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BioC 2.13: CHECK report for Category on moscato1

This page was generated on 2014-04-05 09:49:12 -0700 (Sat, 05 Apr 2014).

Package 112/750HostnameOS / ArchBUILDCHECKBUILD BIN
Category 2.28.0
Bioconductor Package Maintainer
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/Category
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  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: Category
Version: 2.28.0
Command: rm -rf Category.buildbin-libdir && mkdir Category.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Category.buildbin-libdir Category_2.28.0.tar.gz >Category-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=Category.buildbin-libdir --install="check:Category-install.out" --force-multiarch --no-vignettes --timings Category_2.28.0.tar.gz && mv Category.buildbin-libdir/* Category.Rcheck/ && rmdir Category.buildbin-libdir
StartedAt: 2014-04-05 02:46:34 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 02:54:20 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 466.0 seconds
RetCode: 0
Status:  OK  
CheckDir: Category.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/Category.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 'Category/DESCRIPTION' ... OK
* this is package 'Category' version '2.28.0'
* 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 'Category' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'BiocGenerics' 'methods' 'Biobase' 'AnnotationDbi' 'graph' 'genefilter'
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
Packages in Depends field not imported from:
  'GO.db' 'Matrix'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'DatPkgFactory'
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 ... OK
* 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 installed files from 'inst/doc' ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'Category.Rnw', 'ChromBand.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [41s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
ChrBandTree-class 11.10   0.12   11.23
MAPAmat            8.08   0.03    8.11
makeChrBandGraph   7.66   0.00    7.66
** running examples for arch 'x64' ... [51s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
ChrBandTree-class 13.37   0.11   13.49
MAPAmat           11.36   0.02   11.37
makeChrBandGraph  10.20   0.02   10.22
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
  Running 'runTests.R' [54s]
 [54s] OK
** running tests for arch 'x64'
  Running 'runTests.R' [58s]
 [58s] 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

NOTE: There were 3 notes.
See
  'D:/biocbld/bbs-2.13-bioc/meat/Category.Rcheck/00check.log'
for details.

Category.Rcheck/00install.out:


install for i386

* installing *source* package 'Category' ...
** R
** 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 'Category' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Category' as Category_2.28.0.zip
* DONE (Category)

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

nameusersystemelapsed
ChrBandTree-class11.10 0.1211.23
ChrMapHyperGParams-class0.020.000.01
ChrMapHyperGResult-class000
ChrMapLinearMParams-class000
ChrMapLinearMResult-class000
DatPkg-class0.080.000.08
HyperGResult-accessors0.700.020.71
LinearMResult-class000
MAPAmat8.080.038.11
applyByCategory0.010.000.01
cateGOryMatrix0.310.020.33
cb_parse_band_Hs0.020.000.02
cb_parse_band_Mm0.010.000.01
findAMstats000
getPathNames0.090.000.09
gseattperm1.700.011.72
hyperg0.850.021.43
makeChrBandGraph7.660.007.66
makeEBcontr0.420.010.44
probes2MAP0.370.020.39
probes2Path0.110.020.12
ttperm0.030.000.03

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

nameusersystemelapsed
ChrBandTree-class13.37 0.1113.49
ChrMapHyperGParams-class000
ChrMapHyperGResult-class0.010.000.01
ChrMapLinearMParams-class000
ChrMapLinearMResult-class000
DatPkg-class0.060.010.08
HyperGResult-accessors1.050.001.04
LinearMResult-class000
MAPAmat11.36 0.0211.37
applyByCategory0.020.000.01
cateGOryMatrix0.310.030.38
cb_parse_band_Hs000
cb_parse_band_Mm0.020.000.01
findAMstats0.010.000.02
getPathNames0.100.000.09
gseattperm1.870.031.90
hyperg0.820.030.84
makeChrBandGraph10.20 0.0210.22
makeEBcontr0.320.030.34
probes2MAP0.250.010.27
probes2Path0.040.030.42
ttperm0.010.000.01