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Package 439/671HostnameOS / ArchBUILDCHECKBUILD BIN
netresponse 1.12.0
Leo Lahti
Snapshot Date: 2013-04-30 17:01:37 -0700 (Tue, 30 Apr 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/netresponse
Last Changed Rev: 75263 / Revision: 76155
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 
pelham Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ WARNINGS ] OK 

Summary

Package: netresponse
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch netresponse_1.12.0.tar.gz
StartedAt: 2013-05-01 08:37:25 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 08:47:27 -0700 (Wed, 01 May 2013)
EllapsedTime: 601.6 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: netresponse.Rcheck
Warnings: 1

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/netresponse.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'netresponse/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'netresponse' version '1.12.0'
* 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 ... [18s/20s] WARNING
Found the following significant warnings:
  netresponse.c:686:6: warning: variable 'KsiAlpha' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  netresponse.c:686:6: warning: variable 'BetaKsi' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  netresponse.c:696:6: warning: variable 'U_p' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  netresponse.c:686:6: warning: variable 'KsiBeta' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  netresponse.c:686:6: warning: variable 'S2mu' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  netresponse.c:686:6: warning: variable 'Mumu' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  netresponse.c:696:6: warning: variable 'U_hat' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  netresponse.c:686:6: warning: variable 'AlphaKsi' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  netresponse.c:686:6: warning: variable 'Mubar' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  netresponse.c:686:6: warning: variable 'Mutilde' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
See '/Users/biocbuild/bbs-2.12-bioc/meat/netresponse.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package 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 for unstated 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 ... NOTE
File 'netresponse/R/firstlib.R':
  .onLoad calls:
    packageStartupMessage("\nnetresponse Copyright (C) 2008-2013 Leo Lahti.\nThis program comes with ABSOLUTELY NO WARRANTY.\nThis is free software, and you are welcome to redistribute it under GNU GPL >=2, see the licensing terms for details.\n")

See section 'Good practice' in '?.onAttach'.
* 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 for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [266s/271s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
ICMg.combined.sampler 222.898  0.618 227.188
detect.responses       14.476  1.280  16.228
netresponse-package     8.751  0.727  10.044
ICMg.links.sampler      7.368  0.114   7.637
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'ICMg.test.R' [47s/49s]
  Running 'bicmixture.R' [8s/8s]
  Running 'mixture.model.test.R' [8s/8s]
  Running 'mixture.model.test.multimodal.R' [12s/12s]
  Running 'mixture.model.test.singlemode.R' [8s/9s]
  Running 'timing.R' [0s/1s]
  Running 'toydata2.R' [1s/1s]
  Running 'validate.netresponse.R' [23s/23s]
  Running 'validate.pca.basis.R' [36s/37s]
  Running 'vdpmixture.R' [8s/8s]
 [150s/156s] 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
NOTE: There were 2 notes.
See
  '/Users/biocbuild/bbs-2.12-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    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c netresponse.c -o netresponse.o
netresponse.c:147:37: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    *U_hat_table=(double ***)malloc(dim2 * sizeof(double*));
                                    ^˜˜˜ ˜
netresponse.c:148:31: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    *data2_int=(int **)malloc(dim2 * sizeof(int*));
                              ^˜˜˜ ˜
netresponse.c:151:38: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
    (*data2_int)[j]  = (int *)malloc(datalen * sizeof(int));
                                     ^˜˜˜˜˜˜ ˜
netresponse.c:152:40: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    (*U_hat_table)[j]=(double**)malloc(ncentroids * sizeof(double*));
                                       ^˜˜˜˜˜˜˜˜˜ ˜
netresponse.c:154:47: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
      (*U_hat_table)[j][i] =(double *)malloc(((int)(Ns[j]))*sizeof(double));
                                              ^˜˜˜˜˜˜˜˜˜˜˜ ˜
netresponse.c:221:50: warning: implicit conversion turns floating-point number into integer: 'double' to 'R_xlen_t' (aka 'long') [-Wconversion]
    PROTECT(U_hat_j_SEXP = NEW_NUMERIC(ncentroids*Ns[j]));
                           ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rdefines.h:73:45: note: expanded from macro 'NEW_NUMERIC'
#define NEW_NUMERIC(n)          allocVector(REALSXP,n)
                                                    ^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
netresponse.c:264:15: warning: unused variable 'prior_fields' [-Wunused-variable]
  const char *prior_fields[]={"Mumu","S2mu",
              ^
netresponse.c:530:32: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  *Temp    = (double **)malloc(ncentroids * sizeof(double*));
                               ^˜˜˜˜˜˜˜˜˜ ˜
netresponse.c:532:34: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    *S2_x    = (double **)malloc(ncentroids * sizeof(double*));
                                 ^˜˜˜˜˜˜˜˜˜ ˜
netresponse.c:533:34: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    *Ksi_log = (double **)malloc(ncentroids * sizeof(double*));
                                 ^˜˜˜˜˜˜˜˜˜ ˜
netresponse.c:536:37: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    *U_hat_table=(double ***)malloc(dim2 * sizeof(double*));
                                    ^˜˜˜ ˜
netresponse.c:537:31: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    *data2_int=(int **)malloc(dim2 * sizeof(int*));
                              ^˜˜˜ ˜
netresponse.c:540:38: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
    (*Temp)[i]    = (double *)malloc(datalen * sizeof(double));
                                     ^˜˜˜˜˜˜ ˜
netresponse.c:542:40: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
      (*S2_x)[i]    = (double *)malloc(dim1 * sizeof(double));
                                       ^˜˜˜ ˜
netresponse.c:543:40: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
      (*Ksi_log)[i] = (double *)malloc(dim1 * sizeof(double));
                                       ^˜˜˜ ˜
netresponse.c:547:38: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
    (*data2_int)[j]  = (int *)malloc(datalen * sizeof(int));
                                     ^˜˜˜˜˜˜ ˜
netresponse.c:548:40: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    (*U_hat_table)[j]=(double**)malloc(ncentroids * sizeof(double*));
                                       ^˜˜˜˜˜˜˜˜˜ ˜
netresponse.c:550:47: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
      (*U_hat_table)[j][i] =(double *)malloc(((int)(Ns[j]))*sizeof(double));
                                              ^˜˜˜˜˜˜˜˜˜˜˜ ˜
netresponse.c:629:30: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
  log_p_of_z_given_other_z_c(datalen, ncentroids, post_gamma, log_lambda);
  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
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 '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: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: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: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 '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: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
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 '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
29 warnings generated.
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/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-2.12-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.sampler222.898 0.618227.188
ICMg.links.sampler7.3680.1147.637
NetResponseModel-class0.0070.0060.026
PlotMixture0.0020.0040.005
PlotMixtureBivariate0.0050.0040.009
PlotMixtureMultivariate0.0050.0030.008
PlotMixtureMultivariate.deprecated0.0020.0040.006
PlotMixtureUnivariate0.0050.0040.010
add.ellipse0.0050.0030.009
centerData0.0020.0030.005
check.matrix0.0060.0040.009
check.network0.0050.0030.009
detect.responses14.476 1.28016.228
dna0.0430.0120.055
enrichment.list.factor0.0030.0030.005
filter.netw0.0020.0040.006
filter.network0.0020.0040.005
find.similar.features0.9350.0981.046
generate.toydata0.0020.0020.004
get.dat0.0110.0060.016
get.mis0.0100.0040.014
get.model.parameters0.0180.0100.029
get.subnets0.0030.0030.006
getqofz0.0100.0040.014
independent.models0.0160.0030.019
list.significant.responses0.0080.0030.011
model.stats0.0090.0060.014
netresponse-package 8.751 0.72710.044
order.responses0.0030.0050.007
osmo0.0660.0170.085
pick.model.pairs0.0060.0040.010
pick.model.parameters0.0060.0040.011
plot.data0.0060.0040.010
plot.expression0.0060.0040.011
plot.response0.0030.0030.005
plot.responses0.0020.0030.005
plot.scale0.0020.0040.006
plot.subnet0.0030.0040.007
plotAssociations0.0020.0040.006
plotPCA0.0020.0040.006
read.sif0.0020.0040.006
remove.negative.edges0.0020.0040.007
response.enrichment0.0020.0040.006
response2sample0.0160.0100.027
sample2response0.0090.0060.015
set.breaks0.0030.0040.008
toydata0.0110.0080.018
update.model.pair0.0070.0040.011
vdp.mixt0.1290.0210.155
write.netresponse.results0.0020.0030.006