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BioC 3.1: CHECK report for trio on moscato2

This page was generated on 2015-10-09 09:30:35 -0700 (Fri, 09 Oct 2015).

Package 989/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
trio 3.6.0
Holger Schwender
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/trio
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: trio
Version: 3.6.0
Command: rm -rf trio.buildbin-libdir trio.Rcheck && mkdir trio.buildbin-libdir trio.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=trio.buildbin-libdir trio_3.6.0.tar.gz >trio.Rcheck\00install.out 2>&1 && cp trio.Rcheck\00install.out trio-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=trio.buildbin-libdir --install="check:trio-install.out" --force-multiarch --no-vignettes --timings trio_3.6.0.tar.gz
StartedAt: 2015-10-09 06:57:05 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 07:00:59 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 234.7 seconds
RetCode: 0
Status:  OK  
CheckDir: trio.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf trio.buildbin-libdir trio.Rcheck && mkdir trio.buildbin-libdir trio.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=trio.buildbin-libdir trio_3.6.0.tar.gz >trio.Rcheck\00install.out 2>&1 && cp trio.Rcheck\00install.out trio-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=trio.buildbin-libdir --install="check:trio-install.out" --force-multiarch --no-vignettes --timings trio_3.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/trio.Rcheck'
* using R version 3.2.2 (2015-08-14)
* 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 '3.6.0'
* 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 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
** checking loading without being on the library search path ... 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 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
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [67s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
trioFS        11.57   0.00   11.58
print.trioFS  11.39   0.02   11.42
trio.permTest 11.39   0.02   11.41
plot.trioLR    7.09   0.03    7.97
colGxGPerms    6.21   0.03    6.24
** running examples for arch 'x64' ... [82s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
print.trioFS  12.87   0.03   12.91
trio.permTest 12.20   0.02   12.22
trioFS        12.14   0.00   12.15
colGxGPerms    9.68   0.01    9.71
plot.trioLR    8.35   0.11    9.66
print.trioLR   6.41   0.00    6.41
trio.prepare   5.71   0.00    5.71
* 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
  'E:/biocbld/bbs-3.1-bioc/meat/trio.Rcheck/00check.log'
for details.


trio.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'trio' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'trio' as trio_3.6.0.zip
* DONE (trio)

trio.Rcheck/examples_i386/trio-Ex.timings:

nameusersystemelapsed
allelicTDT0.030.000.03
colEMlrt0.190.000.19
colGxE0.010.020.03
colGxGPerms6.210.036.24
colPOlrt0.030.000.03
colTDTmaxTest0.140.000.14
colTDTsam0.670.010.69
findLDblocks0.110.000.11
getLD0.030.000.03
getMatPseudo0.020.000.01
lrControl000
ped2geno000
plot.LDblocks0.120.000.13
plot.getLD0.070.020.08
plot.trioLR7.090.037.97
poly4root000
print.colGxE0.060.000.06
print.trioFS11.39 0.0211.42
print.trioLR4.460.014.48
probTDT0.190.000.19
read.pedfile000
removeSNPs000
scoreTDT0.010.020.03
tdt0.030.000.03
tdtGxG2.080.012.09
trio.check0.90.00.9
trio.data000
trio.permTest11.39 0.0211.41
trio.power0.020.000.01
trio.prepare3.800.003.81
trio.sim0.240.000.23
trioFS11.57 0.0011.58
trioLR4.620.004.62

trio.Rcheck/examples_x64/trio-Ex.timings:

nameusersystemelapsed
allelicTDT0.050.000.05
colEMlrt0.170.000.17
colGxE000
colGxGPerms9.680.019.71
colPOlrt0.060.000.06
colTDTmaxTest0.220.000.22
colTDTsam1.370.031.40
findLDblocks0.220.020.24
getLD0.060.000.06
getMatPseudo0.020.000.01
lrControl000
ped2geno000
plot.LDblocks0.090.000.09
plot.getLD0.140.020.16
plot.trioLR8.350.119.66
poly4root000
print.colGxE0.090.010.10
print.trioFS12.87 0.0312.91
print.trioLR6.410.006.41
probTDT0.080.020.09
read.pedfile000
removeSNPs0.010.000.02
scoreTDT0.030.000.03
tdt0.050.000.05
tdtGxG2.530.002.53
trio.check1.770.001.78
trio.data0.020.000.01
trio.permTest12.20 0.0212.22
trio.power0.020.000.02
trio.prepare5.710.005.71
trio.sim0.410.000.40
trioFS12.14 0.0012.15
trioLR4.830.004.84