netresponse 1.35.0
Leo Lahti
| Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/netresponse | | Last Changed Rev: 122712 / Revision: 127142 | | Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | WARNINGS | OK | |
| toluca2 | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | WARNINGS | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ WARNINGS ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings netresponse_1.35.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/netresponse.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* 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 ‘1.35.0’
* 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 36.206 0.069 36.294
* 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 -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-3.5-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)