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BioC 3.0: CHECK report for inveRsion on perceval

This page was generated on 2015-04-10 09:55:40 -0700 (Fri, 10 Apr 2015).

Package 461/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
inveRsion 1.14.0
Alejandro Caceres
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/inveRsion
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: inveRsion
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch inveRsion_1.14.0.tar.gz
StartedAt: 2015-04-10 02:56:09 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 02:56:52 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 42.9 seconds
RetCode: 0
Status:  OK 
CheckDir: inveRsion.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch inveRsion_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/inveRsion.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 ‘inveRsion/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘inveRsion’ version ‘1.14.0’
* 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 ‘inveRsion’ can be installed ... [3s/5s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘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
* 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: ‘haplo.stats’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File ‘inveRsion/R/zzz.R’:
  .onLoad calls:
    packageStartupMessage("\n")
    packageStartupMessage("Hola!\n")
    packageStartupMessage("welcome to inevRsion package. \n \n \n")
    packageStartupMessage("type: manual() for full manual \n      vignette(\"inveRsion\") for a quick start \n")

See section ‘Good practice’ in '?.onAttach'.

encodeGeno: no visible global function definition for ‘setupGeno’
encodeGeno: no visible global function definition for ‘haplo.em’
encodeGeno: no visible global function definition for
  ‘haplo.em.control’
encodeGenoAcross: no visible global function definition for ‘setupGeno’
encodeGenoAcross: no visible global function definition for ‘haplo.em’
encodeGenoAcross: no visible global function definition for
  ‘haplo.em.control’
* 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 compilation flags in Makevars ... OK
* checking for GNU extensions 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 ... [4s/4s] 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 were 3 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/inveRsion.Rcheck/00check.log’
for details.

inveRsion.Rcheck/00install.out:

* installing *source* package ‘inveRsion’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c init_inveRsion.c -o init_inveRsion.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c inversionModel.c -o inversionModel.o
inversionModel.c: In function ‘blockAndLev’:
inversionModel.c:185: warning: suggest parentheses around comparison in operand of &
inversionModel.c:167: warning: unused variable ‘ncol’
inversionModel.c:316:4: warning: "/*" within comment
inversionModel.c: In function ‘inversionModel’:
inversionModel.c:360: warning: suggest parentheses around comparison in operand of &
inversionModel.c:237: warning: unused variable ‘i’
inversionModel.c:237: warning: unused variable ‘ncol’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c writeGenoDat.c -o writeGenoDat.o
writeGenoDat.c: In function ‘writeGenoDat’:
writeGenoDat.c:36: warning: unused variable ‘fm’
writeGenoDat.c:36: warning: unused variable ‘fa’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -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 inveRsion.so init_inveRsion.o inversionModel.o writeGenoDat.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64 -L/usr/local/lib/x86_64 -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3 -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.0-bioc/meat/inveRsion.Rcheck/inveRsion/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘inveRsion’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (inveRsion)

inveRsion.Rcheck/inveRsion-Ex.timings:

nameusersystemelapsed
GenoDat-class0.0690.0040.073
GenoDatROI-class0.0080.0010.009
HaploCode-class0.1530.0060.160
ac0.0060.0010.006
accBic1.8870.0101.899
accuracy-class0.0050.0020.015
codeHaplo0.0680.0020.070
gDat0.0060.0010.016
getClassif-methods0.1990.0010.200
getInv-methods0.0020.0000.003
getROIs-methods0.0030.0010.002
hapCode0.0110.0030.013
invList0.0030.0010.004
inveRsion-package0.0000.0000.001
inversionList-class0.0040.0010.005
listInv-methods0.7240.0310.757
scan-class0.0120.0020.024
scanInv0.0400.0070.054
scanRes0.0090.0020.017
setUpGenoDatFile0.0100.0030.014