BioC 3.5: CHECK report for netresponse on veracruz2

Package: netresponse

Version: 1.36.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings netresponse_1.36.0.tar.gz

StartedAt: 2017-10-18 06:46:33 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 06:50:04 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 211.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: netresponse.Rcheck

Warnings: 1

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings netresponse_1.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/netresponse.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.36.0’
* 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 ‘netresponse’ can be installed ... OK
* checking installed package size ... OK
* checking package 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 files in ‘vignettes’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘NetResponse.Rmd’, ‘NetResponse.md’, ‘TODO/TODO.Rmd’,
    ‘fig/NetResponse2-1.png’, ‘fig/NetResponse2b-1.png’,
    ‘fig/NetResponse3-1.png’, ‘fig/NetResponse4-1.png’,
    ‘fig/NetResponse5-1.png’, ‘fig/NetResponse7-1.png’,
    ‘fig/vdp-1.png’, ‘main.R’, ‘netresponse.bib’, ‘netresponse.pdf’
Package has no Sweave vignette sources and no VignetteBuilder field.
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
ICMg.combined.sampler 33.252  0.206  34.541
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘ICMg.test.R’
  Running ‘bicmixture.R’
  Running ‘mixture.model.test.R’
  Running ‘mixture.model.test.multimodal.R’
  Running ‘mixture.model.test.singlemode.R’
  Running ‘timing.R’
  Running ‘toydata2.R’
  Running ‘validate.netresponse.R’
  Running ‘validate.pca.basis.R’
  Running ‘vdpmixture.R’
 OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/netresponse.Rcheck/00check.log’
for details.

* installing *source* package ‘netresponse’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -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-3.5-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)

name	user	system	elapsed
ICMg.combined.sampler	33.252	0.206	34.541
ICMg.links.sampler	1.822	0.030	1.919
NetResponseModel-class	0.002	0.001	0.002
PlotMixture	0.000	0.000	0.001
PlotMixtureBivariate	0	0	0
PlotMixtureMultivariate	0	0	0
PlotMixtureMultivariate.deprecated	0	0	0
PlotMixtureUnivariate	0.000	0.001	0.001
add.ellipse	0.001	0.000	0.000
centerData	0.000	0.000	0.001
check.matrix	0.000	0.000	0.001
check.network	0.000	0.000	0.001
detect.responses	0.002	0.001	0.003
dna	0.020	0.005	0.024
enrichment.list.factor	0.001	0.000	0.000
enrichment.list.factor.minimal	0.000	0.000	0.001
filter.netw	0.000	0.001	0.000
filter.network	0	0	0
find.similar.features	0.607	0.011	0.632
generate.toydata	0.000	0.000	0.001
get.dat-NetResponseModel-method	0.000	0.000	0.001
get.mis	0	0	0
get.model.parameters	0.004	0.002	0.008
get.subnets-NetResponseModel-method	0.000	0.000	0.001
getqofz-NetResponseModel-method	0	0	0
independent.models	0.001	0.000	0.000
list.significant.responses	0.001	0.000	0.000
listify.groupings	0	0	0
model.stats	0.004	0.001	0.005
netresponse-package	3.714	0.043	3.862
order.responses	0	0	0
osmo	0.040	0.004	0.046
pick.model.pairs	0.001	0.000	0.001
pick.model.parameters	0.000	0.000	0.001
plotPCA	0	0	0
plot_associations	0.000	0.000	0.001
plot_data	0.000	0.000	0.001
plot_expression	0.001	0.001	0.001
plot_matrix	0.006	0.000	0.007
plot_response	0.000	0.000	0.001
plot_responses	0.001	0.000	0.000
plot_scale	0.000	0.000	0.001
plot_subnet	0.001	0.000	0.001
read.sif	0.000	0.000	0.001
remove.negative.edges	0.000	0.000	0.001
response.enrichment	0	0	0
response2sample	0.006	0.002	0.007
sample2response	0.000	0.000	0.001
set.breaks	0.001	0.000	0.001
toydata	0.002	0.001	0.003
update.model.pair	0.001	0.000	0.000
vdp.mixt	0.073	0.005	0.079
vectorize.groupings	0.000	0.000	0.001
write.netresponse.results	0.000	0.000	0.001