BioC 3.4: CHECK report for ASpli on zin1

Package: ASpli

Version: 0.99.13

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings ASpli_0.99.13.tar.gz

StartedAt: 2016-09-20 03:20:08 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 03:35:27 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 918.7 seconds

RetCode: 0

Status:  OK

CheckDir: ASpli.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings ASpli_0.99.13.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/ASpli.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 ‘ASpli/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ASpli’ version ‘0.99.13’
* 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    120.608  0.224 120.841
ASpli-package       86.496  0.416  88.961
AsDiscover-methods  72.364  0.156  72.532
acc_AS              70.372  0.896  71.366
plotTopTags         67.380  0.196  67.587
acc_DU              62.704  0.500  63.206
DUreport            59.420  0.224  59.648
acc_counts          54.796  0.868  55.665
readCounts          53.444  0.104  53.549
loadBAM             11.280  0.084  11.364
acc_features         8.448  0.004   8.450
binGenome            8.352  0.008   8.360
* 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
  ‘/home/biocbuild/bbs-3.4-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	86.496	0.416	88.961
AsDiscover-methods	72.364	0.156	72.532
DUreport	59.420	0.224	59.648
DUreport_DEXSeq	120.608	0.224	120.841
acc_AS	70.372	0.896	71.366
acc_DU	62.704	0.500	63.206
acc_counts	54.796	0.868	55.665
acc_features	8.448	0.004	8.450
binGenome	8.352	0.008	8.360
loadBAM	11.280	0.084	11.364
plotTopTags	67.380	0.196	67.587
readCounts	53.444	0.104	53.549