nem 2.51.0
Holger Froehlich
| Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/nem | | Last Changed Rev: 129129 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings nem_2.51.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/nem.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘2.51.0’
* 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 ... OK
* 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
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’ ... 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: 5 NOTEs
See
‘/Users/biocbuild/bbs-3.6-bioc/meat/nem.Rcheck/00check.log’
for details.
* 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: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;
^
MCMC.c:403:10: warning: unused variable 'stored2' [-Wunused-variable]
long stored2 = 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 /Users/biocbuild/bbs-3.6-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)