BioC 3.5: CHECK report for ppiStats on malbec2
This page was generated on 2017-08-16 13:12:44 -0400 (Wed, 16 Aug 2017).
ppiStats 1.42.0 Bioconductor Package Maintainer
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/ppiStats | Last Changed Rev: 129126 / Revision: 131943 | Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 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 |  |
veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |  |
Summary
Package: ppiStats |
Version: 1.42.0 |
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings ppiStats_1.42.0.tar.gz |
StartedAt: 2017-08-16 01:21:46 -0400 (Wed, 16 Aug 2017) |
EndedAt: 2017-08-16 01:23:54 -0400 (Wed, 16 Aug 2017) |
EllapsedTime: 127.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ppiStats.Rcheck |
Warnings: 0 |
Command output
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### Running command:
###
### /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings ppiStats_1.42.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/ppiStats.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ppiStats/DESCRIPTION’ ... OK
* this is package ‘ppiStats’ version ‘1.42.0’
* 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 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
‘/home/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 | 2.696 | 1.244 | 3.943 |
|
bpMatrix | 0.252 | 0.384 | 0.639 |
|
calcInOutDegStats | 0.036 | 0.000 | 0.035 |
|
createSummaryTables | 0.148 | 0.012 | 0.159 |
|
degreeEstimates | 0.032 | 0.000 | 0.030 |
|
estErrProbMethodOfMoments | 0.000 | 0.000 | 0.002 |
|
estimateCCMErrorRates | 1.364 | 0.884 | 2.251 |
|
estimatePPIErrorRates | 3.324 | 0.608 | 3.936 |
|
genBPGraph | 0.172 | 0.000 | 0.170 |
|
idProteinErrorType | 1.120 | 0.760 | 1.881 |
|
idProteinType | 0.024 | 0.000 | 0.026 |
|
inOutScatterCharts | 0.000 | 0.000 | 0.001 |
|
nullDistDoublyTestedEdges | 0.216 | 0.024 | 0.242 |
|
twPERM | 0.004 | 0.000 | 0.000 |
|
viabilityCharts | 0.752 | 0.032 | 0.784 |
|