BioC 3.1: CHECK report for netresponse on zin2
This page was generated on 2015-10-09 09:24:07 -0700 (Fri, 09 Oct 2015).
netresponse 1.18.0 Leo Lahti
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/netresponse | Last Changed Rev: 102591 / Revision: 109384 | Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK |  |
petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK |  |
morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK |  |
Summary
Package: netresponse |
Version: 1.18.0 |
Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings netresponse_1.18.0.tar.gz |
StartedAt: 2015-10-09 03:56:48 -0700 (Fri, 09 Oct 2015) |
EndedAt: 2015-10-09 04:01:23 -0700 (Fri, 09 Oct 2015) |
EllapsedTime: 275.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: netresponse.Rcheck |
Warnings: 0 |
Command output
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###
### Running command:
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### /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings netresponse_1.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/netresponse.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (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 ‘1.18.0’
* 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 ... [7s/7s] 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 ... [58s/58s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
ICMg.combined.sampler 42.016 0.023 42.078
detect.responses 5.862 0.012 5.881
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘ICMg.test.R’ [10s/10s]
Running ‘bicmixture.R’ [3s/3s]
Running ‘mixture.model.test.R’ [3s/3s]
Running ‘mixture.model.test.multimodal.R’ [5s/5s]
Running ‘mixture.model.test.singlemode.R’ [3s/3s]
Running ‘timing.R’ [0s/0s]
Running ‘toydata2.R’ [0s/0s]
Running ‘validate.netresponse.R’ [73s/73s]
Running ‘validate.pca.basis.R’ [47s/47s]
Running ‘vdpmixture.R’ [3s/3s]
[147s/147s] OK
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/home/biocbuild/bbs-3.1-bioc/meat/netresponse.Rcheck/00check.log’
for details.
netresponse.Rcheck/00install.out:
* installing *source* package ‘netresponse’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c netresponse.c -o netresponse.o
netresponse.c: In function ‘mHPpost’:
netresponse.c:264:15: warning: unused variable ‘prior_fields’ [-Wunused-variable]
const char *prior_fields[]={"Mumu","S2mu",
^
netresponse.c: In function ‘mLogLambda’:
netresponse.c:713:20: warning: ‘U_p’ may be used uninitialized in this function [-Wmaybe-uninitialized]
vdp_mk_log_lambda(Mumu, S2mu, Mubar, Mutilde,
^
netresponse.c:713:20: warning: ‘KsiBeta’ may be used uninitialized in this function [-Wmaybe-uninitialized]
netresponse.c:713:20: warning: ‘KsiAlpha’ may be used uninitialized in this function [-Wmaybe-uninitialized]
netresponse.c:713:20: warning: ‘BetaKsi’ may be used uninitialized in this function [-Wmaybe-uninitialized]
netresponse.c:713:20: warning: ‘AlphaKsi’ may be used uninitialized in this function [-Wmaybe-uninitialized]
netresponse.c:713:20: warning: ‘Mutilde’ may be used uninitialized in this function [-Wmaybe-uninitialized]
netresponse.c:713:20: warning: ‘Mubar’ may be used uninitialized in this function [-Wmaybe-uninitialized]
netresponse.c:713:20: warning: ‘S2mu’ may be used uninitialized in this function [-Wmaybe-uninitialized]
netresponse.c:713:20: warning: ‘Mumu’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.1-bioc/R/lib -L/usr/local/lib -o netresponse.so netresponse.o -L/home/biocbuild/bbs-3.1-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.1-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 | 42.016 | 0.023 | 42.078 |
|
ICMg.links.sampler | 3.442 | 0.008 | 3.452 |
|
NetResponseModel-class | 0.001 | 0.000 | 0.001 |
|
PlotMixture | 0 | 0 | 0 |
|
PlotMixtureBivariate | 0 | 0 | 0 |
|
PlotMixtureMultivariate | 0 | 0 | 0 |
|
PlotMixtureMultivariate.deprecated | 0.001 | 0.000 | 0.001 |
|
PlotMixtureUnivariate | 0.001 | 0.000 | 0.001 |
|
add.ellipse | 0 | 0 | 0 |
|
centerData | 0 | 0 | 0 |
|
check.matrix | 0 | 0 | 0 |
|
check.network | 0.000 | 0.000 | 0.001 |
|
detect.responses | 5.862 | 0.012 | 5.881 |
|
dna | 0.023 | 0.000 | 0.023 |
|
enrichment.list.factor | 0 | 0 | 0 |
|
enrichment.list.factor.minimal | 0.001 | 0.000 | 0.000 |
|
filter.netw | 0.000 | 0.000 | 0.001 |
|
filter.network | 0 | 0 | 0 |
|
find.similar.features | 0.423 | 0.000 | 0.423 |
|
generate.toydata | 0.000 | 0.000 | 0.001 |
|
get.dat-NetResponseModel-method | 0.001 | 0.000 | 0.001 |
|
get.mis | 0.001 | 0.000 | 0.000 |
|
get.model.parameters | 0.004 | 0.000 | 0.004 |
|
get.subnets-NetResponseModel-method | 0.000 | 0.000 | 0.001 |
|
getqofz-NetResponseModel-method | 0.001 | 0.000 | 0.000 |
|
independent.models | 0.001 | 0.000 | 0.000 |
|
list.significant.responses | 0 | 0 | 0 |
|
listify.groupings | 0.000 | 0.000 | 0.001 |
|
model.stats | 0.003 | 0.000 | 0.003 |
|
netresponse-package | 3.771 | 0.012 | 3.786 |
|
order.responses | 0 | 0 | 0 |
|
osmo | 0.04 | 0.00 | 0.04 |
|
pick.model.pairs | 0 | 0 | 0 |
|
pick.model.parameters | 0.000 | 0.000 | 0.001 |
|
plot.data | 0.001 | 0.000 | 0.001 |
|
plot.expression | 0.001 | 0.000 | 0.000 |
|
plot.response | 0 | 0 | 0 |
|
plot.responses | 0 | 0 | 0 |
|
plot.scale | 0.000 | 0.000 | 0.001 |
|
plot.subnet | 0.001 | 0.000 | 0.000 |
|
plotPCA | 0 | 0 | 0 |
|
plot_associations | 0 | 0 | 0 |
|
plot_matrix | 0.006 | 0.000 | 0.006 |
|
read.sif | 0 | 0 | 0 |
|
remove.negative.edges | 0.000 | 0.000 | 0.001 |
|
response.enrichment | 0.001 | 0.000 | 0.001 |
|
response2sample | 0.005 | 0.000 | 0.004 |
|
sample2response | 0 | 0 | 0 |
|
set.breaks | 0.001 | 0.000 | 0.001 |
|
toydata | 0.002 | 0.000 | 0.002 |
|
update.model.pair | 0 | 0 | 0 |
|
vdp.mixt | 0.047 | 0.000 | 0.047 |
|
vectorize.groupings | 0 | 0 | 0 |
|
write.netresponse.results | 0.000 | 0.000 | 0.001 |
|