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CHECK report for Oscope on tokay1

This page was generated on 2019-04-13 11:25:45 -0400 (Sat, 13 Apr 2019).

Package 1105/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Oscope 1.12.1
Ning Leng
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/Oscope
Branch: RELEASE_3_8
Last Commit: 34d9912
Last Changed Date: 2019-01-04 13:42:37 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Oscope
Version: 1.12.1
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Oscope.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings Oscope_1.12.1.tar.gz
StartedAt: 2019-04-13 04:20:29 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 04:23:02 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 153.2 seconds
RetCode: 0
Status:  OK  
CheckDir: Oscope.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Oscope.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings Oscope_1.12.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/Oscope.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Oscope/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Oscope' version '1.12.1'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 'Oscope' 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
AbsCor: no visible global function definition for 'cor'
CalcMV: no visible binding for global variable 'median'
CalcMV: no visible global function definition for 'lm'
CalcMV: no visible global function definition for 'coef'
CalcMV: no visible global function definition for 'plot'
CalcMV: no visible global function definition for 'lines'
CalcMV: no visible global function definition for 'points'
CalcMV: no visible global function definition for 'abline'
FlagCluster: no visible global function definition for 'quantile'
ImpShift: no visible global function definition for 'txtProgressBar'
ImpShift: no visible global function definition for 'setTxtProgressBar'
NISFun: no visible global function definition for 'str'
NormForSine : <anonymous>: no visible global function definition for
  'quantile'
PipeR : <anonymous>: no visible global function definition for
  'residuals'
PipeR : <anonymous>: no visible global function definition for 'lm'
PipeShiftCDF : <anonymous>: no visible global function definition for
  'quantile'
PipeShiftCDF : <anonymous>: no visible global function definition for
  'ecdf'
SineOptim: no visible global function definition for 'optim'
scanK: no visible global function definition for 'quantile'
scanK: no visible global function definition for 'dist'
scanK : <anonymous>: no visible global function definition for 'median'
Undefined global functions or variables:
  abline coef cor dist ecdf lines lm median optim plot points quantile
  residuals setTxtProgressBar str txtProgressBar
Consider adding
  importFrom("graphics", "abline", "lines", "plot", "points")
  importFrom("stats", "coef", "cor", "dist", "ecdf", "lm", "median",
             "optim", "quantile", "residuals")
  importFrom("utils", "setTxtProgressBar", "str", "txtProgressBar")
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 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
** running examples for arch 'x64' ... 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
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/Oscope.Rcheck/00check.log'
for details.



Installation output

Oscope.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/Oscope_1.12.1.tar.gz && rm -rf Oscope.buildbin-libdir && mkdir Oscope.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Oscope.buildbin-libdir Oscope_1.12.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL Oscope_1.12.1.zip && rm Oscope_1.12.1.tar.gz Oscope_1.12.1.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  534k  100  534k    0     0  11.5M      0 --:--:-- --:--:-- --:--:-- 12.7M

install for i386

* installing *source* package 'Oscope' ...
** R
** data
** demo
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Oscope'
    finding HTML links ... done
    AbsCor                                  html  
    CalcMV                                  html  
    FlagCluster                             html  
    FormatSineOut                           html  
    ImpShift                                html  
    NISFun                                  html  
    NormForSine                             html  
    Opt2Shift                               html  
    Oscope-package                          html  
    OscopeENI                               html  
    OscopeExampleData                       html  
    OscopeKM                                html  
    OscopeSine                              html  
    PermuCut                                html  
    PipeR                                   html  
    PipeShiftCDF                            html  
    SineFun                                 html  
    SineOptim                               html  
    scanK                                   html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'Oscope' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Oscope' as Oscope_1.12.1.zip
* DONE (Oscope)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'Oscope' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

Oscope.Rcheck/examples_i386/Oscope-Ex.timings

nameusersystemelapsed
AbsCor000
CalcMV0.020.000.02
FlagCluster0.460.000.47
FormatSineOut000
ImpShift0.520.000.52
NISFun1.040.001.04
NormForSine0.020.000.02
Opt2Shift0.970.000.97
OscopeENI2.030.022.05
OscopeExampleData000
OscopeKM0.440.000.43
OscopeSine000
PermuCut404
PipeR000
PipeShiftCDF0.010.000.02
SineFun000
SineOptim000
scanK0.390.000.39

Oscope.Rcheck/examples_x64/Oscope-Ex.timings

nameusersystemelapsed
AbsCor000
CalcMV000
FlagCluster0.470.020.48
FormatSineOut000
ImpShift0.60.00.6
NISFun1.220.001.22
NormForSine000
Opt2Shift1.180.001.18
OscopeENI3.440.003.44
OscopeExampleData0.000.020.02
OscopeKM0.840.000.84
OscopeSine0.020.000.02
PermuCut4.660.004.67
PipeR0.010.000.01
PipeShiftCDF000
SineFun000
SineOptim000
scanK0.40.00.4