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BioC 3.0: CHECK report for simulatorZ on perceval

This page was generated on 2015-04-10 10:00:23 -0700 (Fri, 10 Apr 2015).

Package 828/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
simulatorZ 1.0.0
Yuqing 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/simulatorZ
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  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: simulatorZ
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch simulatorZ_1.0.0.tar.gz
StartedAt: 2015-04-10 06:29:52 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 06:36:16 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 384.0 seconds
RetCode: 0
Status:  OK 
CheckDir: simulatorZ.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch simulatorZ_1.0.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/simulatorZ.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘simulatorZ/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘simulatorZ’ version ‘1.0.0’
* 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 ‘simulatorZ’ can be installed ... [31s/34s] 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
cvSubsets: no visible global function definition for ‘assay’
funCV: no visible global function definition for ‘assay’
geneFilter: no visible global function definition for ‘assay’
getTrueModel: no visible global function definition for ‘assay’
simData: no visible global function definition for ‘assay’
simTime: no visible global function definition for ‘assay’
zmatrix: no visible global function definition for ‘assay’
* 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 C/C++/Fortran sources/headers ... 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 ... [76s/77s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
geneFilter   15.027  0.337  15.473
zmatrix      11.112  0.103  11.222
simTime       7.179  0.105   7.291
simBootstrap  6.857  0.100   6.967
getTrueModel  5.824  0.102   5.932
simData       4.938  0.080   5.024
cvSubsets     4.846  0.092   5.078
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [17s/17s]
 [17s/17s] 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

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/simulatorZ.Rcheck/00check.log’
for details.

simulatorZ.Rcheck/00install.out:

* installing *source* package ‘simulatorZ’ ...
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c coxformatrices.cpp -o coxformatrices.o
coxformatrices.cpp:80: warning: missing braces around initializer for ‘const R_CMethodDef’
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -L/usr/local/lib -o simulatorZ.so coxformatrices.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.0-bioc/meat/simulatorZ.Rcheck/simulatorZ/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (simulatorZ)

simulatorZ.Rcheck/simulatorZ-Ex.timings:

nameusersystemelapsed
cvSubsets4.8460.0925.078
funCV2.5390.1012.654
geneFilter15.027 0.33715.473
getTrueModel5.8240.1025.932
masomenos1.2270.0181.244
plusMinus1.0110.0161.028
rowCoxTests1.2820.0531.337
simBootstrap6.8570.1006.967
simData4.9380.0805.024
simTime7.1790.1057.291
zmatrix11.112 0.10311.222