BioC 3.3: CHECK report for PCpheno on windows2.bioconductor.org

Package: PCpheno

Version: 1.33.0

Command: rm -rf PCpheno.buildbin-libdir PCpheno.Rcheck && mkdir PCpheno.buildbin-libdir PCpheno.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=PCpheno.buildbin-libdir PCpheno_1.33.0.tar.gz >PCpheno.Rcheck\00install.out 2>&1 && cp PCpheno.Rcheck\00install.out PCpheno-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=PCpheno.buildbin-libdir --install="check:PCpheno-install.out" --force-multiarch --no-vignettes --timings PCpheno_1.33.0.tar.gz

StartedAt: 2015-10-27 04:53:33 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 04:56:53 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 200.1 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 && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=PCpheno.buildbin-libdir PCpheno_1.33.0.tar.gz >PCpheno.Rcheck\00install.out 2>&1 && cp PCpheno.Rcheck\00install.out PCpheno-install.out  && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=PCpheno.buildbin-libdir --install="check:PCpheno-install.out" --force-multiarch --no-vignettes --timings PCpheno_1.33.0.tar.gz
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* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/PCpheno.Rcheck'
* using R Under development (unstable) (2015-09-22 r69418)
* using platform: x86_64-w64-mingw32 (64-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 '1.33.0'
* 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' ... [24s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
gtResult-class 4.24   1.08    5.31
** running examples for arch 'x64' ... [25s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
gtResult-class 4.36    0.8    5.15
* 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
  'c:/biocbld/bbs-3.3-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 "Biobase" for requests: listlen
No methods found in "annotate" for requests: pubmed, buildPubMedAbst
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 "Biobase" for requests: listlen
No methods found in "annotate" for requests: pubmed, buildPubMedAbst
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 "Biobase" for requests: listlen
No methods found in "annotate" for requests: pubmed, buildPubMedAbst
No methods found in "BiocGenerics" for requests: plot
* MD5 sums
packaged installation of 'PCpheno' as PCpheno_1.33.0.zip
* DONE (PCpheno)

name	user	system	elapsed
CoHyperGResult-class	0.28	0.00	0.28
Dudley	0	0	0
Giaever	0.14	0.00	0.14
HI	0	0	0
KEGG2SCISI	0.36	0.01	0.64
Kastenmayer	0.02	0.02	0.03
Lesage	0	0	0
Osterberg	0.02	0.00	0.02
SGDphenoL	0.03	0.00	0.03
YEASTOHNOLOG	0	0	0
buildFDMat	0.17	0.03	0.20
categoryToEntrezBuilder	0.25	0.01	0.27
complexStatus	0.55	0.04	0.58
deResult-class	0.07	0.00	0.08
densityEstimate	1.93	0.09	2.01
getDescr	0.54	0.03	0.66
getFDgene	0.13	0.02	0.14
graphTheory	4.12	0.15	4.28
gtResult-class	4.24	1.08	5.31
overlap	0	0	0
plot	1.58	0.14	1.72
ppiInteraction	2.65	0.27	2.95
reduceM	0	0	0
truncName	0	0	0

name	user	system	elapsed
CoHyperGResult-class	0.33	0.04	0.36
Dudley	0.00	0.01	0.02
Giaever	0.11	0.00	0.11
HI	0.02	0.00	0.01
KEGG2SCISI	0.42	0.00	0.43
Kastenmayer	0.01	0.00	0.01
Lesage	0	0	0
Osterberg	0.02	0.02	0.03
SGDphenoL	0.02	0.00	0.02
YEASTOHNOLOG	0.01	0.00	0.01
buildFDMat	0.16	0.03	0.19
categoryToEntrezBuilder	0.30	0.03	0.33
complexStatus	0.44	0.03	0.46
deResult-class	0.31	0.02	0.33
densityEstimate	1.64	0.04	1.69
getDescr	0.67	0.00	0.67
getFDgene	0.11	0.00	0.11
graphTheory	4.16	0.14	4.30
gtResult-class	4.36	0.80	5.15
overlap	0	0	0
plot	1.37	0.07	1.45
ppiInteraction	3.36	0.04	3.39
reduceM	0	0	0
truncName	0	0	0