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BioC 3.0: CHECK report for nem on perceval

This page was generated on 2015-04-10 09:53:11 -0700 (Fri, 10 Apr 2015).

Package 599/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
nem 2.40.0
Holger Froehlich
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/nem
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: nem
Version: 2.40.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch nem_2.40.0.tar.gz
StartedAt: 2015-04-10 04:20:06 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 04:22:11 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 125.2 seconds
RetCode: 0
Status:  OK 
CheckDir: nem.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch nem_2.40.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/nem.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘nem/DESCRIPTION’ ... OK
* this is package ‘nem’ version ‘2.40.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages which this enhances but not available for checking: ‘doMC’ ‘Rglpk’

Depends: includes the non-default packages:
  ‘e1071’ ‘graph’ ‘plotrix’ ‘limma’ ‘cluster’ ‘statmod’ ‘Hmisc’
  ‘Rgraphviz’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘nem’ can be installed ... [10s/12s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘e1071’ ‘graph’ ‘Rgraphviz’
A package should be listed in only one of these fields.
* 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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘cluster’ ‘Hmisc’ ‘limma’ ‘plotrix’ ‘statmod’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': ‘boot:::boot’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘nem’ ‘network.AIC’ ‘score’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
get.insertions: warning in transitive.closure(Phinew, mat = TRUE, loop
  = TRUE): partial argument match of 'loop' to 'loops'
moduleNetwork: warning in transitive.closure(modeltotal, mat = TRUE,
  loop = TRUE): partial argument match of 'loop' to 'loops'
nem.calcSignificance : modify.rand: warning in
  transitive.closure(Phinew, mat = TRUE, loop = TRUE): partial argument
  match of 'loop' to 'loops'
sampleRndNetwork: warning in transitive.closure(S, mat = TRUE, loop =
  FALSE): partial argument match of 'loop' to 'loops'
nem.calcSignificance: no visible global function definition for
  ‘registerDoMC’
nem.calcSignificance: no visible global function definition for
  ‘%dopar%’
nem.calcSignificance: no visible global function definition for
  ‘foreach’
nem.calcSignificance: no visible global function definition for ‘permp’
nem.featureselection: no visible global function definition for
  ‘registerDoMC’
nem.featureselection: no visible global function definition for
  ‘%dopar%’
nem.featureselection: no visible global function definition for
  ‘foreach’
nem.featureselection: no visible binding for global variable ‘d’
nemModelSelection: no visible global function definition for
  ‘registerDoMC’
nemModelSelection: no visible global function definition for ‘%dopar%’
nemModelSelection: no visible global function definition for ‘foreach’
nemModelSelection: no visible binding for global variable ‘lam’
nemModelSelection: no visible binding for global variable ‘r’
plotEffects: no visible global function definition for ‘color.legend’
plotnem: no visible global function definition for ‘color.legend’
quicknem: no visible global function definition for ‘exprs’
quicknem: no visible global function definition for
  ‘normalizeQuantiles’
quicknem: no visible binding for global variable ‘makeContrasts’
quicknem: no visible global function definition for ‘lmFit’
quicknem: no visible global function definition for ‘contrasts.fit’
quicknem: no visible global function definition for ‘eBayes’
score.aux: no visible global function definition for ‘registerDoMC’
score.aux: no visible global function definition for ‘%dopar%’
score.aux: no visible global function definition for ‘foreach’
score.aux: no visible binding for global variable ‘m’
transitive.reduction : solve.problem: no visible global function
  definition for ‘Rglpk_solve_LP’
* 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 compiled code ... NOTE
File ‘nem/libs/nem.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘MCMC.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘MCMC.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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [12s/12s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

NOTE: There were 5 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/nem.Rcheck/00check.log’
for details.

nem.Rcheck/00install.out:

* installing *source* package ‘nem’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c MCMC.c -o MCMC.o
MCMC.c: In function ‘network_likelihood’:
MCMC.c:116: warning: suggest parentheses around comparison in operand of &
MCMC.c:125: warning: suggest parentheses around comparison in operand of &
MCMC.c: In function ‘MCMCrun’:
MCMC.c:403: warning: unused variable ‘stored2’
MCMC.c:402: warning: unused variable ‘stored’
MCMC.c:359: warning: unused variable ‘mutinf’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c netlearn.c -o netlearn.o
netlearn.c: In function ‘learn_network’:
netlearn.c:168: warning: unused variable ‘lik_switch’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c wrapper.c -o wrapper.o
wrapper.c: In function ‘MCMCrunWrapper’:
wrapper.c:107: warning: suggest parentheses around comparison in operand of &
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -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 -L/usr/local/lib -o nem.so MCMC.o netlearn.o wrapper.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.0-bioc/meat/nem.Rcheck/nem/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 (nem)

nem.Rcheck/nem-Ex.timings:

nameusersystemelapsed
BFSlevel000
BoutrosRNAi20020.0350.0040.039
Ivanova2006RNAiTimeSeries0.0030.0000.003
NiederbergerMediator20120.0130.0020.016
SCCgraph0.3220.0200.341
SahinRNAi20080.0040.0010.005
enumerate.models0.0030.0010.004
generateNetwork0.4640.0250.775
infer.edge.type0.3830.0100.408
local.model.prior0.0010.0000.002
nem3.3440.0553.413
nem.bootstrap0.0000.0000.001
nem.calcSignificance0.0000.0000.001
nem.consensus0.0000.0010.001
nem.cont.preprocess0.2110.0040.215
nem.discretize0.1980.0070.205
nem.jackknife0.0000.0000.001
nemModelSelection0.4490.0120.464
network.AIC0.2360.0060.241
plotEffects0.2030.0090.368
prior.EgeneAttach.EB0.4520.0070.461
prune.graph0.0570.0030.096
quicknem0.0010.0000.001
selectEGenes0.5840.0070.592
set.default.parameters0.0010.0000.001
sim.intervention0.1770.0060.182
subsets0.0010.0000.000
transitive.closure0.0510.0030.134
transitive.reduction0.0410.0010.045