BioC 3.2: CHECK report for GraphAT on windows1.bioconductor.org

Package: GraphAT

Version: 1.42.0

Command: rm -rf GraphAT.buildbin-libdir GraphAT.Rcheck && mkdir GraphAT.buildbin-libdir GraphAT.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GraphAT.buildbin-libdir GraphAT_1.42.0.tar.gz >GraphAT.Rcheck\00install.out 2>&1 && cp GraphAT.Rcheck\00install.out GraphAT-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=GraphAT.buildbin-libdir --install="check:GraphAT-install.out" --force-multiarch --no-vignettes --timings GraphAT_1.42.0.tar.gz

StartedAt: 2015-10-27 02:29:19 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 02:29:59 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 40.1 seconds

RetCode: 0

Status:  OK

CheckDir: GraphAT.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf GraphAT.buildbin-libdir GraphAT.Rcheck && mkdir GraphAT.buildbin-libdir GraphAT.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GraphAT.buildbin-libdir GraphAT_1.42.0.tar.gz >GraphAT.Rcheck\00install.out 2>&1 && cp GraphAT.Rcheck\00install.out GraphAT-install.out  && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=GraphAT.buildbin-libdir --install="check:GraphAT-install.out" --force-multiarch --no-vignettes --timings GraphAT_1.42.0.tar.gz
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* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/GraphAT.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GraphAT/DESCRIPTION' ... OK
* this is package 'GraphAT' version '1.42.0'
* 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 'GraphAT' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'graph' 'methods'
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 ... OK
* 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 ... NOTE
prepare_Rd: depthmat.Rd:28: Dropping empty section \references
* 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 examples ...
** running examples for arch 'i386' ... [3s] OK
** running examples for arch 'x64' ... [4s] OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'C:/biocbld/bbs-3.2-bioc/meat/GraphAT.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'GraphAT' ...
** R
** data
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded

install for x64

* installing *source* package 'GraphAT' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GraphAT' as GraphAT_1.42.0.zip
* DONE (GraphAT)

name	user	system	elapsed
Phenoclusters	0.43	0.11	0.55
causton	0.27	0.02	0.28
cellcycle	0.17	0.05	0.22
clust2Mat	0	0	0
depthmat	0.27	0.04	0.31
getpvalue	0	0	0
giaever	0.31	0.00	0.31
mRNAclusters	0.17	0.10	0.27
makeClustM	0	0	0
mat2UndirG	0	0	0
permPower	0.49	0.02	0.50
perms	0	0	0

name	user	system	elapsed
Phenoclusters	0.47	0.08	0.55
causton	0.31	0.02	0.33
cellcycle	0.17	0.01	0.19
clust2Mat	0	0	0
depthmat	0.28	0.05	0.33
getpvalue	0.02	0.00	0.01
giaever	0.45	0.00	0.45
mRNAclusters	0.22	0.11	0.33
makeClustM	0	0	0
mat2UndirG	0.02	0.00	0.02
permPower	0.87	0.01	0.89
perms	0	0	0