BioC 3.5: CHECK report for trio on malbec2

Package: trio

Version: 3.14.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings trio_3.14.0.tar.gz

StartedAt: 2017-10-18 02:59:27 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 03:01:08 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 101.1 seconds

RetCode: 0

Status:  OK

CheckDir: trio.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings trio_3.14.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/trio.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (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 ‘3.14.0’
* 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 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  7.360   0.02   7.403
trioFS        6.472   0.00   6.479
trio.permTest 6.092   0.00   6.092
colGxGPerms   5.876   0.02   5.897
plot.trioLR   5.412   0.02   5.614
* 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
  ‘/home/biocbuild/bbs-3.5-bioc/meat/trio.Rcheck/00check.log’
for details.

* 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)

name	user	system	elapsed
allelicTDT	0.024	0.004	0.028
colEMlrt	0.224	0.004	0.231
colGxE	0.200	0.004	0.203
colGxGPerms	5.876	0.020	5.897
colPOlrt	0.060	0.000	0.061
colTDTmaxTest	0.184	0.008	0.192
colTDTsam	0.776	0.004	0.779
findLDblocks	0.212	0.000	0.213
getLD	0.016	0.000	0.017
getMatPseudo	0.008	0.000	0.008
lrControl	0.004	0.000	0.001
ped2geno	0	0	0
plot.LDblocks	0.136	0.004	0.139
plot.getLD	0.032	0.000	0.031
plot.trioLR	5.412	0.020	5.614
poly4root	0.000	0.000	0.002
print.colGxE	0.176	0.008	0.186
print.trioFS	7.360	0.020	7.403
print.trioLR	2.588	0.000	2.588
probTDT	0.124	0.008	0.129
read.pedfile	0.000	0.000	0.001
removeSNPs	0.008	0.000	0.006
scoreTDT	0.044	0.000	0.044
tdt	0.072	0.000	0.072
tdtGxG	1.368	0.004	1.370
trio.check	0.620	0.000	0.618
trio.data	0.004	0.000	0.006
trio.permTest	6.092	0.000	6.092
trio.power	3.560	0.000	3.562
trio.prepare	2.220	0.000	2.221
trio.sim	1.276	0.000	1.277
trioFS	6.472	0.000	6.479
trioLR	2.400	0.000	2.402