BioC 3.5: CHECK report for GenomicFiles on toluca2
This page was generated on 2017-04-23 14:38:28 -0400 (Sun, 23 Apr 2017).
GenomicFiles 1.11.6 Bioconductor Package Maintainer
Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017) | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicFiles | Last Changed Rev: 127991 / Revision: 129046 | Last Changed Date: 2017-04-03 09:47:33 -0400 (Mon, 03 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | |
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |
toluca2 | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ OK ] | OK | |
veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | ERROR | skipped | skipped | |
Summary
Package: GenomicFiles |
Version: 1.11.6 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GenomicFiles_1.11.6.tar.gz |
StartedAt: 2017-04-23 04:27:51 -0400 (Sun, 23 Apr 2017) |
EndedAt: 2017-04-23 04:35:40 -0400 (Sun, 23 Apr 2017) |
EllapsedTime: 468.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GenomicFiles.Rcheck |
Warnings: 0 |
Command output
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GenomicFiles_1.11.6.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/GenomicFiles.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 ‘GenomicFiles/DESCRIPTION’ ... OK
* this is package ‘GenomicFiles’ version ‘1.11.6’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
‘BiocGenerics’ ‘GenomicRanges’ ‘SummarizedExperiment’ ‘BiocParallel’
‘Rsamtools’ ‘rtracklayer’
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 ‘GenomicFiles’ 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 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 ... OK
* 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
VcfStack-class 12.036 0.281 12.418
reduceByYield 1.386 0.425 29.431
GenomicFiles-class 1.010 0.375 11.325
reduceByFile-methods 0.306 0.375 24.636
reduceByRange-methods 0.305 0.217 22.837
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘GenomicFiles_unit_tests.R’
OK
* 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: 1 NOTE
See
‘/Users/biocbuild/bbs-3.5-bioc/meat/GenomicFiles.Rcheck/00check.log’
for details.
GenomicFiles.Rcheck/00install.out:
* installing *source* package ‘GenomicFiles’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GenomicFiles)
GenomicFiles.Rcheck/GenomicFiles-Ex.timings:
name | user | system | elapsed
|
GenomicFiles-class | 1.010 | 0.375 | 11.325 |
|
VcfStack-class | 12.036 | 0.281 | 12.418 |
|
pack-methods | 1.262 | 0.008 | 1.280 |
|
reduceByFile-methods | 0.306 | 0.375 | 24.636 |
|
reduceByRange-methods | 0.305 | 0.217 | 22.837 |
|
reduceByYield | 1.386 | 0.425 | 29.431 |
|
registry-utils | 0.001 | 0.000 | 0.001 |
|
unpack-methods | 0.496 | 0.122 | 4.334 |
|