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BioC 3.4: CHECK report for ASpli on morelia

This page was generated on 2017-04-15 16:27:57 -0400 (Sat, 15 Apr 2017).

Package 70/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ASpli 1.0.0
Estefania Mancini
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/ASpli
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: ASpli
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ASpli_1.0.0.tar.gz
StartedAt: 2017-04-14 22:47:35 -0700 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 23:08:54 -0700 (Fri, 14 Apr 2017)
EllapsedTime: 1279.5 seconds
RetCode: 0
Status:  OK 
CheckDir: ASpli.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ASpli_1.0.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/ASpli.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.0.0’
* 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 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    139.719  9.483 149.612
acc_AS              99.186 12.921 112.422
ASpli-package       99.304 10.396 111.287
AsDiscover-methods  92.326 10.428 102.957
DUreport            80.853  8.945  90.067
acc_DU              79.756  9.349  89.328
plotTopTags         75.859  8.814  84.894
acc_counts          72.758 10.663  90.705
readCounts          65.986  8.498  74.584
binGenome           13.113  0.053  13.175
acc_features        12.492  0.040  12.573
loadBAM             11.445  0.830  12.282
* 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-3.4-bioc/meat/ASpli.Rcheck/00check.log’
for details.


ASpli.Rcheck/00install.out:

* 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)

ASpli.Rcheck/ASpli-Ex.timings:

nameusersystemelapsed
ASpli-package 99.304 10.396111.287
AsDiscover-methods 92.326 10.428102.957
DUreport80.853 8.94590.067
DUreport_DEXSeq139.719 9.483149.612
acc_AS 99.186 12.921112.422
acc_DU79.756 9.34989.328
acc_counts72.75810.66390.705
acc_features12.492 0.04012.573
binGenome13.113 0.05313.175
loadBAM11.445 0.83012.282
plotTopTags75.859 8.81484.894
readCounts65.986 8.49874.584