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BioC 3.1: CHECK report for netresponse on moscato2

This page was generated on 2015-10-09 09:28:57 -0700 (Fri, 09 Oct 2015).

Package 656/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
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 UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  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: 1.18.0
Command: rm -rf netresponse.buildbin-libdir netresponse.Rcheck && mkdir netresponse.buildbin-libdir netresponse.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=netresponse.buildbin-libdir netresponse_1.18.0.tar.gz >netresponse.Rcheck\00install.out 2>&1 && cp netresponse.Rcheck\00install.out netresponse-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=netresponse.buildbin-libdir --install="check:netresponse-install.out" --force-multiarch --no-vignettes --timings netresponse_1.18.0.tar.gz
StartedAt: 2015-10-09 04:23:38 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 04:34:56 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 677.1 seconds
RetCode: 0
Status:  OK  
CheckDir: netresponse.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf netresponse.buildbin-libdir netresponse.Rcheck && mkdir netresponse.buildbin-libdir netresponse.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=netresponse.buildbin-libdir netresponse_1.18.0.tar.gz >netresponse.Rcheck\00install.out 2>&1 && cp netresponse.Rcheck\00install.out netresponse-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=netresponse.buildbin-libdir --install="check:netresponse-install.out" --force-multiarch --no-vignettes --timings netresponse_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/netresponse.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'E:/biocbld/bbs-3.1-bioc/meat/netresponse.buildbin-libdir/netresponse/libs/i386/netresponse.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'E:/biocbld/bbs-3.1-bioc/meat/netresponse.buildbin-libdir/netresponse/libs/x64/netresponse.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)

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.
The detected symbols are linked into the code but might come from
libraries and not actually be called.

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 ...
** running examples for arch 'i386' ... [75s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
ICMg.combined.sampler 54.83   0.05   54.90
detect.responses       6.68   0.02    6.69
netresponse-package    5.82   0.00    5.82
** running examples for arch 'x64' ... [69s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
ICMg.combined.sampler 50.78   0.00   50.80
detect.responses       6.39   0.01    6.42
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'ICMg.test.R' [12s]
  Running 'bicmixture.R' [3s]
  Running 'mixture.model.test.R' [3s]
  Running 'mixture.model.test.multimodal.R' [6s]
  Running 'mixture.model.test.singlemode.R' [3s]
  Running 'timing.R' [0s]
  Running 'toydata2.R' [0s]
  Running 'validate.netresponse.R' [97s]
  Running 'validate.pca.basis.R' [59s]
  Running 'vdpmixture.R' [3s]
 [188s] OK
** running tests for arch 'x64' ...
  Running 'ICMg.test.R' [14s]
  Running 'bicmixture.R' [4s]
  Running 'mixture.model.test.R' [4s]
  Running 'mixture.model.test.multimodal.R' [7s]
  Running 'mixture.model.test.singlemode.R' [4s]
  Running 'timing.R' [0s]
  Running 'toydata2.R' [0s]
  Running 'validate.netresponse.R' [98s]
  Running 'validate.pca.basis.R' [60s]
  Running 'vdpmixture.R' [4s]
 [195s] OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  'E:/biocbld/bbs-3.1-bioc/meat/netresponse.Rcheck/00check.log'
for details.


netresponse.Rcheck/00install.out:


install for i386

* installing *source* package 'netresponse' ...
** libs
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c netresponse.c -o netresponse.o
netresponse.c: In function 'mHPpost':
netresponse.c:264:15: warning: unused variable 'prior_fields' [-Wunused-variable]
netresponse.c: In function 'mLogLambda':
netresponse.c:713:20: warning: 'U_p' may be used uninitialized in this function [-Wuninitialized]
netresponse.c:713:20: warning: 'KsiBeta' may be used uninitialized in this function [-Wuninitialized]
netresponse.c:713:20: warning: 'KsiAlpha' may be used uninitialized in this function [-Wuninitialized]
netresponse.c:713:20: warning: 'BetaKsi' may be used uninitialized in this function [-Wuninitialized]
netresponse.c:713:20: warning: 'AlphaKsi' may be used uninitialized in this function [-Wuninitialized]
netresponse.c:713:20: warning: 'Mutilde' may be used uninitialized in this function [-Wuninitialized]
netresponse.c:713:20: warning: 'Mubar' may be used uninitialized in this function [-Wuninitialized]
netresponse.c:713:20: warning: 'S2mu' may be used uninitialized in this function [-Wuninitialized]
netresponse.c:713:20: warning: 'Mumu' may be used uninitialized in this function [-Wuninitialized]
gcc -m32 -shared -s -static-libgcc -o netresponse.dll tmp.def netresponse.o -Ld:/RCompile/r-compiling/local/local320/lib/i386 -Ld:/RCompile/r-compiling/local/local320/lib -LE:/biocbld/BBS-3˜1.1-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-3.1-bioc/meat/netresponse.buildbin-libdir/netresponse/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'netresponse' ...
** libs
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c netresponse.c -o netresponse.o
netresponse.c: In function 'mHPpost':
netresponse.c:264:15: warning: unused variable 'prior_fields' [-Wunused-variable]
netresponse.c: In function 'mLogLambda':
netresponse.c:713:20: warning: 'U_p' may be used uninitialized in this function [-Wuninitialized]
netresponse.c:713:20: warning: 'KsiBeta' may be used uninitialized in this function [-Wuninitialized]
netresponse.c:713:20: warning: 'KsiAlpha' may be used uninitialized in this function [-Wuninitialized]
netresponse.c:713:20: warning: 'BetaKsi' may be used uninitialized in this function [-Wuninitialized]
netresponse.c:713:20: warning: 'AlphaKsi' may be used uninitialized in this function [-Wuninitialized]
netresponse.c:713:20: warning: 'Mutilde' may be used uninitialized in this function [-Wuninitialized]
netresponse.c:713:20: warning: 'Mubar' may be used uninitialized in this function [-Wuninitialized]
netresponse.c:713:20: warning: 'S2mu' may be used uninitialized in this function [-Wuninitialized]
netresponse.c:713:20: warning: 'Mumu' may be used uninitialized in this function [-Wuninitialized]
gcc -m64 -shared -s -static-libgcc -o netresponse.dll tmp.def netresponse.o -Ld:/RCompile/r-compiling/local/local320/lib/x64 -Ld:/RCompile/r-compiling/local/local320/lib -LE:/biocbld/BBS-3˜1.1-B/R/bin/x64 -lR
installing to E:/biocbld/bbs-3.1-bioc/meat/netresponse.buildbin-libdir/netresponse/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'netresponse' as netresponse_1.18.0.zip
* DONE (netresponse)

netresponse.Rcheck/examples_i386/netresponse-Ex.timings:

nameusersystemelapsed
ICMg.combined.sampler54.83 0.0554.90
ICMg.links.sampler3.340.003.33
NetResponseModel-class000
PlotMixture0.010.000.02
PlotMixtureBivariate000
PlotMixtureMultivariate000
PlotMixtureMultivariate.deprecated000
PlotMixtureUnivariate000
add.ellipse000
centerData000
check.matrix000
check.network000
detect.responses6.680.026.69
dna0.050.000.05
enrichment.list.factor000
enrichment.list.factor.minimal000
filter.netw000
filter.network000
find.similar.features0.640.000.63
generate.toydata000
get.dat-NetResponseModel-method0.020.000.02
get.mis000
get.model.parameters000
get.subnets-NetResponseModel-method000
getqofz-NetResponseModel-method000
independent.models000
list.significant.responses000
listify.groupings000
model.stats0.010.000.01
netresponse-package5.820.005.82
order.responses000
osmo0.050.000.05
pick.model.pairs000
pick.model.parameters000
plot.data000
plot.expression000
plot.response000
plot.responses000
plot.scale000
plot.subnet000
plotPCA000
plot_associations000
plot_matrix0.020.000.02
read.sif000
remove.negative.edges000
response.enrichment000
response2sample0.010.000.01
sample2response000
set.breaks000
toydata000
update.model.pair000
vdp.mixt0.070.000.07
vectorize.groupings000
write.netresponse.results000

netresponse.Rcheck/examples_x64/netresponse-Ex.timings:

nameusersystemelapsed
ICMg.combined.sampler50.78 0.0050.80
ICMg.links.sampler3.540.003.54
NetResponseModel-class000
PlotMixture000
PlotMixtureBivariate000
PlotMixtureMultivariate000
PlotMixtureMultivariate.deprecated000
PlotMixtureUnivariate000
add.ellipse000
centerData000
check.matrix000
check.network000
detect.responses6.390.016.42
dna0.020.000.01
enrichment.list.factor000
enrichment.list.factor.minimal000
filter.netw000
filter.network000
find.similar.features0.420.000.42
generate.toydata000
get.dat-NetResponseModel-method000
get.mis000
get.model.parameters000
get.subnets-NetResponseModel-method0.020.000.01
getqofz-NetResponseModel-method000
independent.models000
list.significant.responses000
listify.groupings000
model.stats000
netresponse-package4.470.004.48
order.responses000
osmo0.050.000.05
pick.model.pairs000
pick.model.parameters000
plot.data0.020.000.01
plot.expression000
plot.response000
plot.responses000
plot.scale000
plot.subnet000
plotPCA000
plot_associations000
plot_matrix0.000.000.08
read.sif000
remove.negative.edges000
response.enrichment000
response2sample000
sample2response000
set.breaks000
toydata0.000.010.01
update.model.pair000
vdp.mixt0.050.000.05
vectorize.groupings000
write.netresponse.results000