nem 2.32.1
Holger Froehlich
| Snapshot Date: 2012-09-23 17:01:39 -0700 (Sun, 23 Sep 2012) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/nem | | Last Changed Rev: 66525 / Revision: 69725 | | Last Changed Date: 2012-06-08 10:11:11 -0700 (Fri, 08 Jun 2012) |
| lamb2 | Linux (openSUSE 11.4) / x86_64 | OK | [ OK ] | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| petty | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/nem.Rcheck’
* using R version 2.15.1 (2012-06-22)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘nem/DESCRIPTION’ ... OK
* this is package ‘nem’ version ‘2.32.1’
* 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 whether package ‘nem’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 for unstated 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
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: no visible global function definition for ‘dynoNEM_MCMC’
nem: no visible global function definition for
‘dynoNEM.posteriorEGenePos’
nem.calcSignificance: no visible binding for global variable
‘inference’
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’
score: no visible global function definition for ‘registerDoMC’
score: no visible global function definition for ‘%dopar%’
score: no visible global function definition for ‘foreach’
score: no visible binding for global variable ‘m’
sim.intervention : <anonymous>: no visible global function definition
for ‘dynoNEM.perturb’
* 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 for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK
NOTE: There was 1 note.
See
‘/loc/home/biocbuild/bbs-2.10-bioc/meat/nem.Rcheck/00check.log’
for details.
* installing *source* package ‘nem’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c MCMC.c -o MCMC.o
MCMC.c: In function ‘network_likelihood’:
MCMC.c:128:41: warning: suggest parentheses around comparison in operand of ‘&’
MCMC.c:137:6: warning: suggest parentheses around comparison in operand of ‘&’
MCMC.c: In function ‘MCMCrun’:
MCMC.c:423:10: warning: unused variable ‘stored2’
MCMC.c:422:10: warning: unused variable ‘stored’
MCMC.c:380:35: warning: unused variable ‘mutinf’
MCMC.c: In function ‘network_likelihood’:
MCMC.c:117:16: warning: ‘loglik0’ may be used uninitialized in this function
MCMC.c: In function ‘MCMCrun’:
MCMC.c:427:55: warning: ‘priorScale_new’ may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c wrapper.c -o wrapper.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o nem.so MCMC.o wrapper.o -L/home/biocbuild/bbs-2.10-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.10-bioc/meat/nem.Rcheck/nem/libs
** R
** data
** inst
** preparing 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)