BioC 2.14: CHECK report for PCpheno on moscato2

Package: PCpheno

Version: 1.26.0

Command: rm -rf PCpheno.buildbin-libdir && mkdir PCpheno.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=PCpheno.buildbin-libdir PCpheno_1.26.0.tar.gz >PCpheno-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=PCpheno.buildbin-libdir --install="check:PCpheno-install.out" --force-multiarch --no-vignettes --timings PCpheno_1.26.0.tar.gz

StartedAt: 2014-10-08 03:45:28 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 03:51:13 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 344.7 seconds

RetCode: 0

Status:  OK

CheckDir: PCpheno.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf PCpheno.buildbin-libdir && mkdir PCpheno.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=PCpheno.buildbin-libdir PCpheno_1.26.0.tar.gz >PCpheno-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=PCpheno.buildbin-libdir --install="check:PCpheno-install.out" --force-multiarch --no-vignettes --timings PCpheno_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/PCpheno.Rcheck'
* using R version 3.1.1 (2014-07-10)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'PCpheno/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PCpheno' version '1.26.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'Category' 'ScISI' 'SLGI' 'ppiStats' 'ppiData' 'annotate'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'PCpheno' 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:
  'Category' 'ScISI' 'KEGG.db' 'GO.db'
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
** 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
Packages in Depends field not imported from:
  'SLGI' 'annotate' 'ppiData' 'ppiStats'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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 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' ... [37s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
graphTheory    7.00   0.10    7.10
gtResult-class 5.63   0.61    6.24
** running examples for arch 'x64' ... [45s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
gtResult-class 8.51   0.71    9.24
graphTheory    8.77   0.08    8.84
ppiInteraction 5.57   0.08    5.65
* 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
  'E:/biocbld/bbs-2.14-bioc/meat/PCpheno.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'PCpheno' ...
** R
** data
** inst
** preparing package for lazy loading
No methods found in "BiocGenerics" for requests: plot
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "BiocGenerics" for requests: plot

install for x64

* installing *source* package 'PCpheno' ...
** testing if installed package can be loaded
No methods found in "BiocGenerics" for requests: plot
* MD5 sums
packaged installation of 'PCpheno' as PCpheno_1.26.0.zip
* DONE (PCpheno)

name	user	system	elapsed
CoHyperGResult-class	0.51	0.00	0.56
Dudley	0.01	0.00	0.01
Giaever	0.33	0.00	0.33
HI	0	0	0
KEGG2SCISI	0.31	0.02	1.17
Kastenmayer	0.02	0.00	0.02
Lesage	0	0	0
Osterberg	0.01	0.01	0.03
SGDphenoL	0.03	0.00	0.03
YEASTOHNOLOG	0.00	0.02	0.01
buildFDMat	0.36	0.02	0.38
categoryToEntrezBuilder	0.33	0.00	0.34
complexStatus	1.28	0.03	1.36
deResult-class	0.06	0.04	0.11
densityEstimate	1.75	0.14	1.89
getDescr	0.87	0.00	1.19
getFDgene	0.17	0.00	0.17
graphTheory	7.0	0.1	7.1
gtResult-class	5.63	0.61	6.24
overlap	0	0	0
plot	1.48	0.04	1.53
ppiInteraction	4.34	0.10	4.63
reduceM	0	0	0
truncName	0	0	0

name	user	system	elapsed
CoHyperGResult-class	0.69	0.00	0.68
Dudley	0.02	0.00	0.01
Giaever	0.39	0.00	0.39
HI	0	0	0
KEGG2SCISI	0.55	0.03	0.58
Kastenmayer	0.02	0.00	0.01
Lesage	0.01	0.00	0.02
Osterberg	0.03	0.00	0.03
SGDphenoL	0.03	0.00	0.03
YEASTOHNOLOG	0	0	0
buildFDMat	0.39	0.04	0.42
categoryToEntrezBuilder	0.35	0.01	0.36
complexStatus	1.62	0.02	1.64
deResult-class	0.10	0.00	0.11
densityEstimate	2.08	0.12	2.20
getDescr	1	0	1
getFDgene	0.14	0.02	0.16
graphTheory	8.77	0.08	8.84
gtResult-class	8.51	0.71	9.24
overlap	0	0	0
plot	2.23	0.14	2.37
ppiInteraction	5.57	0.08	5.65
reduceM	0	0	0
truncName	0	0	0