BioC 3.3: CHECK report for netresponse on linux2.bioconductor.org
This page was generated on 2015-10-27 12:11:52 -0400 (Tue, 27 Oct 2015).
netresponse 1.21.0
Leo Lahti
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/netresponse | | Last Changed Rev: 109592 / Revision: 109948 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK | |
Summary
| Package: netresponse |
| Version: 1.21.0 |
| Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings netresponse_1.21.0.tar.gz |
| StartedAt: 2015-10-27 06:18:20 -0400 (Tue, 27 Oct 2015) |
| EndedAt: 2015-10-27 06:22:56 -0400 (Tue, 27 Oct 2015) |
| EllapsedTime: 275.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: netresponse.Rcheck |
| Warnings: 0 |
Command output
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###
### Running command:
###
### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings netresponse_1.21.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/netresponse.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* 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 ‘1.21.0’
* 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 ... [8s/8s] 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’
Undefined global functions or variables:
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 ... [56s/56s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
ICMg.combined.sampler 39.413 0.015 39.484
detect.responses 5.981 0.008 5.997
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘ICMg.test.R’ [11s/11s]
Running ‘bicmixture.R’ [3s/3s]
Running ‘mixture.model.test.R’ [2s/2s]
Running ‘mixture.model.test.multimodal.R’ [5s/5s]
Running ‘mixture.model.test.singlemode.R’ [4s/4s]
Running ‘timing.R’ [0s/0s]
Running ‘toydata2.R’ [0s/0s]
Running ‘validate.netresponse.R’ [76s/76s]
Running ‘validate.pca.basis.R’ [44s/44s]
Running ‘vdpmixture.R’ [3s/3s]
[147s/147s] OK
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/home/biocbuild/bbs-3.3-bioc/meat/netresponse.Rcheck/00check.log’
for details.
netresponse.Rcheck/00install.out:
* installing *source* package ‘netresponse’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c netresponse.c -o netresponse.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.3-bioc/R/lib -L/usr/local/lib -o netresponse.so netresponse.o -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-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 | 39.413 | 0.015 | 39.484 |
|
| ICMg.links.sampler | 3.165 | 0.008 | 3.173 |
|
| NetResponseModel-class | 0.001 | 0.000 | 0.001 |
|
| PlotMixture | 0 | 0 | 0 |
|
| PlotMixtureBivariate | 0 | 0 | 0 |
|
| PlotMixtureMultivariate | 0 | 0 | 0 |
|
| PlotMixtureMultivariate.deprecated | 0 | 0 | 0 |
|
| PlotMixtureUnivariate | 0 | 0 | 0 |
|
| add.ellipse | 0 | 0 | 0 |
|
| centerData | 0 | 0 | 0 |
|
| check.matrix | 0 | 0 | 0 |
|
| check.network | 0 | 0 | 0 |
|
| detect.responses | 5.981 | 0.008 | 5.997 |
|
| dna | 0.03 | 0.00 | 0.03 |
|
| enrichment.list.factor | 0.001 | 0.000 | 0.001 |
|
| enrichment.list.factor.minimal | 0.001 | 0.000 | 0.000 |
|
| filter.netw | 0.001 | 0.000 | 0.000 |
|
| filter.network | 0.000 | 0.000 | 0.001 |
|
| find.similar.features | 0.552 | 0.004 | 0.556 |
|
| generate.toydata | 0 | 0 | 0 |
|
| get.dat-NetResponseModel-method | 0.000 | 0.000 | 0.001 |
|
| get.mis | 0.000 | 0.000 | 0.001 |
|
| get.model.parameters | 0.006 | 0.000 | 0.005 |
|
| get.subnets-NetResponseModel-method | 0.000 | 0.000 | 0.001 |
|
| getqofz-NetResponseModel-method | 0 | 0 | 0 |
|
| independent.models | 0 | 0 | 0 |
|
| list.significant.responses | 0.000 | 0.000 | 0.001 |
|
| listify.groupings | 0.000 | 0.000 | 0.001 |
|
| model.stats | 0.004 | 0.000 | 0.004 |
|
| netresponse-package | 4.193 | 0.000 | 4.195 |
|
| order.responses | 0.000 | 0.000 | 0.001 |
|
| osmo | 0.050 | 0.008 | 0.059 |
|
| pick.model.pairs | 0.001 | 0.000 | 0.001 |
|
| pick.model.parameters | 0.001 | 0.000 | 0.001 |
|
| plot.data | 0.001 | 0.000 | 0.001 |
|
| plot.expression | 0 | 0 | 0 |
|
| plot.response | 0 | 0 | 0 |
|
| plot.responses | 0 | 0 | 0 |
|
| plot.scale | 0.001 | 0.000 | 0.001 |
|
| plot.subnet | 0.001 | 0.000 | 0.001 |
|
| plotPCA | 0.001 | 0.000 | 0.001 |
|
| plot_associations | 0.001 | 0.000 | 0.001 |
|
| plot_matrix | 0.009 | 0.000 | 0.010 |
|
| read.sif | 0 | 0 | 0 |
|
| remove.negative.edges | 0.001 | 0.000 | 0.001 |
|
| response.enrichment | 0.001 | 0.000 | 0.001 |
|
| response2sample | 0.006 | 0.000 | 0.006 |
|
| sample2response | 0.001 | 0.000 | 0.001 |
|
| set.breaks | 0.001 | 0.000 | 0.001 |
|
| toydata | 0.004 | 0.000 | 0.004 |
|
| update.model.pair | 0 | 0 | 0 |
|
| vdp.mixt | 0.068 | 0.004 | 0.071 |
|
| vectorize.groupings | 0.000 | 0.000 | 0.001 |
|
| write.netresponse.results | 0.000 | 0.004 | 0.001 |
|