BioC 3.4: CHECK report for ASpli on malbec1

Package: ASpli

Version: 1.0.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings ASpli_1.0.0.tar.gz

StartedAt: 2017-04-14 21:02:30 -0400 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 21:18:18 -0400 (Fri, 14 Apr 2017)

EllapsedTime: 948.4 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_1.0.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/ASpli.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.0.0’
* 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 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    110.744  0.196 111.013
ASpli-package       81.652  0.228  81.937
acc_AS              79.204  1.000  80.289
AsDiscover-methods  75.340  0.148  75.546
DUreport            68.388  0.172  68.626
plotTopTags         67.032  0.188  67.281
acc_DU              60.692  0.276  61.028
acc_counts          56.696  0.736  57.491
readCounts          54.172  0.176  54.395
loadBAM             10.788  0.128  10.926
binGenome           10.428  0.008  10.452
acc_features        10.152  0.008  10.172
* 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	81.652	0.228	81.937
AsDiscover-methods	75.340	0.148	75.546
DUreport	68.388	0.172	68.626
DUreport_DEXSeq	110.744	0.196	111.013
acc_AS	79.204	1.000	80.289
acc_DU	60.692	0.276	61.028
acc_counts	56.696	0.736	57.491
acc_features	10.152	0.008	10.172
binGenome	10.428	0.008	10.452
loadBAM	10.788	0.128	10.926
plotTopTags	67.032	0.188	67.281
readCounts	54.172	0.176	54.395