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BioC 3.0: CHECK report for RTCA on moscato1

This page was generated on 2015-04-10 09:45:58 -0700 (Fri, 10 Apr 2015).

Package 783/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RTCA 1.18.0
Jitao David Zhang
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/RTCA
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  WARNINGS 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ WARNINGS ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  WARNINGS  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK 

Summary

Package: RTCA
Version: 1.18.0
Command: rm -rf RTCA.buildbin-libdir RTCA.Rcheck && mkdir RTCA.buildbin-libdir RTCA.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RTCA.buildbin-libdir RTCA_1.18.0.tar.gz >RTCA.Rcheck\00install.out 2>&1 && cp RTCA.Rcheck\00install.out RTCA-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=RTCA.buildbin-libdir --install="check:RTCA-install.out" --force-multiarch --no-vignettes --timings RTCA_1.18.0.tar.gz
StartedAt: 2015-04-10 05:17:36 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 05:19:01 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 85.6 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: RTCA.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf RTCA.buildbin-libdir RTCA.Rcheck && mkdir RTCA.buildbin-libdir RTCA.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RTCA.buildbin-libdir RTCA_1.18.0.tar.gz >RTCA.Rcheck\00install.out 2>&1 && cp RTCA.Rcheck\00install.out RTCA-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=RTCA.buildbin-libdir --install="check:RTCA-install.out" --force-multiarch --no-vignettes --timings RTCA_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/RTCA.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RTCA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RTCA' version '1.18.0'
* 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 'RTCA' 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
** 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 ... NOTE
'library' or 'require' call to 'RColorBrewer' which was already attached by Depends.
  Please remove these calls from your code.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
parseRTCA: warning in read.table(file, skip = skipnum, sep = "\t", head
  = TRUE, dec = dec, ...): partial argument match of 'head' to 'header'
* 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... WARNING
Found the following file(s) containing GNU extensions:
  Makefile
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif. See section 'Writing portable packages' in
the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [6s] OK
** running examples for arch 'x64' ... [10s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'essentials.R' [4s]
 [5s] OK
** running tests for arch 'x64' ...
  Running 'essentials.R' [4s]
 [5s] 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

WARNING: There was 1 warning.
NOTE: There were 2 notes.
See
  'D:/biocbld/bbs-3.0-bioc/meat/RTCA.Rcheck/00check.log'
for details.

RTCA.Rcheck/00install.out:


install for i386

* installing *source* package 'RTCA' ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'time' from package 'stats' in package 'RTCA'
Creating a generic function for 'plot' from package 'graphics' in package 'RTCA'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'RTCA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RTCA' as RTCA_1.18.0.zip
* DONE (RTCA)

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

nameusersystemelapsed
RTCA-class0.200.020.22
RTCAtimeline-class000
alphaNames000
combineRTCA0.220.000.21
controlView0.260.000.78
derivativeTransform0.280.000.28
factor2numeric0.010.000.02
interpolationTransform0.570.000.56
nearestTimeIndex0.20.00.2
parseRTCA0.700.020.71
plateView0.390.000.39
plotGridEffect0.470.000.47
ratioTransform0.190.000.19
rgrTransform0.540.000.55
sliceRTCA0.190.000.18
smoothTransform0.340.000.35
spectramaxImport0.020.000.01

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

nameusersystemelapsed
RTCA-class0.320.000.32
RTCAtimeline-class000
alphaNames000
combineRTCA0.420.020.44
controlView0.350.000.36
derivativeTransform0.270.010.28
factor2numeric000
interpolationTransform0.750.000.75
nearestTimeIndex0.260.000.27
parseRTCA1.240.021.24
plateView0.510.000.52
plotGridEffect0.890.010.92
ratioTransform0.410.000.41
rgrTransform0.920.000.92
sliceRTCA0.250.000.25
smoothTransform0.460.000.46
spectramaxImport0.020.000.02