BioC 3.0: CHECK report for PCpheno on moscato1

Package: PCpheno

Version: 1.28.0

Command: rm -rf PCpheno.buildbin-libdir PCpheno.Rcheck && mkdir PCpheno.buildbin-libdir PCpheno.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=PCpheno.buildbin-libdir PCpheno_1.28.0.tar.gz >PCpheno.Rcheck\00install.out 2>&1 && cp PCpheno.Rcheck\00install.out PCpheno-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=PCpheno.buildbin-libdir --install="check:PCpheno-install.out" --force-multiarch --no-vignettes --timings PCpheno_1.28.0.tar.gz

StartedAt: 2015-04-10 04:03:26 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 04:10:16 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 410.0 seconds

RetCode: 0

Status:  OK

CheckDir: PCpheno.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf PCpheno.buildbin-libdir PCpheno.Rcheck && mkdir PCpheno.buildbin-libdir PCpheno.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=PCpheno.buildbin-libdir PCpheno_1.28.0.tar.gz >PCpheno.Rcheck\00install.out 2>&1 && cp PCpheno.Rcheck\00install.out PCpheno-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=PCpheno.buildbin-libdir --install="check:PCpheno-install.out" --force-multiarch --no-vignettes --timings PCpheno_1.28.0.tar.gz
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* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/PCpheno.Rcheck'
* using R version 3.1.3 (2015-03-09)
* 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 '1.28.0'
* 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
'library' or 'require' calls in package code:
  'GO.db' 'KEGG.db'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
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.
* 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' ... [44s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
graphTheory    7.48   0.10    7.56
gtResult-class 5.72   0.71    6.45
ppiInteraction 6.12   0.09    7.93
** running examples for arch 'x64' ... [43s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
gtResult-class 7.47   0.63    8.10
graphTheory    7.13   0.12    7.25
* 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

NOTE: There were 3 notes.
See
  'D:/biocbld/bbs-3.0-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_1.28.0.zip
* DONE (PCpheno)

name	user	system	elapsed
CoHyperGResult-class	0.77	0.00	0.78
Dudley	0.01	0.00	0.01
Giaever	0.14	0.01	0.16
HI	0	0	0
KEGG2SCISI	0.47	0.00	1.34
Kastenmayer	0.01	0.00	0.01
Lesage	0	0	0
Osterberg	0.01	0.00	0.01
SGDphenoL	0.02	0.02	0.03
YEASTOHNOLOG	0	0	0
buildFDMat	0.17	0.05	0.22
categoryToEntrezBuilder	0.32	0.00	1.35
complexStatus	1.25	0.03	2.31
deResult-class	0.10	0.01	0.11
densityEstimate	1.76	0.10	1.86
getDescr	0.90	0.00	1.12
getFDgene	0.14	0.01	0.16
graphTheory	7.48	0.10	7.56
gtResult-class	5.72	0.71	6.45
overlap	0	0	0
plot	1.53	0.08	1.60
ppiInteraction	6.12	0.09	7.93
reduceM	0	0	0
truncName	0	0	0

name	user	system	elapsed
CoHyperGResult-class	0.92	0.03	0.95
Dudley	0	0	0
Giaever	0.12	0.00	0.12
HI	0.00	0.01	0.02
KEGG2SCISI	0.58	0.04	0.61
Kastenmayer	0.02	0.00	0.01
Lesage	0	0	0
Osterberg	0.02	0.00	0.01
SGDphenoL	0.03	0.00	0.04
YEASTOHNOLOG	0.02	0.00	0.01
buildFDMat	0.43	0.04	0.48
categoryToEntrezBuilder	0.38	0.02	0.39
complexStatus	1.43	0.00	1.44
deResult-class	0.10	0.01	0.11
densityEstimate	1.66	0.11	1.78
getDescr	0.95	0.05	1.02
getFDgene	0.14	0.00	0.14
graphTheory	7.13	0.12	7.25
gtResult-class	7.47	0.63	8.10
overlap	0	0	0
plot	1.58	0.12	1.70
ppiInteraction	4.88	0.05	4.93
reduceM	0	0	0
truncName	0	0	0