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BioC 3.0: CHECK report for trio on perceval

This page was generated on 2015-04-10 09:58:33 -0700 (Fri, 10 Apr 2015).

Package 900/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
trio 3.4.0
Holger Schwender
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/trio
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
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: trio
Version: 3.4.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch trio_3.4.0.tar.gz
StartedAt: 2015-04-10 07:12:40 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 07:15:31 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 171.6 seconds
RetCode: 0
Status:  OK 
CheckDir: trio.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch trio_3.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/trio.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘trio/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘trio’ version ‘3.4.0’
* 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 ‘trio’ can be installed ... [3s/8s] 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
'library' or 'require' calls in package code:
  ‘haplo.stats’ ‘logicFS’ ‘LogicReg’ ‘mcbiopi’ ‘siggenes’ ‘splines’
  ‘survival’ ‘VariantAnnotation’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
  .Fortran("slogreg", ..., PACKAGE = "LogicReg")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
colGxG: no visible global function definition for ‘clogit’
colGxGlrt: no visible global function definition for ‘clogit’
colTDTebam: no visible global function definition for ‘ebam’
colTDTepistatic: no visible global function definition for ‘clogit’
colTDTsam: no visible global function definition for ‘sam’
estimateRatioTDT: no visible global function definition for ‘ns’
freqmap.reconstruct: no visible global function definition for
  ‘haplo.em’
getOriginalStat: no visible global function definition for ‘clogit’
getPermStat: no visible global function definition for ‘clogit’
gtdt.null.approx2: no visible global function definition for ‘denspr’
printTrioTree: no visible global function definition for ‘getPImps’
tdt: no visible global function definition for ‘clogit’
tdtEpistatic: no visible global function definition for ‘clogit’
tdtGxG: no visible global function definition for ‘clogit’
trio.permTest: no visible global function definition for ‘evalTree’
trioFS.formula: no visible global function definition for ‘getXy’
trioLR.formula: no visible global function definition for ‘getXy’
trioPImp: no visible global function definition for ‘getPImps’
vimTrio: no visible global function definition for ‘clogit’
vimTrio.oneprime: no visible global function definition for ‘clogit’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [68s/69s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
print.trioFS  9.969  0.031  10.034
trioFS        9.782  0.020   9.807
trio.permTest 9.319  0.025   9.352
colGxGPerms   8.375  0.025   8.406
print.trioLR  5.842  0.017   5.859
plot.trioLR   5.497  0.049   5.622
trioLR        5.450  0.018   5.476
trio.prepare  5.339  0.017   5.359
* 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

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/trio.Rcheck/00check.log’
for details.

trio.Rcheck/00install.out:

* installing *source* package ‘trio’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (trio)

trio.Rcheck/trio-Ex.timings:

nameusersystemelapsed
allelicTDT0.0460.0070.053
colEMlrt0.2450.0030.249
colGxE0.0140.0010.015
colGxGPerms8.3750.0258.406
colPOlrt0.0460.0070.052
colTDTmaxTest0.1710.0150.186
colTDTsam1.4250.0431.476
findLDblocks0.2020.0090.211
getLD0.0430.0020.045
getMatPseudo0.0160.0020.019
lrControl0.0010.0000.001
ped2geno0.0010.0000.001
plot.LDblocks0.0820.0040.098
plot.getLD0.1930.0040.214
plot.trioLR5.4970.0495.622
poly4root0.0010.0000.001
print.colGxE0.1000.0050.105
print.trioFS 9.969 0.03110.034
print.trioLR5.8420.0175.859
probTDT0.1120.0150.127
read.pedfile0.0010.0000.001
removeSNPs0.0100.0010.011
scoreTDT0.0170.0010.018
tdt0.0720.0030.075
tdtGxG2.3780.0052.383
trio.check1.6270.0171.657
trio.data0.0080.0010.008
trio.permTest9.3190.0259.352
trio.power0.0190.0000.020
trio.prepare5.3390.0175.359
trio.sim0.3160.0010.318
trioFS9.7820.0209.807
trioLR5.4500.0185.476