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BioC 3.0: CHECK report for BUS on oaxaca

This page was generated on 2015-04-10 10:03:39 -0700 (Fri, 10 Apr 2015).

Package 118/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BUS 1.22.0
Yuanhua Liu
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/BUS
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: BUS
Version: 1.22.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch BUS_1.22.0.tar.gz
StartedAt: 2015-04-09 21:54:07 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 21:54:39 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 31.6 seconds
RetCode: 0
Status:  OK 
CheckDir: BUS.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch BUS_1.22.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/BUS.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BUS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BUS’ version ‘1.22.0’
* 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 ‘BUS’ can be installed ... [2s/3s] 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: ‘minet’
  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 ... NOTE
Call with DUP != TRUE:
   .Call("MINempirical", mat, nat, N, n1, n2, DUP = FALSE)
DUP = FALSE is deprecated and will be disabled in future versions of R.
* checking R code for possible problems ... NOTE
gene.pvalue : fi: warning in matrix(1:nrow(EXP), nc = 1): partial
  argument match of 'nc' to 'ncol'
gene.pvalue: warning in matrix(1:nrow(EXP), nc = 1): partial argument
  match of 'nc' to 'ncol'
gene.pvalue : fi: warning in matrix(1:ncol(real), nc = 1): partial
  argument match of 'nc' to 'ncol'
gene.pvalue: warning in matrix(1:nrow(real), nc = 1): partial argument
  match of 'nc' to 'ncol'
gene.pvalue : fi1: warning in matrix(1:ncol(real), nc = 1): partial
  argument match of 'nc' to 'ncol'
gene.trait.pvalue: warning in matrix(0, nr = nrow(EXP), nc =
  nrow(trait)): partial argument match of 'nr' to 'nrow'
gene.trait.pvalue: warning in matrix(0, nr = nrow(EXP), nc =
  nrow(trait)): partial argument match of 'nc' to 'ncol'
gene.trait.pvalue : fi: warning in matrix(1:nrow(trait), nc = 1):
  partial argument match of 'nc' to 'ncol'
gene.trait.pvalue: warning in matrix(1:nrow(EXP), nc = 1): partial
  argument match of 'nc' to 'ncol'
gene.trait.pvalue : fi: warning in matrix(1:ncol(real), nc = 1):
  partial argument match of 'nc' to 'ncol'
gene.trait.pvalue: warning in matrix(1:nrow(real), nc = 1): partial
  argument match of 'nc' to 'ncol'
gene.trait.pvalue : fj: warning in matrix(1:nrow(real), nc = 1):
  partial argument match of 'nc' to 'ncol'
gene.trait.pvalue: warning in matrix(1:ncol(real), nc = 1): partial
  argument match of 'nc' to 'ncol'
gene.pvalue: multiple local function definitions for ‘fi’ with
  different formal arguments
gene.similarity : s.similarity: no visible global function definition
  for ‘build.mim’
gene.similarity : s.similarity: no visible global function definition
  for ‘mrnet’
gene.similarity : s.similarity: no visible global function definition
  for ‘aracne’
gene.similarity : s.similarity: no visible global function definition
  for ‘clr’
gene.trait.pvalue: multiple local function definitions for ‘fi’ with
  different formal arguments
* 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 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 ... [5s/6s] 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/BUS.Rcheck/00check.log’
for details.

BUS.Rcheck/00install.out:

* installing *source* package ‘BUS’ ...
** 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 BUS.cpp -o BUS.o
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 BUS.so BUS.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.0-bioc/meat/BUS.Rcheck/BUS/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 (BUS)

BUS.Rcheck/BUS-Ex.timings:

nameusersystemelapsed
BUS0.0660.0040.069
gene.pvalue1.7030.0221.758
gene.similarity0.0050.0000.005
gene.trait.pvalue1.3360.0071.350
gene.trait.similarity0.0200.0020.022
pred.network1.5850.0281.614
tumors.mRNA0.0170.0010.018
tumors.miRNA0.0030.0010.003