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CHECK report for trio on tokay1

This page was generated on 2019-04-13 11:23:06 -0400 (Sat, 13 Apr 2019).

Package 1588/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
trio 3.20.0
Holger Schwender
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/trio
Branch: RELEASE_3_8
Last Commit: 16aad35
Last Changed Date: 2018-10-30 11:41:51 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  NA 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: trio
Version: 3.20.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:trio.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings trio_3.20.0.tar.gz
StartedAt: 2019-04-13 06:02:02 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 06:07:56 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 353.8 seconds
RetCode: 0
Status:  OK  
CheckDir: trio.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:trio.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings trio_3.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/trio.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'trio/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'trio' version '3.20.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
.onAttach: no visible global function definition for 'winMenuAdd'
.onAttach: no visible global function definition for 'winMenuAddItem'
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 winMenuAdd winMenuAddItem 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", "winMenuAdd", "winMenuAddItem", "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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
colGxGPerms   39.03   0.15   46.20
print.trioFS  16.42   0.02   16.43
trioFS        14.93   0.02   14.94
tdtGxG        12.38   0.02   12.39
trio.permTest  9.20   0.03    9.23
plot.trioLR    5.47   0.38    5.85
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
colGxGPerms   35.75   0.12   35.88
print.trioFS  16.45   0.03   16.48
trioFS        15.96   0.00   15.95
tdtGxG        12.66   0.00   12.67
trio.permTest  8.14   0.02    8.15
* 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
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/trio.Rcheck/00check.log'
for details.



Installation output

trio.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/trio_3.20.0.tar.gz && rm -rf trio.buildbin-libdir && mkdir trio.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=trio.buildbin-libdir trio_3.20.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL trio_3.20.0.zip && rm trio_3.20.0.tar.gz trio_3.20.0.zip
###
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##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  724k  100  724k    0     0  15.7M      0 --:--:-- --:--:-- --:--:-- 17.2M

install for i386

* installing *source* package 'trio' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'trio'
    finding HTML links ... done
    allelicTDT                              html  
    colEMlrt                                html  
    colGxE                                  html  
    colGxGPerms                             html  
    colPOlrt                                html  
    colTDTmaxTest                           html  
    colTDTsam                               html  
    findLDblocks                            html  
    getLD                                   html  
    getMatPseudo                            html  
    lrControl                               html  
    ped2geno                                html  
    plot.LDblocks                           html  
    plot.getLD                              html  
    plot.trioLR                             html  
    poly4root                               html  
    print.colGxE                            html  
    print.trioFS                            html  
    print.trioLR                            html  
    probTDT                                 html  
    read.pedfile                            html  
    removeSNPs                              html  
    scoreTDT                                html  
    tdt                                     html  
    tdtGxG                                  html  
    trio.check                              html  
    trio.data                               html  
    trio.permTest                           html  
    trio.power                              html  
    trio.prepare                            html  
    trio.sim                                html  
    trioFS                                  html  
    trioLR                                  html  
    vcf2geno                                html  
** building package indices
** installing vignettes
   'trio.Rnw' 
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'trio' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'trio' as trio_3.20.0.zip
* DONE (trio)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'trio' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

trio.Rcheck/examples_i386/trio-Ex.timings

nameusersystemelapsed
allelicTDT0.040.000.05
colEMlrt0.160.020.17
colGxE0.020.000.02
colGxGPerms39.03 0.1546.20
colPOlrt0.020.020.03
colTDTmaxTest0.080.000.08
colTDTsam0.700.040.75
findLDblocks0.050.000.05
getLD0.030.000.03
getMatPseudo0.010.000.02
lrControl000
ped2geno000
plot.LDblocks0.110.000.11
plot.getLD0.050.000.04
plot.trioLR5.470.385.85
poly4root000
print.colGxE0.10.00.1
print.trioFS16.42 0.0216.43
print.trioLR2.980.013.00
probTDT0.030.020.05
read.pedfile000
removeSNPs0.000.010.02
scoreTDT0.020.000.01
tdt0.280.000.28
tdtGxG12.38 0.0212.39
trio.check0.590.010.61
trio.data0.000.020.02
trio.permTest9.200.039.23
trio.power0.020.000.02
trio.prepare2.050.002.04
trio.sim0.320.000.33
trioFS14.93 0.0214.94
trioLR2.430.012.45

trio.Rcheck/examples_x64/trio-Ex.timings

nameusersystemelapsed
allelicTDT0.030.000.03
colEMlrt0.100.000.09
colGxE0.020.000.01
colGxGPerms35.75 0.1235.88
colPOlrt0.010.020.03
colTDTmaxTest0.050.000.05
colTDTsam0.560.010.57
findLDblocks0.020.020.04
getLD0.030.000.03
getMatPseudo0.010.000.01
lrControl000
ped2geno000
plot.LDblocks0.070.000.07
plot.getLD0.040.000.04
plot.trioLR4.540.114.78
poly4root000
print.colGxE0.080.000.08
print.trioFS16.45 0.0316.48
print.trioLR2.900.012.92
probTDT0.050.000.05
read.pedfile000
removeSNPs0.020.000.01
scoreTDT0.010.000.02
tdt0.170.000.17
tdtGxG12.66 0.0012.67
trio.check0.780.000.78
trio.data0.020.000.02
trio.permTest8.140.028.15
trio.power0.010.000.02
trio.prepare2.140.002.14
trio.sim0.330.000.33
trioFS15.96 0.0015.95
trioLR2.790.002.80