.085  85.257
plotTopTags         69.650  6.214  76.423
acc_DU              62.644  6.678  70.097
acc_counts          61.246  7.698  69.603
DUreport            59.900  6.005  66.714
readCounts          52.541  5.193  57.826
acc_features        14.076  0.047  14.232
loadBAM             12.110  0.863  13.383
binGenome           12.820  0.037  13.041
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/ASpli.Rcheck/00check.log’
for details.

* installing *source* package ‘ASpli’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ASpli)

name	user	system	elapsed
ASpli-package	92.170	6.571	98.863
AsDiscover-methods	77.475	7.085	85.257
DUreport	59.900	6.005	66.714
DUreport_DEXSeq	125.583	6.598	133.597
acc_AS	79.632	9.071	89.546
acc_DU	62.644	6.678	70.097
acc_counts	61.246	7.698	69.603
acc_features	14.076	0.047	14.232
binGenome	12.820	0.037	13.041
loadBAM	12.110	0.863	13.383
plotTopTags	69.650	6.214	76.423
readCounts	52.541	5.193	57.826