BioC 3.5: CHECK report for gespeR on tokay2

Package: gespeR

Version: 1.8.0

Command: rm -rf gespeR.buildbin-libdir gespeR.Rcheck && mkdir gespeR.buildbin-libdir gespeR.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=gespeR.buildbin-libdir gespeR_1.8.0.tar.gz >gespeR.Rcheck\00install.out 2>&1 && cp gespeR.Rcheck\00install.out gespeR-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=gespeR.buildbin-libdir --install="check:gespeR-install.out" --force-multiarch --no-vignettes --timings gespeR_1.8.0.tar.gz

StartedAt: 2017-08-16 00:07:52 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 00:14:58 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 426.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: gespeR.Rcheck

Warnings: 1

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### Running command:
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###   rm -rf gespeR.buildbin-libdir gespeR.Rcheck && mkdir gespeR.buildbin-libdir gespeR.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=gespeR.buildbin-libdir gespeR_1.8.0.tar.gz >gespeR.Rcheck\00install.out 2>&1 && cp gespeR.Rcheck\00install.out gespeR-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=gespeR.buildbin-libdir --install="check:gespeR-install.out" --force-multiarch --no-vignettes --timings gespeR_1.8.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/gespeR.Rcheck'
* using R version 3.4.1 (2017-06-30)
* 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 '1.8.0'
* 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.cv: no visible global function definition for 'coef'
.select.model: no visible global function definition for 'predict'
concordance: no visible global function definition for 'cor'
lasso.rand: no visible global function definition for 'runif'
plot.gespeR: no visible global function definition for 'hist'
stability.selection: no visible global function definition for 'lm'
Phenotypes,character: no visible global function definition for
  'read.delim'
Undefined global functions or variables:
  coef cor hist lm predict read.delim runif
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "coef", "cor", "lm", "predict", "runif")
  importFrom("utils", "read.delim")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'c,Phenotypes-method':
\S4method{c}{Phenotypes}
  Code: function(x, ...)
  Docs: function(x, ..., recursive = FALSE)
  Argument names in docs not in code:
    recursive

* 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' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
gespeR-package    8.58   0.20   47.66
gespeR-class      0.98   0.04   10.06
stability-methods 0.13   0.02    9.60
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
gespeR-package    11.84   0.16   49.83
gespeR-class       0.66   0.03   11.43
stability-methods  0.14   0.07   10.03
* 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 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/gespeR.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'gespeR' ...
** R
** data
** 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 'gespeR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'gespeR' as gespeR_1.8.0.zip
* DONE (gespeR)

name	user	system	elapsed
Phenotypes-class	0.02	0.00	0.02
TargetRelations-class	0.01	0.00	0.01
annotate.gsp-methods	0.16	0.00	0.16
as.data.frame-Phenotypes-method	0.08	0.02	0.09
c-Phenotypes-method	0.14	0.00	0.14
concordance	1.25	0.01	1.27
gespeR-class	0.98	0.04	10.06
gespeR-package	8.58	0.20	47.66
gspssp-methods	0.22	0.01	0.23
join-methods	0.03	0.00	0.03
lasso.rand	0	0	0
na.rem-methods	0.03	0.00	0.03
path-methods	0.02	0.00	0.02
rbo	0	0	0
scores-methods	0.21	0.00	0.22
simData	0.02	0.00	0.01
stability-methods	0.13	0.02	9.60
stabilityfits	0.21	0.00	0.22
target-relations-methods	0.22	0.00	0.22
trmatrix-methods	0.24	0.00	0.23
values-methods	0.04	0.00	0.05

name	user	system	elapsed
Phenotypes-class	0.02	0.00	0.01
TargetRelations-class	0.02	0.00	0.02
annotate.gsp-methods	0.12	0.01	0.14
as.data.frame-Phenotypes-method	0.08	0.00	0.08
c-Phenotypes-method	0.19	0.00	0.18
concordance	1.59	0.00	1.60
gespeR-class	0.66	0.03	11.43
gespeR-package	11.84	0.16	49.83
gspssp-methods	0.22	0.00	0.22
join-methods	0.01	0.00	0.02
lasso.rand	0.02	0.00	0.01
na.rem-methods	0.03	0.00	0.03
path-methods	0	0	0
rbo	0	0	0
scores-methods	0.17	0.01	0.18
simData	0.02	0.00	0.02
stability-methods	0.14	0.07	10.03
stabilityfits	0.24	0.00	0.23
target-relations-methods	0.21	0.00	0.22
trmatrix-methods	0.18	0.00	0.17
values-methods	0.04	0.00	0.05