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BioC 3.5: CHECK report for stepNorm on tokay2

This page was generated on 2017-08-16 13:18:50 -0400 (Wed, 16 Aug 2017).

Package 1281/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
stepNorm 1.48.0
Yuanyuan Xiao
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/stepNorm
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: stepNorm
Version: 1.48.0
Command: rm -rf stepNorm.buildbin-libdir stepNorm.Rcheck && mkdir stepNorm.buildbin-libdir stepNorm.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=stepNorm.buildbin-libdir stepNorm_1.48.0.tar.gz >stepNorm.Rcheck\00install.out 2>&1 && cp stepNorm.Rcheck\00install.out stepNorm-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=stepNorm.buildbin-libdir --install="check:stepNorm-install.out" --force-multiarch --no-vignettes --timings stepNorm_1.48.0.tar.gz
StartedAt: 2017-08-16 03:11:12 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 03:13:42 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 150.0 seconds
RetCode: 0
Status:  OK  
CheckDir: stepNorm.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf stepNorm.buildbin-libdir stepNorm.Rcheck && mkdir stepNorm.buildbin-libdir stepNorm.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=stepNorm.buildbin-libdir stepNorm_1.48.0.tar.gz >stepNorm.Rcheck\00install.out 2>&1 && cp stepNorm.Rcheck\00install.out stepNorm-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=stepNorm.buildbin-libdir --install="check:stepNorm-install.out" --force-multiarch --no-vignettes --timings stepNorm_1.48.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/stepNorm.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 'stepNorm/DESCRIPTION' ... OK
* this is package 'stepNorm' version '1.48.0'
* 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 '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
** 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
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 19.79   0.04   19.84
fitWithin      18.01   0.02   18.03
fit2DWithin     8.39   0.00    8.39
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
stepWithinNorm 22.37   0.02   22.39
fitWithin      20.00   0.00   20.00
fit2DWithin     8.68   0.01    8.71
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/stepNorm.Rcheck/00check.log'
for details.


stepNorm.Rcheck/00install.out:


install for i386

* installing *source* package 'stepNorm' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded

install for x64

* installing *source* package 'stepNorm' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'stepNorm' as stepNorm_1.48.0.zip
* DONE (stepNorm)

stepNorm.Rcheck/examples_i386/stepNorm-Ex.timings:

nameusersystemelapsed
calcAIC0.200.010.22
calcBIC0.190.020.20
fit2DWithin8.390.008.39
fitWithin18.01 0.0218.03
maCompPlate20.050.000.05
makeStepList0.090.000.09
marrayFitClass0.080.010.10
seqWithinNorm0.250.020.27
stepWithinNorm19.79 0.0419.84
withinNorm0.110.020.13

stepNorm.Rcheck/examples_x64/stepNorm-Ex.timings:

nameusersystemelapsed
calcAIC0.240.000.23
calcBIC0.350.000.34
fit2DWithin8.680.018.71
fitWithin20 020
maCompPlate20.070.000.06
makeStepList0.120.000.12
marrayFitClass0.090.020.11
seqWithinNorm0.350.000.35
stepWithinNorm22.37 0.0222.39
withinNorm0.070.000.06