BioC 3.1: CHECK report for gespeR on moscato2

Package: gespeR

Version: 1.0.0

Command: rm -rf gespeR.buildbin-libdir gespeR.Rcheck && mkdir gespeR.buildbin-libdir gespeR.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=gespeR.buildbin-libdir gespeR_1.0.0.tar.gz >gespeR.Rcheck\00install.out 2>&1 && cp gespeR.Rcheck\00install.out gespeR-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=gespeR.buildbin-libdir --install="check:gespeR-install.out" --force-multiarch --no-vignettes --timings gespeR_1.0.0.tar.gz

StartedAt: 2015-10-09 02:16:42 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 02:23:38 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 416.0 seconds

RetCode: 0

Status:  OK

CheckDir: gespeR.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf gespeR.buildbin-libdir gespeR.Rcheck && mkdir gespeR.buildbin-libdir gespeR.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=gespeR.buildbin-libdir gespeR_1.0.0.tar.gz >gespeR.Rcheck\00install.out 2>&1 && cp gespeR.Rcheck\00install.out gespeR-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=gespeR.buildbin-libdir --install="check:gespeR-install.out" --force-multiarch --no-vignettes --timings gespeR_1.0.0.tar.gz
###
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* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/gespeR.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 'gespeR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'gespeR' version '1.0.0'
* 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 'gespeR' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... NOTE
gespeR,Phenotypes-TargetRelations : .local: warning in
  Phenotypes(phenotype = gsp, ids = names(gsp), type = "GSP"): partial
  argument match of 'phenotype' to 'phenotypes'
* 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' ... [76s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
gespeR-package    7.72   0.12   46.07
gespeR-class      0.51   0.00    9.25
stability-methods 0.14   0.02    9.08
** running examples for arch 'x64' ... [82s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
gespeR-package    6.33   0.14   49.74
gespeR-class      0.24   0.04   11.74
stability-methods 0.11   0.02    9.11
* 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
  'E:/biocbld/bbs-3.1-bioc/meat/gespeR.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'gespeR' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
Creating a generic function for 'as.data.frame' from package 'base' in package 'gespeR'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'

install for x64

* installing *source* package 'gespeR' ...
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* MD5 sums
packaged installation of 'gespeR' as gespeR_1.0.0.zip
* DONE (gespeR)

name	user	system	elapsed
Phenotypes-class	0.02	0.00	0.01
TargetRelations-class	0	0	0
annotate.gsp-methods	0.53	0.03	0.56
as.data.frame-Phenotypes-method	0.01	0.02	0.03
c-Phenotypes-method	0.02	0.00	0.02
concordance	0.78	0.00	0.78
gespeR-class	0.51	0.00	9.25
gespeR-package	7.72	0.12	46.07
gspssp-methods	0.28	0.00	0.28
join-methods	0.02	0.00	0.02
lasso.rand	0	0	0
na.rem-methods	0.01	0.00	0.01
path-methods	0	0	0
rbo	0	0	0
scores-methods	0.25	0.05	0.30
simData	0.02	0.00	0.02
stability-methods	0.14	0.02	9.08
stabilityfits	0.39	0.01	0.40
target-relations-methods	0.40	0.02	0.42
trmatrix-methods	0.39	0.00	0.39
values-methods	0.02	0.00	0.01

name	user	system	elapsed
Phenotypes-class	0	0	0
TargetRelations-class	0	0	0
annotate.gsp-methods	0.27	0.00	0.27
as.data.frame-Phenotypes-method	0.03	0.00	0.03
c-Phenotypes-method	0.02	0.00	0.02
concordance	0.92	0.05	0.96
gespeR-class	0.24	0.04	11.74
gespeR-package	6.33	0.14	49.74
gspssp-methods	0.32	0.00	0.33
join-methods	0.02	0.00	0.02
lasso.rand	0.01	0.00	0.01
na.rem-methods	0	0	0
path-methods	0.02	0.00	0.02
rbo	0	0	0
scores-methods	0.25	0.00	0.25
simData	0.02	0.00	0.02
stability-methods	0.11	0.02	9.11
stabilityfits	0.26	0.00	0.26
target-relations-methods	0.64	0.00	0.64
trmatrix-methods	0.23	0.00	0.23
values-methods	0.02	0.00	0.02