BioC 3.5: CHECK report for ASpli on oaxaca

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: 2017-03-03 23:15:19 -0800 (Fri, 03 Mar 2017)

EndedAt: 2017-03-03 23:34:15 -0800 (Fri, 03 Mar 2017)

EllapsedTime: 1135.6 seconds

RetCode: 0

Status:  OK

CheckDir: ASpli.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ASpli_1.1.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/ASpli.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* 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    123.580  7.040 130.701
ASpli-package       94.511  7.389 102.340
acc_AS              85.549  9.639  95.285
AsDiscover-methods  75.869  8.285  84.213
plotTopTags         71.980  6.627  81.161
acc_counts          66.080  7.617  73.794
acc_DU              66.083  6.642  72.785
DUreport            62.014  6.264  68.338
readCounts          55.995  5.803  62.412
acc_features        13.730  0.041  13.782
loadBAM             12.082  0.927  13.016
binGenome           12.281  0.040  12.329
* 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	94.511	7.389	102.340
AsDiscover-methods	75.869	8.285	84.213
DUreport	62.014	6.264	68.338
DUreport_DEXSeq	123.580	7.040	130.701
acc_AS	85.549	9.639	95.285
acc_DU	66.083	6.642	72.785
acc_counts	66.080	7.617	73.794
acc_features	13.730	0.041	13.782
binGenome	12.281	0.040	12.329
loadBAM	12.082	0.927	13.016
plotTopTags	71.980	6.627	81.161
readCounts	55.995	5.803	62.412