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CHECK report for stepNorm on tokay1

This page was generated on 2019-04-13 11:19:31 -0400 (Sat, 13 Apr 2019).

Package 1518/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
stepNorm 1.54.0
Yuanyuan Xiao
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/stepNorm
Branch: RELEASE_3_8
Last Commit: 422b547
Last Changed Date: 2018-10-30 11:41:42 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  NA 
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: stepNorm
Version: 1.54.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:stepNorm.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings stepNorm_1.54.0.tar.gz
StartedAt: 2019-04-13 05:46:33 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 05:49:51 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 198.3 seconds
RetCode: 0
Status:  OK  
CheckDir: stepNorm.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:stepNorm.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings stepNorm_1.54.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/stepNorm.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 'stepNorm/DESCRIPTION' ... OK
* this is package 'stepNorm' version '1.54.0'
* 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 'stepNorm' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'marray' 'methods'
A package should be listed in only one of these fields.
* 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
loess2Dfit: warning in loess.control(trace.hat = "approximate",
  iteration = 5, surface = "direct"): partial argument match of
  'iteration' to 'iterations'
loessfit: warning in loess.control(trace.hat = "approximate", iteration
  = 5, surface = "direct"): partial argument match of 'iteration' to
  'iterations'
* 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 examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
stepWithinNorm 24.68   0.03   24.70
fitWithin      20.03   0.00   20.03
fit2DWithin     8.42   0.02    8.44
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
stepWithinNorm 23.21   0.04   23.24
fitWithin      18.99   0.02   19.00
fit2DWithin     8.06   0.01    8.08
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/stepNorm.Rcheck/00check.log'
for details.



Installation output

stepNorm.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/stepNorm_1.54.0.tar.gz && rm -rf stepNorm.buildbin-libdir && mkdir stepNorm.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=stepNorm.buildbin-libdir stepNorm_1.54.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL stepNorm_1.54.0.zip && rm stepNorm_1.54.0.tar.gz stepNorm_1.54.0.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  459k  100  459k    0     0  11.3M      0 --:--:-- --:--:-- --:--:-- 12.4M

install for i386

* installing *source* package 'stepNorm' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'stepNorm'
    finding HTML links ... done
    calcAIC                                 html  
    calcBIC                                 html  
    fit2DWithin                             html  
    fitWithin                               html  
    maCompPlate2                            html  
    makeStepList                            html  
    marrayFitClass                          html  
    seqWithinNorm                           html  
    stepNorm-internal                       html  
    stepWithinNorm                          html  
    withinNorm                              html  
** building package indices
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'stepNorm' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'stepNorm' as stepNorm_1.54.0.zip
* DONE (stepNorm)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'stepNorm' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

stepNorm.Rcheck/examples_i386/stepNorm-Ex.timings

nameusersystemelapsed
calcAIC0.110.020.12
calcBIC0.080.030.11
fit2DWithin8.420.028.44
fitWithin20.03 0.0020.03
maCompPlate20.010.000.01
makeStepList0.080.020.10
marrayFitClass0.140.000.14
seqWithinNorm0.280.010.30
stepWithinNorm24.68 0.0324.70
withinNorm0.060.000.06

stepNorm.Rcheck/examples_x64/stepNorm-Ex.timings

nameusersystemelapsed
calcAIC0.110.000.11
calcBIC0.080.000.08
fit2DWithin8.060.018.08
fitWithin18.99 0.0219.00
maCompPlate2000
makeStepList0.060.000.06
marrayFitClass0.080.000.08
seqWithinNorm0.230.010.25
stepWithinNorm23.21 0.0423.24
withinNorm0.060.000.06