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BioC 3.0: CHECK report for netresponse on oaxaca

This page was generated on 2015-04-10 10:04:24 -0700 (Fri, 10 Apr 2015).

Package 602/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
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 

Summary

Package: netresponse
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch netresponse_1.16.0.tar.gz
StartedAt: 2015-04-10 01:47:23 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 01:51:55 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 272.0 seconds
RetCode: 0
Status:  OK 
CheckDir: netresponse.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch netresponse_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/netresponse.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 ‘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 ... [12s/13s] 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [70s/72s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
ICMg.combined.sampler 47.996  0.074  48.411
detect.responses       8.575  0.059   8.843
netresponse-package    5.220  0.041   5.376
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘ICMg.test.R’ [14s/14s]
  Running ‘bicmixture.R’ [5s/5s]
  Running ‘mixture.model.test.R’ [5s/5s]
  Running ‘mixture.model.test.multimodal.R’ [7s/7s]
  Running ‘mixture.model.test.singlemode.R’ [5s/5s]
  Running ‘timing.R’ [0s/0s]
  Running ‘toydata2.R’ [0s/0s]
  Running ‘validate.netresponse.R’ [15s/15s]
  Running ‘validate.pca.basis.R’ [21s/21s]
  Running ‘vdpmixture.R’ [4s/4s]
 [77s/78s] 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
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/netresponse.Rcheck/00check.log’
for details.

netresponse.Rcheck/00install.out:

* installing *source* package ‘netresponse’ ...
** 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 netresponse.c -o netresponse.o
netresponse.c:264:15: warning: unused variable 'prior_fields' [-Wunused-variable]
  const char *prior_fields[]={"Mumu","S2mu",
              ^
netresponse.c:686:6: warning: variable 'Mumu' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  if(dim1) {
     ^˜˜˜
netresponse.c:713:21: note: uninitialized use occurs here
  vdp_mk_log_lambda(Mumu, S2mu, Mubar, Mutilde, 
                    ^˜˜˜
netresponse.c:686:3: note: remove the 'if' if its condition is always true
  if(dim1) {
  ^˜˜˜˜˜˜˜˜
netresponse.c:655:15: note: initialize the variable 'Mumu' to silence this warning
  double *Mumu, *S2mu, *Mubar, *Mutilde, 
              ^
               = NULL
netresponse.c:686:6: warning: variable 'S2mu' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  if(dim1) {
     ^˜˜˜
netresponse.c:713:27: note: uninitialized use occurs here
  vdp_mk_log_lambda(Mumu, S2mu, Mubar, Mutilde, 
                          ^˜˜˜
netresponse.c:686:3: note: remove the 'if' if its condition is always true
  if(dim1) {
  ^˜˜˜˜˜˜˜˜
netresponse.c:655:22: note: initialize the variable 'S2mu' to silence this warning
  double *Mumu, *S2mu, *Mubar, *Mutilde, 
                     ^
                      = NULL
netresponse.c:686:6: warning: variable 'Mubar' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  if(dim1) {
     ^˜˜˜
netresponse.c:713:33: note: uninitialized use occurs here
  vdp_mk_log_lambda(Mumu, S2mu, Mubar, Mutilde, 
                                ^˜˜˜˜
netresponse.c:686:3: note: remove the 'if' if its condition is always true
  if(dim1) {
  ^˜˜˜˜˜˜˜˜
netresponse.c:655:30: note: initialize the variable 'Mubar' to silence this warning
  double *Mumu, *S2mu, *Mubar, *Mutilde, 
                             ^
                              = NULL
netresponse.c:686:6: warning: variable 'Mutilde' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  if(dim1) {
     ^˜˜˜
netresponse.c:713:40: note: uninitialized use occurs here
  vdp_mk_log_lambda(Mumu, S2mu, Mubar, Mutilde, 
                                       ^˜˜˜˜˜˜
netresponse.c:686:3: note: remove the 'if' if its condition is always true
  if(dim1) {
  ^˜˜˜˜˜˜˜˜
netresponse.c:655:40: note: initialize the variable 'Mutilde' to silence this warning
  double *Mumu, *S2mu, *Mubar, *Mutilde, 
                                       ^
                                        = NULL
netresponse.c:686:6: warning: variable 'AlphaKsi' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  if(dim1) {
     ^˜˜˜
netresponse.c:714:7: note: uninitialized use occurs here
                    AlphaKsi, BetaKsi, KsiAlpha, KsiBeta, 
                    ^˜˜˜˜˜˜˜
netresponse.c:686:3: note: remove the 'if' if its condition is always true
  if(dim1) {
  ^˜˜˜˜˜˜˜˜
netresponse.c:656:14: note: initialize the variable 'AlphaKsi' to silence this warning
    *AlphaKsi, *BetaKsi, *KsiAlpha, *KsiBeta, *U_p, *prior_alpha,
             ^
              = NULL
netresponse.c:686:6: warning: variable 'BetaKsi' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  if(dim1) {
     ^˜˜˜
netresponse.c:714:17: note: uninitialized use occurs here
                    AlphaKsi, BetaKsi, KsiAlpha, KsiBeta, 
                              ^˜˜˜˜˜˜
netresponse.c:686:3: note: remove the 'if' if its condition is always true
  if(dim1) {
  ^˜˜˜˜˜˜˜˜
netresponse.c:656:24: note: initialize the variable 'BetaKsi' to silence this warning
    *AlphaKsi, *BetaKsi, *KsiAlpha, *KsiBeta, *U_p, *prior_alpha,
                       ^
                        = NULL
netresponse.c:686:6: warning: variable 'KsiAlpha' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  if(dim1) {
     ^˜˜˜
netresponse.c:714:26: note: uninitialized use occurs here
                    AlphaKsi, BetaKsi, KsiAlpha, KsiBeta, 
                                       ^˜˜˜˜˜˜˜
netresponse.c:686:3: note: remove the 'if' if its condition is always true
  if(dim1) {
  ^˜˜˜˜˜˜˜˜
netresponse.c:656:35: note: initialize the variable 'KsiAlpha' to silence this warning
    *AlphaKsi, *BetaKsi, *KsiAlpha, *KsiBeta, *U_p, *prior_alpha,
                                  ^
                                   = NULL
netresponse.c:686:6: warning: variable 'KsiBeta' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  if(dim1) {
     ^˜˜˜
netresponse.c:714:36: note: uninitialized use occurs here
                    AlphaKsi, BetaKsi, KsiAlpha, KsiBeta, 
                                                 ^˜˜˜˜˜˜
netresponse.c:686:3: note: remove the 'if' if its condition is always true
  if(dim1) {
  ^˜˜˜˜˜˜˜˜
netresponse.c:656:45: note: initialize the variable 'KsiBeta' to silence this warning
    *AlphaKsi, *BetaKsi, *KsiAlpha, *KsiBeta, *U_p, *prior_alpha,
                                            ^
                                             = NULL
netresponse.c:696:6: warning: variable 'U_p' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  if(dim2) {
     ^˜˜˜
netresponse.c:716:7: note: uninitialized use occurs here
                    U_p, U_hat,
                    ^˜˜
netresponse.c:696:3: note: remove the 'if' if its condition is always true
  if(dim2) {
  ^˜˜˜˜˜˜˜˜
netresponse.c:656:51: note: initialize the variable 'U_p' to silence this warning
    *AlphaKsi, *BetaKsi, *KsiAlpha, *KsiBeta, *U_p, *prior_alpha,
                                                  ^
                                                   = NULL
netresponse.c:696:6: warning: variable 'U_hat' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  if(dim2) {
     ^˜˜˜
netresponse.c:716:12: note: uninitialized use occurs here
                    U_p, U_hat,
                         ^˜˜˜˜
netresponse.c:696:3: note: remove the 'if' if its condition is always true
  if(dim2) {
  ^˜˜˜˜˜˜˜˜
netresponse.c:661:14: note: initialize the variable 'U_hat' to silence this warning
  SEXP* U_hat;
             ^
              = NULL
11 warnings 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 netresponse.so netresponse.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/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)

netresponse.Rcheck/netresponse-Ex.timings:

nameusersystemelapsed
ICMg.combined.sampler47.996 0.07448.411
ICMg.links.sampler2.6190.0202.706
NetResponseModel-class0.0020.0000.002
PlotMixture0.0010.0000.001
PlotMixtureBivariate0.0010.0000.001
PlotMixtureMultivariate0.0010.0010.001
PlotMixtureMultivariate.deprecated0.0000.0000.001
PlotMixtureUnivariate000
add.ellipse0.0010.0000.000
centerData0.0010.0000.000
check.matrix0.0010.0000.000
check.network000
detect.responses8.5750.0598.843
dna0.0260.0030.029
enrichment.list.factor0.0000.0000.001
enrichment.list.factor.minimal0.0010.0000.001
filter.netw0.0010.0000.001
filter.network0.0010.0000.001
find.similar.features0.5780.0050.591
generate.toydata0.0010.0000.001
get.dat0.0010.0000.001
get.mis0.0000.0000.001
get.model.parameters0.0050.0010.007
get.subnets0.0010.0000.000
getqofz0.0000.0000.001
independent.models0.0000.0000.001
list.significant.responses0.0000.0000.001
listify.groupings000
model.stats0.0050.0010.006
netresponse-package5.2200.0415.376
order.responses0.0000.0000.001
osmo0.0510.0040.055
pick.model.pairs0.0000.0000.001
pick.model.parameters0.0000.0000.001
plot.data0.0000.0010.001
plot.expression0.0010.0000.001
plot.response0.0010.0000.000
plot.responses0.0010.0000.000
plot.scale0.0000.0000.001
plot.subnet0.0000.0000.001
plotAssociations000
plotPCA000
read.sif0.0010.0000.000
remove.negative.edges0.0010.0000.001
response.enrichment0.0010.0000.001
response2sample0.0080.0020.009
sample2response0.0010.0000.000
set.breaks0.0010.0000.001
toydata0.0040.0000.004
update.model.pair0.0010.0000.001
vdp.mixt0.0750.0010.076
vectorize.groupings0.0010.0000.001
write.netresponse.results0.0000.0000.001