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BioC 3.4: CHECK report for stepNorm on moscato1

This page was generated on 2016-09-21 03:41:26 -0700 (Wed, 21 Sep 2016).

Package 1170/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
stepNorm 1.45.0
Yuanyuan Xiao
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/stepNorm
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: stepNorm
Version: 1.45.0
Command: rm -rf stepNorm.buildbin-libdir stepNorm.Rcheck && mkdir stepNorm.buildbin-libdir stepNorm.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=stepNorm.buildbin-libdir stepNorm_1.45.0.tar.gz >stepNorm.Rcheck\00install.out 2>&1 && cp stepNorm.Rcheck\00install.out stepNorm-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=stepNorm.buildbin-libdir --install="check:stepNorm-install.out" --force-multiarch --no-vignettes --timings stepNorm_1.45.0.tar.gz
StartedAt: 2016-09-20 17:12:42 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 17:16:47 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 245.1 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 && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=stepNorm.buildbin-libdir stepNorm_1.45.0.tar.gz >stepNorm.Rcheck\00install.out 2>&1 && cp stepNorm.Rcheck\00install.out stepNorm-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=stepNorm.buildbin-libdir --install="check:stepNorm-install.out" --force-multiarch --no-vignettes --timings stepNorm_1.45.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/stepNorm.Rcheck'
* using R version 3.3.1 (2016-06-21)
* 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 '1.45.0'
* 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 44.06   0.01   44.07
fitWithin      39.72   0.00   39.72
fit2DWithin    17.68   0.00   17.67
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
stepWithinNorm 42.51   0.00   42.51
fitWithin      38.38   0.00   38.38
fit2DWithin    16.86   0.01   16.88
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'D:/biocbld/bbs-3.4-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_1.45.0.zip
* DONE (stepNorm)

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

nameusersystemelapsed
calcAIC0.180.010.20
calcBIC0.160.000.16
fit2DWithin17.68 0.0017.67
fitWithin39.72 0.0039.72
maCompPlate20.030.000.03
makeStepList0.060.020.08
marrayFitClass0.170.000.17
seqWithinNorm0.390.000.39
stepWithinNorm44.06 0.0144.07
withinNorm0.060.000.06

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

nameusersystemelapsed
calcAIC0.190.000.19
calcBIC0.190.020.20
fit2DWithin16.86 0.0116.88
fitWithin38.38 0.0038.38
maCompPlate20.030.000.03
makeStepList0.060.000.06
marrayFitClass0.110.000.11
seqWithinNorm0.340.000.35
stepWithinNorm42.51 0.0042.51
withinNorm0.070.000.06