Back to Multiple platform build/check report for BioC 3.7 |
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This page was generated on 2018-10-17 08:47:07 -0400 (Wed, 17 Oct 2018).
Package 984/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
nem 2.54.0 Holger Froehlich
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK |
Package: nem |
Version: 2.54.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:nem.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings nem_2.54.0.tar.gz |
StartedAt: 2018-10-16 22:54:38 -0400 (Tue, 16 Oct 2018) |
EndedAt: 2018-10-16 22:55:47 -0400 (Tue, 16 Oct 2018) |
EllapsedTime: 68.6 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: nem.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:nem.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings nem_2.54.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/nem.Rcheck’ * using R version 3.5.1 Patched (2018-07-12 r74967) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘nem/DESCRIPTION’ ... OK * this is package ‘nem’ version ‘2.54.0’ * checking package namespace information ... OK * checking package dependencies ... NOTE Package which this enhances but not available for checking: ‘doMC’ * 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 ... WARNING Found the following significant warnings: MCMC.c:44:45: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value] MCMC.c:72:62: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value] See ‘/Users/biocbuild/bbs-3.7-bioc/meat/nem.Rcheck/00install.out’ for details. * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ 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 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 bum.mle: no visible global function definition for ‘optim’ bum.negLogLik: no visible global function definition for ‘dexp’ nem.bootstrap: no visible global function definition for ‘makeCluster’ 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.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’ quicknem: no visible global function definition for ‘exprs’ quicknem: no visible global function definition for ‘file_test’ 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’ Undefined global functions or variables: %dopar% d dexp exprs file_test foreach lam m makeCluster optim r registerDoMC Consider adding importFrom("stats", "dexp", "optim") importFrom("utils", "file_test") to your NAMESPACE file. * 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 Note: information on .o files is not available File ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/nem/libs/nem.so’: 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 use Fortran I/O nor system RNGs. 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 sizes of PDF files under ‘inst/doc’ ... NOTE ‘qpdf’ made some significant size reductions: compacted ‘markowetz-thesis-2006.pdf’ from 1155Kb to 844Kb consider running tools::compactPDF() on these files * checking installed files from ‘inst/doc’ ... NOTE The following files should probably not be installed: ‘ModuleNetworks1.png’ Consider the use of a .Rinstignore file: see ‘Writing R Extensions’, or move the vignette sources from ‘inst/doc’ to ‘vignettes’. * checking files in ‘vignettes’ ... OK * checking examples ... 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 Status: 1 WARNING, 5 NOTEs See ‘/Users/biocbuild/bbs-3.7-bioc/meat/nem.Rcheck/00check.log’ for details.
nem.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL nem ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘nem’ ... ** libs clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c MCMC.c -o MCMC.o MCMC.c:44:45: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value] p -= inv_nu*abs(net[s][k]-prior[s][k]); ^ MCMC.c:44:45: note: use function 'fabs' instead p -= inv_nu*abs(net[s][k]-prior[s][k]); ^˜˜ fabs MCMC.c:72:62: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value] if(Psi[p][s] != 0 && abs(Psi[p][s]) <= t){ // p is a parent ^ MCMC.c:72:62: note: use function 'fabs' instead if(Psi[p][s] != 0 && abs(Psi[p][s]) <= t){ // p is a parent ^˜˜ fabs MCMC.c:403:10: warning: unused variable 'stored2' [-Wunused-variable] long stored2 = 0; ^ MCMC.c:359:35: warning: unused variable 'mutinf' [-Wunused-variable] double loglikMean, loglikSum, mutinf, delta, logPrior_cur_scale; ^ MCMC.c:402:10: warning: unused variable 'stored' [-Wunused-variable] long stored = 0; ^ 5 warnings generated. clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c netlearn.c -o netlearn.o netlearn.c:171:13: warning: variable 'negenes' used in loop condition not modified in loop body [-Wfor-loop-analysis] for (i=0; negenes; i++) { ^˜˜˜˜˜˜ netlearn.c:168:9: warning: unused variable 'lik_switch' [-Wunused-variable] double lik_switch; ^ 2 warnings generated. clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c wrapper.c -o wrapper.o clang -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 -o nem.so MCMC.o netlearn.o wrapper.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/nem/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ‘nem.Rnw’ using ‘latin1’ ** testing if installed package can be loaded * DONE (nem)
nem.Rcheck/nem-Ex.timings
name | user | system | elapsed | |
BFSlevel | 0.001 | 0.001 | 0.002 | |
BoutrosRNAi2002 | 0.050 | 0.005 | 0.056 | |
Ivanova2006RNAiTimeSeries | 0.002 | 0.001 | 0.003 | |
NiederbergerMediator2012 | 0.009 | 0.001 | 0.011 | |
SCCgraph | 0.438 | 0.011 | 0.455 | |
SahinRNAi2008 | 0.003 | 0.000 | 0.003 | |
enumerate.models | 0.004 | 0.000 | 0.005 | |
generateNetwork | 0.257 | 0.029 | 0.425 | |
infer.edge.type | 0.162 | 0.005 | 0.179 | |
local.model.prior | 0.001 | 0.001 | 0.002 | |
nem | 1.959 | 0.024 | 2.003 | |
nem.bootstrap | 0.002 | 0.000 | 0.002 | |
nem.calcSignificance | 0.002 | 0.001 | 0.003 | |
nem.consensus | 0.001 | 0.000 | 0.002 | |
nem.cont.preprocess | 0.206 | 0.003 | 0.212 | |
nem.discretize | 0.028 | 0.003 | 0.031 | |
nem.jackknife | 0.001 | 0.000 | 0.001 | |
nemModelSelection | 0.341 | 0.008 | 0.361 | |
network.AIC | 0.158 | 0.003 | 0.162 | |
plotEffects | 0.211 | 0.007 | 0.242 | |
prior.EgeneAttach.EB | 0.293 | 0.010 | 0.306 | |
prune.graph | 0.117 | 0.006 | 0.168 | |
quicknem | 0.003 | 0.000 | 0.002 | |
selectEGenes | 0.335 | 0.005 | 0.342 | |
set.default.parameters | 0.001 | 0.000 | 0.001 | |
sim.intervention | 0.103 | 0.004 | 0.108 | |
subsets | 0.001 | 0.000 | 0.001 | |
transitive.closure | 0.093 | 0.005 | 0.109 | |
transitive.reduction | 0.086 | 0.004 | 0.094 | |