netresponse 1.16.0
Leo Lahti
| 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/netresponse | | 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 |
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### Running command:
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### /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings netresponse_1.16.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/netresponse.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘netresponse/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘netresponse’ version ‘1.16.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
‘dmt’ ‘igraph’ ‘infotheo’ ‘ggplot2’ ‘graph’ ‘mclust’ ‘minet’
‘parallel’ ‘qvalue’ ‘RColorBrewer’ ‘reshape’ ‘Rgraphviz’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘netresponse’ can be installed ... [10s/10s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* 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
'library' or 'require' calls to packages already attached by Depends:
‘Rgraphviz’ ‘ggplot2’ ‘graph’ ‘mclust’ ‘minet’ ‘reshape’
Please remove these calls from your code.
'library' or 'require' call to ‘graphics’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
‘RColorBrewer’ ‘Rgraphviz’ ‘dmt’ ‘ggplot2’ ‘graph’ ‘igraph’
‘infotheo’ ‘mclust’ ‘methods’ ‘minet’ ‘parallel’ ‘qvalue’ ‘reshape’
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
PlotMixture: no visible global function definition for ‘aes’
PlotMixture: no visible global function definition for ‘geom_histogram’
PlotMixture: no visible global function definition for ‘theme_bw’
PlotMixture: no visible global function definition for ‘xlab’
PlotMixture: no visible global function definition for ‘ylab’
PlotMixture: no visible global function definition for ‘ggtitle’
PlotMixtureMultivariate: no visible global function definition for
‘theme_set’
PlotMixtureMultivariate: no visible global function definition for
‘theme_bw’
PlotMixtureMultivariate: no visible global function definition for
‘aes’
PlotMixtureMultivariate: no visible global function definition for
‘geom_point’
PlotMixtureMultivariate: no visible global function definition for
‘ggtitle’
PlotMixtureMultivariate: no visible global function definition for
‘xlab’
PlotMixtureMultivariate: no visible global function definition for
‘ylab’
PlotMixtureUnivariate: no visible global function definition for ‘aes’
PlotMixtureUnivariate: no visible global function definition for
‘geom_histogram’
PlotMixtureUnivariate: no visible global function definition for
‘theme_bw’
PlotMixtureUnivariate: no visible global function definition for ‘xlab’
PlotMixtureUnivariate: no visible global function definition for ‘ylab’
PlotMixtureUnivariate: no visible global function definition for
‘ggtitle’
PlotMixtureUnivariate: no visible global function definition for
‘geom_line’
bic.mixture.multivariate: no visible global function definition for
‘Mclust’
bic.mixture.multivariate: no visible global function definition for
‘mclustBIC’
bic.mixture.univariate: no visible global function definition for
‘Mclust’
bic.select.best.mode: no visible global function definition for
‘mclustBIC’
build.mim: no visible global function definition for ‘mutinformation’
check.network: no visible global function definition for
‘igraph.to.graphNEL’
check.network: no visible global function definition for ‘nodes’
check.network: no visible global function definition for
‘igraph.from.graphNEL’
check.network: no visible global function definition for ‘subgraph’
check.network: no visible global function definition for ‘edgeMatrix’
detect.responses: no visible global function definition for
‘igraph.to.graphNEL’
detect.responses: no visible global function definition for
‘graph.data.frame’
detect.responses: no visible global function definition for ‘nodes<-’
list.responses.continuous.multi: no visible global function definition
for ‘qvalue’
list.responses.continuous.single: no visible global function definition
for ‘qvalue’
plot.data: no visible global function definition for ‘ggplot’
plot.data: no visible global function definition for ‘aes’
plot.data: no visible global function definition for ‘facet_wrap’
plot.data: no visible global function definition for ‘geom_boxplot’
plot.data: no visible global function definition for ‘opts’
plot.responses: no visible global function definition for ‘nodes’
plot.responses: no visible global function definition for ‘melt’
plot.responses: no visible global function definition for ‘ggplot’
plot.responses: no visible global function definition for ‘aes’
plot.responses: no visible global function definition for ‘facet_wrap’
plot.responses: no visible global function definition for
‘geom_boxplot’
plot.responses: no visible global function definition for ‘ggtitle’
plot.responses: no visible global function definition for ‘geom_bar’
plot.responses: no visible global function definition for ‘ddply’
plot.responses: no visible global function definition for
‘geom_errorbar’
plot.responses: no visible global function definition for ‘theme_bw’
read.sif: no visible global function definition for ‘graph.edgelist’
read.sif: no visible global function definition for
‘igraph.to.graphNEL’
* 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 ... NOTE
File ‘netresponse/libs/netresponse.so’:
Found ‘rand’, possibly from ‘rand’ (C)
Object: ‘netresponse.o’
Found ‘srand’, possibly from ‘srand’ (C)
Object: ‘netresponse.o’
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [60s/61s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
ICMg.combined.sampler 41.254 0.032 41.800
detect.responses 6.700 0.016 6.725
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘ICMg.test.R’ [11s/12s]
Running ‘bicmixture.R’ [4s/4s]
Running ‘mixture.model.test.R’ [4s/4s]
Running ‘mixture.model.test.multimodal.R’ [7s/7s]
Running ‘mixture.model.test.singlemode.R’ [4s/4s]
Running ‘timing.R’ [0s/0s]
Running ‘toydata2.R’ [0s/0s]
Running ‘validate.netresponse.R’ [14s/14s]
Running ‘validate.pca.basis.R’ [22s/22s]
Running ‘vdpmixture.R’ [4s/4s]
[70s/72s] 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 5 notes.
See
‘/home/biocbuild/bbs-3.0-bioc/meat/netresponse.Rcheck/00check.log’
for details.
* installing *source* package ‘netresponse’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c netresponse.c -o netresponse.o
netresponse.c: In function ‘mHPpost’:
netresponse.c:264:15: warning: unused variable ‘prior_fields’ [-Wunused-variable]
netresponse.c: In function ‘mLogLambda’:
netresponse.c:713:20: warning: ‘U_p’ may be used uninitialized in this function [-Wuninitialized]
netresponse.c:713:20: warning: ‘KsiBeta’ may be used uninitialized in this function [-Wuninitialized]
netresponse.c:713:20: warning: ‘KsiAlpha’ may be used uninitialized in this function [-Wuninitialized]
netresponse.c:713:20: warning: ‘BetaKsi’ may be used uninitialized in this function [-Wuninitialized]
netresponse.c:713:20: warning: ‘AlphaKsi’ may be used uninitialized in this function [-Wuninitialized]
netresponse.c:713:20: warning: ‘Mutilde’ may be used uninitialized in this function [-Wuninitialized]
netresponse.c:713:20: warning: ‘Mubar’ may be used uninitialized in this function [-Wuninitialized]
netresponse.c:713:20: warning: ‘S2mu’ may be used uninitialized in this function [-Wuninitialized]
netresponse.c:713:20: warning: ‘Mumu’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.0-bioc/R/lib -L/usr/local/lib -o netresponse.so netresponse.o -L/home/biocbuild/bbs-3.0-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.0-bioc/meat/netresponse.Rcheck/netresponse/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 (netresponse)