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BioC 3.1: CHECK report for simulatorZ on morelia

This page was generated on 2015-10-09 09:42:14 -0700 (Fri, 09 Oct 2015).

Package 911/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
simulatorZ 1.2.0
Yuqing Zhang
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/simulatorZ
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  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: simulatorZ
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings simulatorZ_1.2.0.tar.gz
StartedAt: 2015-10-09 06:25:18 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 06:28:07 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 169.1 seconds
RetCode: 0
Status:  OK 
CheckDir: simulatorZ.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings simulatorZ_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/simulatorZ.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.2.0’
* 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 ... [11s/11s] 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 ... [53s/53s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
zmatrix      9.537  0.390   9.928
geneFilter   8.066  0.549   8.699
simBootstrap 5.884  0.625   6.510
simTime      5.580  0.322   5.902
getTrueModel 5.199  0.221   5.448
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [8s/8s]
 [8s/8s] 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

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/simulatorZ.Rcheck/00check.log’
for details.


simulatorZ.Rcheck/00install.out:

* installing *source* package ‘simulatorZ’ ...
** 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 coxformatrices.cpp -o coxformatrices.o
coxformatrices.cpp:79:17: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                NULL
                ^˜˜˜
                {   }
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/6.0/include/stddef.h:72:18: note: expanded from macro 'NULL'
#    define NULL __null
                 ^˜˜˜˜˜
1 warning generated.
clang++ -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 -o simulatorZ.so coxformatrices.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.1-bioc/meat/simulatorZ.Rcheck/simulatorZ/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (simulatorZ)

simulatorZ.Rcheck/simulatorZ-Ex.timings:

nameusersystemelapsed
cvSubsets1.9350.0592.063
funCV1.6960.0351.731
geneFilter8.0660.5498.699
getTrueModel5.1990.2215.448
masomenos1.0130.0171.030
plusMinus1.1610.0731.235
rowCoxTests0.5480.0220.570
simBootstrap5.8840.6256.510
simData4.5480.1744.723
simTime5.5800.3225.902
zmatrix9.5370.3909.928