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BioC 2.14: CHECK report for CNORdt on morelia

This page was generated on 2014-10-08 09:05:51 -0700 (Wed, 08 Oct 2014).

Package 168/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNORdt 1.6.0
A. MacNamara
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/CNORdt
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 

Summary

Package: CNORdt
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch CNORdt_1.6.0.tar.gz
StartedAt: 2014-10-07 22:04:45 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 22:06:55 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 129.9 seconds
RetCode: 0
Status:  OK 
CheckDir: CNORdt.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch CNORdt_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/CNORdt.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CNORdt/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CNORdt’ version ‘1.6.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘CNORdt’ can be installed ... [6s/6s] 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
* 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
Package in Depends field not imported from: ‘abind’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [65s/66s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
cutAndPlotResultsDT 31.645  0.087  31.765
gaBinaryDT          30.636  0.066  30.790
* 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

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/CNORdt.Rcheck/00check.log’
for details.

CNORdt.Rcheck/00install.out:

* installing *source* package ‘CNORdt’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c simulatorDT.c -o simulatorDT.o
simulatorDT.c:243:19: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
                        if((track_cond == nCond)) {
                            ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
simulatorDT.c:243:19: note: remove extraneous parentheses around the comparison to silence this warning
                        if((track_cond == nCond)) {
                           ˜           ^       ˜
simulatorDT.c:243:19: note: use '=' to turn this equality comparison into an assignment
                        if((track_cond == nCond)) {
                                       ^˜
                                       =
simulatorDT.c:53:6: warning: unused variable 'nSignals' [-Wunused-variable]
        int nSignals = INTEGER(nSignals_in)[0];
            ^
simulatorDT.c:55:6: warning: unused variable 'nTimes' [-Wunused-variable]
        int nTimes = INTEGER(nTimes_in)[0];
            ^
3 warnings generated.
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o CNORdt.so simulatorDT.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.14-bioc/meat/CNORdt.Rcheck/CNORdt/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CNORdt)

CNORdt.Rcheck/CNORdt-Ex.timings:

nameusersystemelapsed
computeScoreDT0.1780.0020.375
convert2array0.0250.0020.027
cutAndPlotResultsDT31.645 0.08731.765
gaBinaryDT30.636 0.06630.790
getFitDT0.0700.0010.071
simulatorDT0.0270.0010.028