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CHECK report for gespeR on tokay2

This page was generated on 2019-10-16 12:32:12 -0400 (Wed, 16 Oct 2019).

Package 672/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gespeR 1.16.0
Fabian Schmich
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/gespeR
Branch: RELEASE_3_9
Last Commit: 8617a4b
Last Changed Date: 2019-05-02 11:53:52 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: gespeR
Version: 1.16.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:gespeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings gespeR_1.16.0.tar.gz
StartedAt: 2019-10-16 04:03:05 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 04:09:10 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 365.0 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: gespeR.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:gespeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings gespeR_1.16.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/gespeR.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '1.16.0'
* 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
* 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 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
gespeR-package    7.23   0.35   47.27
gespeR-class      0.54   0.01   11.80
stability-methods 0.06   0.05    9.82
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
gespeR-package    5.28   0.16   47.89
gespeR-class      1.11   0.00   10.01
stability-methods 0.08   0.04   10.19
* 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-3.9-bioc/meat/gespeR.Rcheck/00check.log'
for details.



Installation output

gespeR.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/gespeR_1.16.0.tar.gz && rm -rf gespeR.buildbin-libdir && mkdir gespeR.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=gespeR.buildbin-libdir gespeR_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL gespeR_1.16.0.zip && rm gespeR_1.16.0.tar.gz gespeR_1.16.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 24.1M  100 24.1M    0     0  68.9M      0 --:--:-- --:--:-- --:--:-- 70.3M

install for i386

* installing *source* package 'gespeR' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'gespeR'
    finding HTML links ... done
    Phenotypes-class                        html  
    TargetRelations-class                   html  
    annotate.gsp-methods                    html  
    as.data.frame-Phenotypes-method         html  
    as.data.frame.concordance               html  
    c-Phenotypes-method                     html  
    concordance                             html  
    dim-Phenotypes-method                   html  
    gespeR-class                            html  
    finding level-2 HTML links ... done

    gespeR-package                          html  
    gspssp-methods                          html  
    join-methods                            html  
    lasso.rand                              html  
    na.rem-methods                          html  
    path-methods                            html  
    plot.Phenotypes                         html  
    plot.concordance                        html  
    plot.gespeR                             html  
    rbo                                     html  
    scores-methods                          html  
    simData                                 html  
    stability-methods                       html  
    stability.selection                     html  
    stabilityfits                           html  
    sub-Phenotypes-ANY-ANY-ANY-method       html  
    sub-TargetRelations-ANY-ANY-ANY-method
                                            html  
    target-relations-methods                html  
    trmatrix-methods                        html  
    values-methods                          html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'gespeR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'gespeR' as gespeR_1.16.0.zip
* DONE (gespeR)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'gespeR' successfully unpacked and MD5 sums checked

Tests output


Example timings

gespeR.Rcheck/examples_i386/gespeR-Ex.timings

nameusersystemelapsed
Phenotypes-class0.010.000.05
TargetRelations-class0.050.030.22
annotate.gsp-methods0.210.000.22
as.data.frame-Phenotypes-method0.150.010.16
c-Phenotypes-method0.030.000.11
concordance0.570.070.65
gespeR-class 0.54 0.0111.80
gespeR-package 7.23 0.3547.27
gspssp-methods0.170.010.18
join-methods0.020.000.02
lasso.rand000
na.rem-methods0.010.000.02
path-methods0.020.000.01
rbo000
scores-methods0.170.000.17
simData000
stability-methods0.060.059.82
stabilityfits0.160.030.18
target-relations-methods0.160.020.18
trmatrix-methods0.150.000.15
values-methods0.030.000.03

gespeR.Rcheck/examples_x64/gespeR-Ex.timings

nameusersystemelapsed
Phenotypes-class0.010.000.02
TargetRelations-class0.020.000.01
annotate.gsp-methods0.160.010.17
as.data.frame-Phenotypes-method0.090.020.11
c-Phenotypes-method0.050.000.04
concordance0.640.030.68
gespeR-class 1.11 0.0010.01
gespeR-package 5.28 0.1647.89
gspssp-methods0.150.000.15
join-methods0.040.000.04
lasso.rand000
na.rem-methods0.010.000.01
path-methods0.020.000.02
rbo000
scores-methods0.140.000.14
simData0.010.000.01
stability-methods 0.08 0.0410.19
stabilityfits0.170.020.19
target-relations-methods0.180.000.17
trmatrix-methods0.160.000.15
values-methods0.030.000.03