BioC 3.0: CHECK report for MinimumDistance on oaxaca
This page was generated on 2015-04-10 10:06:01 -0700 (Fri, 10 Apr 2015).
MinimumDistance 1.10.2 Robert B Scharpf
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015) | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/MinimumDistance | Last Changed Rev: 99352 / Revision: 102249 | Last Changed Date: 2015-02-10 18:08:54 -0800 (Tue, 10 Feb 2015) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | NotNeeded | OK | OK | |
moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK |
perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK |
oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ OK ] | OK |
Summary
Package: MinimumDistance |
Version: 1.10.2 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MinimumDistance_1.10.2.tar.gz |
StartedAt: 2015-04-10 01:21:27 -0700 (Fri, 10 Apr 2015) |
EndedAt: 2015-04-10 01:28:59 -0700 (Fri, 10 Apr 2015) |
EllapsedTime: 452.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MinimumDistance.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 --no-multiarch MinimumDistance_1.10.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/MinimumDistance.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MinimumDistance/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MinimumDistance’ version ‘1.10.2’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.gigignore
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MinimumDistance’ can be installed ... [29s/30s] 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 ... NOTE
package 'methods' is used but not declared
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [52s/52s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
FilterParamMD 24.054 1.760 25.903
pedigreeGrid 8.565 0.493 9.180
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘doRUnit.R’ [84s/85s]
[84s/85s] OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘BSgenome.Hsapiens.UCSC.hg18’
* 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
NOTE: There were 3 notes.
See
‘/Users/biocbuild/bbs-3.0-bioc/meat/MinimumDistance.Rcheck/00check.log’
for details.
MinimumDistance.Rcheck/00install.out:
* installing *source* package ‘MinimumDistance’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘colMads’ from package ‘matrixStats’ in package ‘MinimumDistance’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MinimumDistance)
MinimumDistance.Rcheck/MinimumDistance-Ex.timings:
name | user | system | elapsed
|
DNAcopyParam | 0.025 | 0.001 | 0.026 |
|
FilterParamMD | 24.054 | 1.760 | 25.903 |
|
MAP2 | 0.437 | 0.035 | 0.473 |
|
MDRanges-class | 0.063 | 0.002 | 0.066 |
|
MinDistGRanges-class | 0.114 | 0.002 | 0.116 |
|
MinDistGRanges | 0.060 | 0.001 | 0.061 |
|
ParentOffspring-class | 0.002 | 0.000 | 0.002 |
|
ParentOffspringList-class | 0.003 | 0.000 | 0.003 |
|
Pedigree | 0.011 | 0.000 | 0.010 |
|
TrioSet | 1.721 | 0.044 | 1.789 |
|
acf2 | 0.004 | 0.000 | 0.004 |
|
md_exp | 0.001 | 0.000 | 0.002 |
|
pedigreeGrid | 8.565 | 0.493 | 9.180 |
|
pedigreeViewports | 0.005 | 0.000 | 0.004 |
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