BioC 3.5: CHECK report for ppiStats on oaxaca
This page was generated on 2016-10-26 16:21:36 -0400 (Wed, 26 Oct 2016).
ppiStats 1.41.0 Bioconductor Package Maintainer
Snapshot Date: 2016-10-25 17:15:05 -0400 (Tue, 25 Oct 2016) | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ppiStats | Last Changed Rev: 122712 / Revision: 123034 | Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK |  |
oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ OK ] | OK |  |
Summary
Package: ppiStats |
Version: 1.41.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ppiStats_1.41.0.tar.gz |
StartedAt: 2016-10-26 04:58:24 -0700 (Wed, 26 Oct 2016) |
EndedAt: 2016-10-26 05:01:02 -0700 (Wed, 26 Oct 2016) |
EllapsedTime: 157.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ppiStats.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 ppiStats_1.41.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/ppiStats.Rcheck’
* using R Under development (unstable) (2016-10-21 r71549)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ppiStats/DESCRIPTION’ ... OK
* this is package ‘ppiStats’ version ‘1.41.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ppiStats’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘lattice’
A package should be listed in only one of these fields.
* 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 ... NOTE
Packages in Depends field not imported from:
‘ScISI’ ‘ppiData’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* 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
* 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/ppiStats.Rcheck/00check.log’
for details.
ppiStats.Rcheck/00install.out:
* installing *source* package ‘ppiStats’ ...
** R
** inst
** preparing package for lazy loading
No methods found in "Biobase" for requests: listlen
No methods found in "annotate" for requests: pubmed, buildPubMedAbst
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "Biobase" for requests: listlen
No methods found in "annotate" for requests: pubmed, buildPubMedAbst
* DONE (ppiStats)
ppiStats.Rcheck/ppiStats-Ex.timings:
name | user | system | elapsed
|
assessSymmetry | 2.776 | 0.379 | 3.156 |
|
bpMatrix | 0.478 | 0.383 | 0.862 |
|
calcInOutDegStats | 0.002 | 0.000 | 0.003 |
|
createSummaryTables | 0.187 | 0.009 | 0.197 |
|
degreeEstimates | 0.003 | 0.001 | 0.003 |
|
estErrProbMethodOfMoments | 0.002 | 0.000 | 0.003 |
|
estimateCCMErrorRates | 1.551 | 0.870 | 2.424 |
|
estimatePPIErrorRates | 3.236 | 0.423 | 3.663 |
|
genBPGraph | 0.146 | 0.007 | 0.152 |
|
idProteinErrorType | 1.581 | 0.411 | 1.993 |
|
idProteinType | 0.036 | 0.008 | 0.045 |
|
inOutScatterCharts | 0.001 | 0.000 | 0.001 |
|
nullDistDoublyTestedEdges | 0.381 | 0.037 | 0.418 |
|
twPERM | 0.001 | 0.000 | 0.001 |
|
viabilityCharts | 0.334 | 0.101 | 0.435 |
|