BUS 1.31.0
Yuanhua Liu
| Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BUS | | Last Changed Rev: 122712 / Revision: 127142 | | Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | |
| toluca2 | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ OK ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BUS_1.31.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/BUS.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* 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 ‘1.31.0’
* 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 ... 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:
.Call("MINempirical", mat, nat, N, n1, n2, DUP = FALSE)
DUP is no longer supported and will be ignored.
* 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
Undefined global functions or variables:
aracne build.mim clr mrnet
* 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 ... 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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.5-bioc/meat/BUS.Rcheck/00check.log’
for details.
* 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-3.5-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)