Multiple platform build/check report for BioC 3.7 - CHECK report for trio on merida2

Package: trio

Version: 3.18.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:trio.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings trio_3.18.0.tar.gz

StartedAt: 2018-10-17 00:30:39 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 00:33:07 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 148.3 seconds

RetCode: 0

Status: OK

CheckDir: trio.Rcheck

Warnings: 0

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:trio.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings trio_3.18.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/trio.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘3.18.0’
* 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 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  7.047  0.062   7.168
colGxGPerms   6.485  0.257   6.815
trio.permTest 6.527  0.046   6.648
trioFS        6.457  0.056   6.563
plot.trioLR   5.424  0.178   5.672
* 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-3.7-bioc/meat/trio.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL trio
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘trio’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘trio.Rnw’ 
** testing if installed package can be loaded
* DONE (trio)

name	user	system	elapsed
allelicTDT	0.042	0.006	0.049
colEMlrt	0.162	0.005	0.172
colGxE	0.011	0.001	0.012
colGxGPerms	6.485	0.257	6.815
colPOlrt	0.029	0.002	0.030
colTDTmaxTest	0.058	0.005	0.062
colTDTsam	0.724	0.025	0.762
findLDblocks	0.025	0.004	0.029
getLD	0.021	0.007	0.029
getMatPseudo	0.015	0.008	0.023
lrControl	0.001	0.000	0.001
ped2geno	0.001	0.001	0.002
plot.LDblocks	0.057	0.007	0.067
plot.getLD	0.043	0.011	0.056
plot.trioLR	5.424	0.178	5.672
poly4root	0.002	0.000	0.002
print.colGxE	0.090	0.006	0.096
print.trioFS	7.047	0.062	7.168
print.trioLR	4.115	0.041	4.212
probTDT	0.082	0.013	0.095
read.pedfile	0.002	0.000	0.003
removeSNPs	0.010	0.002	0.011
scoreTDT	0.018	0.001	0.019
tdt	0.038	0.002	0.041
tdtGxG	1.081	0.069	1.155
trio.check	1.006	0.005	1.017
trio.data	0.006	0.000	0.007
trio.permTest	6.527	0.046	6.648
trio.power	0.020	0.001	0.019
trio.prepare	3.294	0.059	3.387
trio.sim	0.338	0.006	0.344
trioFS	6.457	0.056	6.563
trioLR	3.434	0.047	3.509

CHECK report for trio on merida2

Summary

Command output

Installation output

Tests output

Example timings