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CHECK report for snm on tokay2

This page was generated on 2019-10-16 12:24:29 -0400 (Wed, 16 Oct 2019).

Package 1548/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
snm 1.32.0
John D. Storey
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/snm
Branch: RELEASE_3_9
Last Commit: ff952e9
Last Changed Date: 2019-05-02 11:53:20 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: snm
Version: 1.32.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:snm.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings snm_1.32.0.tar.gz
StartedAt: 2019-10-16 07:13:48 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 07:25:14 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 686.2 seconds
RetCode: 0
Status:  OK  
CheckDir: snm.Rcheck
Warnings: 0

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:snm.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings snm_1.32.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/snm.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 'snm/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'snm' version '1.32.0'
* 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 'snm' 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
buildBasisSplineMatrix : : no visible global function
  definition for 'predict'
calcArrayEffects : : no visible global function definition
  for 'predict'
edge.glr: no visible global function definition for 'pf'
edge.qvalue: no visible global function definition for 'smooth.spline'
edge.qvalue: no visible global function definition for 'predict'
fit.model: no visible binding for global variable 'weighted.mean'
fit.model: no visible global function definition for 'residuals'
getSpanningSet: no visible global function definition for 'quantile'
make.ref.model.matrices: no visible global function definition for
  'model.matrix'
make.ref.model.matrices: no visible global function definition for
  'as.formula'
make.snm.obj: no visible global function definition for 'model.matrix'
sim.doubleChannel: no visible global function definition for 'rchisq'
sim.doubleChannel: no visible global function definition for 'runif'
sim.doubleChannel: no visible global function definition for 'rnorm'
sim.doubleChannel: no visible binding for global variable 'rnorm'
sim.doubleChannel: no visible global function definition for
  'model.matrix'
sim.function.var: no visible global function definition for
  'model.matrix'
sim.intensity.dep: no visible global function definition for
  'model.matrix'
sim.intensity.dep: no visible global function definition for 'predict'
sim.preProcessed: no visible global function definition for 'rchisq'
sim.preProcessed: no visible global function definition for 'runif'
sim.preProcessed: no visible global function definition for 'rnorm'
sim.preProcessed: no visible binding for global variable 'rnorm'
sim.preProcessed: no visible global function definition for
  'model.matrix'
sim.probe.specific: no visible global function definition for
  'model.matrix'
sim.refDesign: no visible global function definition for 'rchisq'
sim.refDesign: no visible global function definition for 'runif'
sim.refDesign: no visible binding for global variable 'rnorm'
sim.refDesign: no visible global function definition for 'rnorm'
sim.refDesign: no visible global function definition for 'model.matrix'
sim.singleChannel: no visible global function definition for 'rchisq'
sim.singleChannel: no visible global function definition for 'runif'
sim.singleChannel: no visible global function definition for 'rnorm'
sim.singleChannel: no visible binding for global variable 'rnorm'
sim.singleChannel: no visible global function definition for
  'model.matrix'
snm.diagnostic.plot: no visible global function definition for 'par'
snm.diagnostic.plot: no visible global function definition for 'plot'
snm.diagnostic.plot: no visible global function definition for 'axis'
snm.diagnostic.plot : : no visible global function
  definition for 'points'
snm.diagnostic.plot: no visible global function definition for 'hist'
snm.diagnostic.plot: no visible global function definition for 'abline'
snm.diagnostic.plot: no visible global function definition for 'mtext'
snm.diagnostic.plot: no visible global function definition for 'title'
snm.plot: no visible global function definition for 'model.matrix'
snm.plot: no visible global function definition for 'rainbow'
snm.plot: no visible global function definition for 'plot'
snm.plot: no visible global function definition for 'points'
snm.plot: no visible global function definition for 'par'
snm.plot: no visible global function definition for 'abline'
snm.plot: no visible global function definition for 'fitted'
snm.plot: no visible global function definition for 'hist'
snm.plot: no visible global function definition for 'mtext'
snm.plot: no visible global function definition for 'title'
Undefined global functions or variables:
  abline as.formula axis fitted hist model.matrix mtext par pf plot
  points predict quantile rainbow rchisq residuals rnorm runif
  smooth.spline title weighted.mean
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "axis", "hist", "mtext", "par",
             "plot", "points", "title")
  importFrom("stats", "as.formula", "fitted", "model.matrix", "pf",
             "predict", "quantile", "rchisq", "residuals", "rnorm",
             "runif", "smooth.spline", "weighted.mean")
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 ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
sim.refDesign 159.57  11.68  171.28
snm           149.14   7.65  156.95
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
snm           135.71   8.45  145.23
sim.refDesign 131.37   5.64  137.35
* 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
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/snm.Rcheck/00check.log'
for details.



Installation output

snm.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/snm_1.32.0.tar.gz && rm -rf snm.buildbin-libdir && mkdir snm.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=snm.buildbin-libdir snm_1.32.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL snm_1.32.0.zip && rm snm_1.32.0.tar.gz snm_1.32.0.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  212k  100  212k    0     0  3601k      0 --:--:-- --:--:-- --:--:-- 4077k

install for i386

* installing *source* package 'snm' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'snm'
    finding HTML links ... done
    fitted.snm                              html  
    plot.snm                                html  
    sim.doubleChannel                       html  
    sim.preProcessed                        html  
    sim.refDesign                           html  
    sim.singleChannel                       html  
    snm-internal                            html  
    snm                                     html  
    summary.snm                             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 'snm' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'snm' as snm_1.32.0.zip
* DONE (snm)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'snm' successfully unpacked and MD5 sums checked

Tests output


Example timings

snm.Rcheck/examples_i386/snm-Ex.timings

nameusersystemelapsed
fitted.snm000
plot.snm000
sim.doubleChannel000
sim.preProcessed2.280.152.44
sim.refDesign159.57 11.68171.28
sim.singleChannel000
snm149.14 7.65156.95
summary.snm000

snm.Rcheck/examples_x64/snm-Ex.timings

nameusersystemelapsed
fitted.snm000
plot.snm000
sim.doubleChannel000
sim.preProcessed3.600.243.82
sim.refDesign131.37 5.64137.35
sim.singleChannel000
snm135.71 8.45145.23
summary.snm000