BioC 3.2: CHECK report for mdgsa on moscato1

Package: mdgsa

Version: 1.1.0

Command: rm -rf mdgsa.buildbin-libdir mdgsa.Rcheck && mkdir mdgsa.buildbin-libdir mdgsa.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=mdgsa.buildbin-libdir mdgsa_1.1.0.tar.gz >mdgsa.Rcheck\00install.out 2>&1 && cp mdgsa.Rcheck\00install.out mdgsa-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=mdgsa.buildbin-libdir --install="check:mdgsa-install.out" --force-multiarch --no-vignettes --timings mdgsa_1.1.0.tar.gz

StartedAt: 2015-08-20 06:46:26 -0700 (Thu, 20 Aug 2015)

EndedAt: 2015-08-20 06:50:43 -0700 (Thu, 20 Aug 2015)

EllapsedTime: 256.6 seconds

RetCode: 0

Status:  OK

CheckDir: mdgsa.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf mdgsa.buildbin-libdir mdgsa.Rcheck && mkdir mdgsa.buildbin-libdir mdgsa.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=mdgsa.buildbin-libdir mdgsa_1.1.0.tar.gz >mdgsa.Rcheck\00install.out 2>&1 && cp mdgsa.Rcheck\00install.out mdgsa-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=mdgsa.buildbin-libdir --install="check:mdgsa-install.out" --force-multiarch --no-vignettes --timings mdgsa_1.1.0.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/mdgsa.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'mdgsa/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'mdgsa' version '1.1.0'
* 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 'mdgsa' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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 ... 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [16s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
propagateGO 5.37   0.04    5.42
** running examples for arch 'x64' ... [16s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
propagateGO  5.7   0.02    5.71
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R' [17s]
 [18s] OK
** running tests for arch 'x64' ...
  Running 'runTests.R' [20s]
 [20s] 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
* DONE

Status: 1 NOTE
See
  'D:/biocbld/bbs-3.2-bioc/meat/mdgsa.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'mdgsa' ...
** 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 'mdgsa' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'mdgsa' as mdgsa_1.1.0.zip
* DONE (mdgsa)

name	user	system	elapsed
annotFilter	0.02	0.00	0.01
annotList2mat	0	0	0
annotMat2list	0	0	0
getGOnames	0.60	0.06	0.67
getKEGGnames	0	0	0
getOntology	0.16	0.00	0.16
goLeaves	3.13	0.09	3.30
indexTransform	0.02	0.00	0.02
mdGsa	0.06	0.02	0.08
mdPat	0.03	0.00	0.03
plotMdGsa	0	0	0
propagateGO	5.37	0.04	5.42
pval2index	0.01	0.00	0.01
revList	0	0	0
splitOntologies	0.64	0.00	0.64
transferIndex	0.05	0.00	0.05
uvGsa	0.01	0.00	0.01
uvPat	0	0	0
uvSignif	0	0	0

name	user	system	elapsed
annotFilter	0.01	0.00	0.02
annotList2mat	0	0	0
annotMat2list	0	0	0
getGOnames	0.78	0.03	0.81
getKEGGnames	0	0	0
getOntology	0.19	0.00	0.18
goLeaves	3.18	0.03	3.22
indexTransform	0.01	0.00	0.01
mdGsa	0.04	0.00	0.03
mdPat	0.01	0.00	0.02
plotMdGsa	0	0	0
propagateGO	5.70	0.02	5.71
pval2index	0.01	0.00	0.02
revList	0	0	0
splitOntologies	0.34	0.01	0.36
transferIndex	0.06	0.00	0.06
uvGsa	0.08	0.00	0.08
uvPat	0.02	0.00	0.02
uvSignif	0	0	0