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BioC 3.4: CHECK report for netresponse on zin1

This page was generated on 2016-09-21 03:37:04 -0700 (Wed, 21 Sep 2016).

Package 816/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
netresponse 1.33.2
Leo Lahti
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/netresponse
Last Changed Rev: 117512 / Revision: 121152
Last Changed Date: 2016-05-15 13:14:22 -0700 (Sun, 15 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: netresponse
Version: 1.33.2
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings netresponse_1.33.2.tar.gz
StartedAt: 2016-09-20 09:57:08 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 10:00:21 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 192.3 seconds
RetCode: 0
Status:  OK 
CheckDir: netresponse.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings netresponse_1.33.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/netresponse.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.33.2’
* 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’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
ICMg.combined.sampler 39.288   0.02  39.308
* 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 NOTE
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/netresponse.Rcheck/00check.log’
for details.


netresponse.Rcheck/00install.out:

* installing *source* package ‘netresponse’ ...
** libs
gcc -I/home/biocbuild/bbs-3.4-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:713:3: warning: ‘U_p’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   vdp_mk_log_lambda(Mumu, S2mu, Mubar, Mutilde, 
   ^
netresponse.c:713:3: warning: ‘KsiBeta’ may be used uninitialized in this function [-Wmaybe-uninitialized]
netresponse.c:713:3: warning: ‘KsiAlpha’ may be used uninitialized in this function [-Wmaybe-uninitialized]
netresponse.c:713:3: warning: ‘BetaKsi’ may be used uninitialized in this function [-Wmaybe-uninitialized]
netresponse.c:713:3: warning: ‘AlphaKsi’ may be used uninitialized in this function [-Wmaybe-uninitialized]
netresponse.c:713:3: warning: ‘Mutilde’ may be used uninitialized in this function [-Wmaybe-uninitialized]
netresponse.c:713:3: warning: ‘Mubar’ may be used uninitialized in this function [-Wmaybe-uninitialized]
netresponse.c:713:3: warning: ‘S2mu’ may be used uninitialized in this function [-Wmaybe-uninitialized]
netresponse.c:713:3: warning: ‘Mumu’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gcc -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o netresponse.so netresponse.o -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-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.sampler39.288 0.02039.308
ICMg.links.sampler2.7320.0042.737
NetResponseModel-class0.0000.0000.001
PlotMixture0.0000.0000.001
PlotMixtureBivariate0.0040.0000.000
PlotMixtureMultivariate000
PlotMixtureMultivariate.deprecated000
PlotMixtureUnivariate000
add.ellipse000
centerData000
check.matrix0.0000.0000.001
check.network0.0000.0000.001
detect.responses0.0000.0000.002
dna0.020.000.02
enrichment.list.factor000
enrichment.list.factor.minimal000
filter.netw000
filter.network000
find.similar.features0.3760.0000.379
generate.toydata0.0000.0000.001
get.dat-NetResponseModel-method000
get.mis000
get.model.parameters0.0040.0000.004
get.subnets-NetResponseModel-method000
getqofz-NetResponseModel-method0.0000.0000.001
independent.models0.0000.0000.001
list.significant.responses0.0000.0000.001
listify.groupings0.0000.0000.001
model.stats0.0040.0000.002
netresponse-package3.5760.0043.585
order.responses000
osmo0.0400.0000.039
pick.model.pairs0.0000.0000.001
pick.model.parameters0.0000.0000.001
plotPCA000
plot_associations000
plot_data000
plot_expression000
plot_matrix0.0040.0000.006
plot_response000
plot_responses000
plot_scale0.0000.0000.001
plot_subnet0.0000.0000.001
read.sif000
remove.negative.edges000
response.enrichment000
response2sample0.0040.0000.004
sample2response0.0000.0000.001
set.breaks0.0000.0000.001
toydata0.0040.0000.002
update.model.pair000
vdp.mixt0.0560.0000.054
vectorize.groupings000
write.netresponse.results000