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BioC 3.5: CHECK report for trio on toluca2

This page was generated on 2017-04-23 14:37:38 -0400 (Sun, 23 Apr 2017).

Package 1331/1377HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
trio 3.13.0
Holger Schwender
Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/trio
Last Changed Rev: 122712 / Revision: 129046
Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: trio
Version: 3.13.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings trio_3.13.0.tar.gz
StartedAt: 2017-04-23 10:57:12 -0400 (Sun, 23 Apr 2017)
EndedAt: 2017-04-23 10:59:42 -0400 (Sun, 23 Apr 2017)
EllapsedTime: 149.9 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 trio_3.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/trio.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 ‘trio/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘trio’ version ‘3.13.0’
* 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 ... 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:
  ‘LogicReg’ ‘VariantAnnotation’ ‘haplo.stats’ ‘logicFS’ ‘mcbiopi’
  ‘siggenes’ ‘splines’ ‘survival’
  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
EvsG2: no visible global function definition for ‘pchisq’
EvsG2split: no visible global function definition for ‘optim’
EvsG4: no visible global function definition for ‘pchisq’
EvsG4split: no visible global function definition for ‘optim’
HRCB.Esp1Rule.sampleKid: no visible global function definition for
  ‘rmultinom’
HRCB.Esp1Rule.spTrioOnBase: no visible global function definition for
  ‘write.csv’
HRCB.applyRule: no visible global function definition for ‘str’
HRCB.applyRule: no visible global function definition for ‘write.csv’
HRCB.famMap.spTrio: no visible global function definition for
  ‘write.csv’
HRCBSpGrp.sp: no visible global function definition for ‘rmultinom’
allelicTDT: no visible global function definition for ‘pchisq’
bkMap.ESp.apply1Rule: no visible global function definition for ‘str’
bkMap.ESp.apply1Rule.stepBy: no visible global function definition for
  ‘str’
bkMap.HRCB.famMap: no visible global function definition for ‘str’
bkMap.LRCB.spTrio: no visible global function definition for
  ‘write.table’
bkMap.constr: no visible global function definition for ‘read.csv’
bkMap.superHRCB: no visible global function definition for ‘str’
bothHetMat: no visible global function definition for ‘rmultinom’
bothHetMat: no visible global function definition for ‘rbinom’
colEMlrt: no visible global function definition for ‘glm’
colEMlrt: no visible global function definition for ‘quasipoisson’
colEMlrt: no visible global function definition for ‘pchisq’
colGxE: no visible global function definition for ‘pchisq’
colGxE: no visible global function definition for ‘qnorm’
colGxEunstructured: no visible global function definition for ‘clogit’
colGxEunstructured: no visible global function definition for ‘is’
colGxEunstructured: no visible global function definition for ‘pchisq’
colGxG: no visible global function definition for ‘clogit’
colGxG: no visible global function definition for ‘is’
colGxG: no visible global function definition for ‘qnorm’
colGxG: no visible global function definition for ‘pchisq’
colGxGPerms: no visible global function definition for ‘is’
colGxGlrt: no visible global function definition for ‘clogit’
colGxGlrt: no visible global function definition for ‘is’
colGxGlrt: no visible global function definition for ‘pchisq’
colPOlrt: no visible global function definition for ‘pchisq’
colTAT: no visible global function definition for ‘pchisq’
colTDTebam: no visible global function definition for ‘ebam’
colTDTepistatic: no visible global function definition for ‘clogit’
colTDTepistatic: no visible global function definition for ‘is’
colTDTepistatic: no visible global function definition for ‘pchisq’
colTDTsam: no visible global function definition for ‘sam’
compBothHet: no visible global function definition for ‘rmultinom’
compBothHet: no visible global function definition for ‘rbinom’
estimateRatioTDT: no visible global function definition for ‘ns’
estimateRatioTDT: no visible global function definition for ‘glm’
estimateRatioTDT: no visible binding for global variable ‘binomial’
estimateRatioTDT: no visible global function definition for ‘predict’
fastGxG: no visible global function definition for ‘pchisq’
fastGxG: no visible global function definition for ‘qnorm’
fastGxG: no visible binding for global variable ‘coef’
fastGxGrec: no visible global function definition for ‘pchisq’
fastGxGrec: no visible global function definition for ‘qnorm’
fastGxGrec: no visible binding for global variable ‘coef’
fastTDTdomSplit: no visible global function definition for ‘qnorm’
fastTDTdomSplit: no visible global function definition for ‘pchisq’
fastTDTrecSplit: no visible global function definition for ‘qnorm’
fastTDTrecSplit: no visible global function definition for ‘pchisq’
fastTDTsplit: no visible global function definition for ‘qnorm’
fastTDTsplit: no visible global function definition for ‘pchisq’
findLDblocks: no visible global function definition for ‘is’
freq.build: no visible global function definition for ‘read.csv’
freqmap.reconstruct: no visible global function definition for
  ‘haplo.em’
getBackParentGeno: no visible global function definition for
  ‘write.table’
getBetaAdd: no visible global function definition for ‘uniroot’
getBetaAdd: no visible global function definition for ‘is’
getBetaDom: no visible global function definition for ‘uniroot’
getBetaDom: no visible global function definition for ‘is’
getBetaRec: no visible global function definition for ‘uniroot’
getBetaRec: no visible global function definition for ‘is’
getCalls4LD: no visible global function definition for ‘qnorm’
getGxEstats: no visible global function definition for ‘is’
getOriginalStat: no visible global function definition for ‘clogit’
getOriginalStat: no visible global function definition for ‘is’
getPermStat: no visible global function definition for ‘clogit’
getPermStat: no visible global function definition for ‘is’
grp.CI : <anonymous>: no visible global function definition for
  ‘segments’
grp.kmStep: no visible global function definition for ‘segments’
grp.kmStep: no visible global function definition for ‘points’
grp.palette: no visible global function definition for ‘jpeg’
grp.palette: no visible global function definition for ‘colors’
grp.palette: no visible global function definition for ‘plot’
grp.palette: no visible global function definition for ‘rect’
grp.palette: no visible global function definition for ‘axis’
grp.palette: no visible global function definition for ‘grid’
grp.palette: no visible global function definition for ‘dev.off’
gtdt.null.add: no visible global function definition for ‘rbinom’
gtdt.null.add: no visible global function definition for ‘rmultinom’
gtdt.null.approx: no visible global function definition for
  ‘na.exclude’
gtdt.null.approx: no visible global function definition for ‘qchisq’
gtdt.null.approx2: no visible global function definition for ‘denspr’
gtdt.null.approx2: no visible global function definition for ‘dchisq’
gtdt.null.dom: no visible global function definition for ‘rbinom’
gtdt.null.rec: no visible global function definition for ‘rbinom’
gxeBetaVadd: no visible global function definition for ‘rbinom’
gxeBetaVadd: no visible global function definition for ‘rmultinom’
gxeBetaVdom: no visible global function definition for ‘rbinom’
gxeBetaVrec: no visible global function definition for ‘rbinom’
impuBk.scheduler: no visible global function definition for
  ‘write.table’
impuBkTDT.scheduler: no visible binding for global variable ‘data’
impuBkTDT.scheduler: no visible global function definition for
  ‘write.table’
noBothHet: no visible global function definition for ‘rbinom’
noBothHetMat: no visible global function definition for ‘rbinom’
plot.LDblocks: no visible global function definition for ‘plot’
plot.LDblocks: no visible global function definition for ‘segments’
plot.getLD: no visible global function definition for ‘par’
plot.getLD: no visible global function definition for ‘gray’
plot.getLD: no visible global function definition for ‘image’
plot.getLD: no visible global function definition for ‘axis’
plot.getLD: no visible global function definition for ‘legend’
plot.getLDlarge: no visible global function definition for ‘gray’
plot.getLDlarge: no visible global function definition for ‘par’
plot.getLDlarge: no visible global function definition for ‘image’
plot.getLDlarge: no visible global function definition for ‘axis’
plot.getLDlarge: no visible global function definition for ‘legend’
plot.trioFS: no visible global function definition for ‘dotchart’
plot.trioFS: no visible global function definition for ‘abline’
plot.trioLR: no visible global function definition for ‘barplot’
plot.trioLR: no visible global function definition for ‘image’
plot.trioLR: no visible global function definition for ‘axis’
plotTrioTree: no visible global function definition for ‘plot’
plotTrioTree: no visible global function definition for ‘text’
plotTrioTree: no visible global function definition for ‘title’
plotTrioTree: no visible global function definition for ‘points’
plotTrioTree: no visible global function definition for ‘lines’
polrtChunk: no visible global function definition for ‘optim’
printTrioTree: no visible global function definition for ‘getPImps’
probTDTdomSplit: no visible global function definition for ‘qnorm’
probTDTdomSplit: no visible global function definition for ‘pchisq’
probTDTrecSplit: no visible global function definition for ‘qnorm’
probTDTrecSplit: no visible global function definition for ‘pchisq’
probTDTsplit: no visible global function definition for ‘qnorm’
probTDTsplit: no visible global function definition for ‘pchisq’
read.pedfile: no visible global function definition for ‘read.table’
scoreGxE: no visible global function definition for ‘pchisq’
scoreGxG: no visible global function definition for ‘pchisq’
scoreTDTdomSplit: no visible global function definition for ‘pchisq’
scoreTDTrecSplit: no visible global function definition for ‘pchisq’
scoreTDTsplit: no visible global function definition for ‘pchisq’
simuHapMap.build: no visible global function definition for ‘read.csv’
snpPREFileMatchTrio: no visible global function definition for
  ‘read.table’
splitBlocks: no visible global function definition for ‘is’
tdt: no visible global function definition for ‘clogit’
tdt: no visible global function definition for ‘qnorm’
tdt: no visible global function definition for ‘pchisq’
tdtEpistatic: no visible global function definition for ‘clogit’
tdtEpistatic: no visible global function definition for ‘is’
tdtEpistatic: no visible global function definition for ‘pchisq’
tdtGxG: no visible global function definition for ‘clogit’
tdtGxG: no visible global function definition for ‘is’
tdtGxG: no visible global function definition for ‘pchisq’
tdtGxG: no visible global function definition for ‘qnorm’
trio.impu: no visible global function definition for ‘read.csv’
trio.impuDev: no visible global function definition for ‘read.csv’
trio.permTest: no visible global function definition for ‘is’
trio.permTest: no visible global function definition for ‘evalTree’
trio.power : single: no visible global function definition for ‘qnorm’
trio.power : single: no visible global function definition for ‘pnorm’
trio.simuDev: no visible global function definition for ‘data’
trio.simuDev: no visible binding for global variable ‘simuBkMap’
trio.simuOLD: no visible global function definition for ‘data’
trio.simuOLD: no visible binding for global variable ‘simuBkMap’
trioBagging: no visible global function definition for ‘packageVersion’
trioFS.formula: no visible global function definition for
  ‘packageVersion’
trioFS.formula: no visible global function definition for ‘getXy’
trioLR.default: no visible global function definition for
  ‘packageVersion’
trioLR.formula: no visible global function definition for
  ‘packageVersion’
trioLR.formula: no visible global function definition for ‘getXy’
trioMerge: no visible global function definition for ‘str’
trioPImp: no visible global function definition for ‘getPImps’
triologreg: no visible global function definition for ‘runif’
txtToGenoMap: no visible global function definition for ‘read.csv’
txtToHapBkMap: no visible global function definition for ‘read.csv’
vcf2geno: no visible global function definition for ‘is’
vim.trioFS: no visible global function definition for ‘is’
vimTrio: no visible global function definition for ‘clogit’
vimTrio.oneprime: no visible global function definition for ‘clogit’
Undefined global functions or variables:
  abline axis barplot binomial clogit coef colors data dchisq denspr
  dev.off dotchart ebam evalTree getPImps getXy glm gray grid haplo.em
  image is jpeg legend lines na.exclude ns optim packageVersion par
  pchisq plot pnorm points predict qchisq qnorm quasipoisson rbinom
  read.csv read.table rect rmultinom runif sam segments simuBkMap str
  text title uniroot write.csv write.table
Consider adding
  importFrom("grDevices", "colors", "dev.off", "gray", "jpeg")
  importFrom("graphics", "abline", "axis", "barplot", "dotchart", "grid",
             "image", "legend", "lines", "par", "plot", "points", "rect",
             "segments", "text", "title")
  importFrom("methods", "is")
  importFrom("stats", "binomial", "coef", "dchisq", "glm", "na.exclude",
             "optim", "pchisq", "pnorm", "predict", "qchisq", "qnorm",
             "quasipoisson", "rbinom", "rmultinom", "runif", "uniroot")
  importFrom("utils", "data", "packageVersion", "read.csv", "read.table",
             "str", "write.csv", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
print.trioFS  8.849  0.052   8.981
colGxGPerms   8.011  0.206   8.257
plot.trioLR   7.541  0.114   7.735
trioFS        7.333  0.041   7.416
trio.permTest 7.264  0.038   7.361
trio.power    5.592  0.017   5.634
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-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
allelicTDT0.0310.0050.036
colEMlrt0.3450.0090.356
colGxE0.3290.0020.333
colGxGPerms8.0110.2068.257
colPOlrt0.0960.0010.098
colTDTmaxTest0.2900.0090.300
colTDTsam1.0420.0121.056
findLDblocks0.5160.0060.521
getLD0.0230.0040.027
getMatPseudo0.0100.0010.010
lrControl0.0010.0000.001
ped2geno0.0010.0000.001
plot.LDblocks0.2230.0040.230
plot.getLD0.0410.0030.043
plot.trioLR7.5410.1147.735
poly4root0.0010.0000.001
print.colGxE0.1600.0040.166
print.trioFS8.8490.0528.981
print.trioLR4.2390.0364.287
probTDT0.2120.0080.222
read.pedfile0.0010.0000.001
removeSNPs0.0080.0010.009
scoreTDT0.0620.0020.063
tdt0.1200.0020.123
tdtGxG1.7290.0211.751
trio.check1.1630.0091.180
trio.data0.0060.0010.007
trio.permTest7.2640.0387.361
trio.power5.5920.0175.634
trio.prepare3.9060.0193.980
trio.sim1.4930.0091.504
trioFS7.3330.0417.416
trioLR4.1760.0484.263