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This page was generated on 2015-10-27 17:39:18 -0400 (Tue, 27 Oct 2015).
| Package 705/1104 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| netresponse 1.20.0 Leo Lahti
| linux1.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK |  | |||||
| windows1.bioconductor.org | Windows Server 2012 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 | |
| Package: netresponse |
| Version: 1.20.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings netresponse_1.20.0.tar.gz |
| StartedAt: 2015-10-27 06:08:03 -0400 (Tue, 27 Oct 2015) |
| EndedAt: 2015-10-27 06:13:12 -0400 (Tue, 27 Oct 2015) |
| EllapsedTime: 309.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: netresponse.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings netresponse_1.20.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/netresponse.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.20.0’
* 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 ... [9s/9s] 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 ... NOTE
plot.responses: no visible global function definition for ‘qplot’
* 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’ ... NOTE
The following directory looks like a leftover from 'knitr':
‘figure’
Please remove from your package.
* checking examples ... [62s/62s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
ICMg.combined.sampler 43.918 0.099 44.059
detect.responses 6.902 0.092 7.001
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘ICMg.test.R’ [11s/11s]
Running ‘bicmixture.R’ [4s/4s]
Running ‘mixture.model.test.R’ [4s/4s]
Running ‘mixture.model.test.multimodal.R’ [6s/6s]
Running ‘mixture.model.test.singlemode.R’ [4s/4s]
Running ‘timing.R’ [0s/0s]
Running ‘toydata2.R’ [0s/0s]
Running ‘validate.netresponse.R’ [70s/70s]
Running ‘validate.pca.basis.R’ [43s/43s]
Running ‘vdpmixture.R’ [3s/3s]
[143s/144s] OK
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.2-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-3.2-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:
| name | user | system | elapsed | |
| ICMg.combined.sampler | 43.918 | 0.099 | 44.059 | |
| ICMg.links.sampler | 2.652 | 0.017 | 2.669 | |
| NetResponseModel-class | 0.001 | 0.000 | 0.001 | |
| PlotMixture | 0.000 | 0.000 | 0.001 | |
| PlotMixtureBivariate | 0.000 | 0.000 | 0.001 | |
| PlotMixtureMultivariate | 0.000 | 0.000 | 0.001 | |
| PlotMixtureMultivariate.deprecated | 0.001 | 0.000 | 0.001 | |
| PlotMixtureUnivariate | 0 | 0 | 0 | |
| add.ellipse | 0 | 0 | 0 | |
| centerData | 0.001 | 0.000 | 0.000 | |
| check.matrix | 0.001 | 0.000 | 0.000 | |
| check.network | 0 | 0 | 0 | |
| detect.responses | 6.902 | 0.092 | 7.001 | |
| dna | 0.024 | 0.004 | 0.028 | |
| enrichment.list.factor | 0.001 | 0.000 | 0.001 | |
| enrichment.list.factor.minimal | 0.001 | 0.000 | 0.001 | |
| filter.netw | 0.000 | 0.001 | 0.001 | |
| filter.network | 0.000 | 0.000 | 0.001 | |
| find.similar.features | 0.437 | 0.012 | 0.450 | |
| generate.toydata | 0 | 0 | 0 | |
| get.dat-NetResponseModel-method | 0 | 0 | 0 | |
| get.mis | 0.001 | 0.000 | 0.000 | |
| get.model.parameters | 0.003 | 0.001 | 0.004 | |
| get.subnets-NetResponseModel-method | 0.000 | 0.000 | 0.001 | |
| getqofz-NetResponseModel-method | 0.001 | 0.001 | 0.000 | |
| independent.models | 0.001 | 0.000 | 0.000 | |
| list.significant.responses | 0 | 0 | 0 | |
| listify.groupings | 0 | 0 | 0 | |
| model.stats | 0.003 | 0.001 | 0.003 | |
| netresponse-package | 4.273 | 0.050 | 4.326 | |
| order.responses | 0.001 | 0.000 | 0.000 | |
| osmo | 0.043 | 0.005 | 0.048 | |
| pick.model.pairs | 0 | 0 | 0 | |
| pick.model.parameters | 0.001 | 0.000 | 0.001 | |
| plot.data | 0 | 0 | 0 | |
| plot.expression | 0 | 0 | 0 | |
| plot.response | 0 | 0 | 0 | |
| plot.responses | 0.000 | 0.000 | 0.001 | |
| plot.scale | 0 | 0 | 0 | |
| plot.subnet | 0.001 | 0.000 | 0.000 | |
| plotPCA | 0 | 0 | 0 | |
| plot_associations | 0.001 | 0.000 | 0.001 | |
| plot_matrix | 0.008 | 0.001 | 0.008 | |
| read.sif | 0 | 0 | 0 | |
| remove.negative.edges | 0 | 0 | 0 | |
| response.enrichment | 0.001 | 0.000 | 0.000 | |
| response2sample | 0.004 | 0.001 | 0.005 | |
| sample2response | 0.000 | 0.000 | 0.001 | |
| set.breaks | 0.001 | 0.000 | 0.000 | |
| toydata | 0.002 | 0.000 | 0.003 | |
| update.model.pair | 0.001 | 0.000 | 0.000 | |
| vdp.mixt | 0.057 | 0.001 | 0.058 | |
| vectorize.groupings | 0 | 0 | 0 | |
| write.netresponse.results | 0.001 | 0.000 | 0.000 | |