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BioC 2.13: CHECK report for MinimumDistance on moscato1

This page was generated on 2014-04-05 09:50:49 -0700 (Sat, 05 Apr 2014).

Package 450/750HostnameOS / ArchBUILDCHECKBUILD BIN
MinimumDistance 1.6.0
Robert B Scharpf
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/MinimumDistance
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  WARNINGS 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ WARNINGS ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  WARNINGS  OK 

Summary

Package: MinimumDistance
Version: 1.6.0
Command: rm -rf MinimumDistance.buildbin-libdir && mkdir MinimumDistance.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MinimumDistance.buildbin-libdir MinimumDistance_1.6.0.tar.gz >MinimumDistance-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=MinimumDistance.buildbin-libdir --install="check:MinimumDistance-install.out" --force-multiarch --no-vignettes --timings MinimumDistance_1.6.0.tar.gz && mv MinimumDistance.buildbin-libdir/* MinimumDistance.Rcheck/ && rmdir MinimumDistance.buildbin-libdir
StartedAt: 2014-04-05 05:09:41 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 05:25:13 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 931.6 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: MinimumDistance.Rcheck
Warnings: 1

Command output

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/MinimumDistance.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MinimumDistance/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MinimumDistance' version '1.6.0'
* 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 'MinimumDistance' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'BiocGenerics'
A package should be listed in only one of these fields.
* 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
Package in Depends field not imported from: 'IRanges'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': 'VanillaICE:::rescale'
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  'Biobase:::annotatedDataFrameFromMatrix' 'Biobase:::assayDataDim'
  'Biobase:::assayDataEnvLock' 'oligoClasses:::.checkOrder'
  'oligoClasses:::.getArm' 'oligoClasses:::setSequenceLengths'
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'initializeLrrAndBafArrays' 'narrowRangeForChromosome'
  'originalNames' 'read.bsfiles2' 'stackListByColIndex'
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.map_trioSet: no visible global function definition for 'ocSamples'
.map_trioSet: no visible binding for global variable 'i'
.map_trioSetList: no visible global function definition for 'ocSamples'
.map_trioSetList: no visible binding for global variable 'i'
computeBayesFactorTrioSet: no visible global function definition for
  'joint4'
close,TrioSet: no visible global function definition for 'isFF'
open,TrioSet: no visible global function definition for 'isFF'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'Pedigree,ANY,ANY,ANY'
  generic '[' and siglist 'TrioSet,ANY,ANY,ANY'
  generic '[' and siglist 'TrioSetList,ANY,ANY,ANY'
  generic '[' and siglist 'ff_array,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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' ... [95s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
computeBayesFactor 40.35   0.69   41.07
callDenovoSegments 17.43   0.03   17.54
narrow              5.50   0.03    5.54
** running examples for arch 'x64' ... [116s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
computeBayesFactor 46.59   1.07   47.68
callDenovoSegments 21.00   0.11   21.11
narrow              9.05   0.01    9.06
TrioSetListLD       5.54   0.11    5.65
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
  Running 'doRUnit.R' [222s]
 [222s] OK
** running tests for arch 'x64'
  Running 'doRUnit.R' [179s]
 [179s] OK
* 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

WARNING: There was 1 warning.
NOTE: There were 3 notes.
See
  'D:/biocbld/bbs-2.13-bioc/meat/MinimumDistance.Rcheck/00check.log'
for details.

MinimumDistance.Rcheck/00install.out:


install for i386

* installing *source* package 'MinimumDistance' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'xyplot' from package 'lattice' in package 'MinimumDistance'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'MinimumDistance' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MinimumDistance' as MinimumDistance_1.6.0.zip
* DONE (MinimumDistance)

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

nameusersystemelapsed
Pedigree-class0.020.000.02
Pedigree0.330.000.33
TrioSet-class3.500.083.57
TrioSet3.060.003.58
TrioSetList-class0.550.020.56
TrioSetListLD3.160.053.29
calculateMindist0.460.010.47
callDenovoSegments17.43 0.0317.54
computeBayesFactor40.35 0.6941.07
isDenovo0.050.000.05
lrr.segs0.020.000.02
mad20.50.00.5
narrow5.500.035.54
phenoData0.480.000.49
segment20.080.000.07
stackRangedDataList0.30.00.3
trioSetList2.740.032.78
trioSetListExample0.370.020.39
xyplotTrio1.420.011.43

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

nameusersystemelapsed
Pedigree-class0.480.000.48
Pedigree0.030.010.04
TrioSet-class3.970.104.07
TrioSet3.810.053.85
TrioSetList-class0.450.010.47
TrioSetListLD5.540.115.65
calculateMindist0.510.080.59
callDenovoSegments21.00 0.1121.11
computeBayesFactor46.59 1.0747.68
isDenovo0.110.000.11
lrr.segs000
mad20.540.020.55
narrow9.050.019.06
phenoData0.420.000.42
segment2000
stackRangedDataList0.370.000.38
trioSetList3.210.023.24
trioSetListExample0.500.030.53
xyplotTrio2.500.032.52