Multiple platform build/check report for BioC 3.6 - CHECK report for birta on veracruz1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings birta_1.22.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/birta.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘birta/DESCRIPTION’ ... OK
* this is package ‘birta’ version ‘1.22.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘birta’ 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘Biobase’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
FisherPretest : <anonymous>: no visible global function definition for
  ‘fisher.test’
FisherPretest: no visible global function definition for ‘p.adjust’
birtaRun: no visible global function definition for ‘median’
birtaRun: no visible global function definition for ‘var’
plotConvergence: no visible global function definition for ‘plot’
plotConvergence: no visible global function definition for ‘abline’
birta,ExpressionSet-ExpressionSet-ExpressionSet: no visible global
  function definition for ‘exprs’
birta,ExpressionSet-ExpressionSet-ExpressionSet: no visible global
  function definition for ‘callGeneric’
birta,ExpressionSet-ExpressionSet-missing: no visible global function
  definition for ‘exprs’
birta,ExpressionSet-ExpressionSet-missing: no visible global function
  definition for ‘callGeneric’
birta,ExpressionSet-missing-ExpressionSet: no visible global function
  definition for ‘exprs’
birta,ExpressionSet-missing-ExpressionSet: no visible global function
  definition for ‘callGeneric’
birta,ExpressionSet-missing-missing: no visible global function
  definition for ‘exprs’
birta,ExpressionSet-missing-missing: no visible global function
  definition for ‘callGeneric’
limmaAnalysis,ExpressionSet-matrix-character: no visible global
  function definition for ‘exprs’
limmaAnalysis,ExpressionSet-matrix-character: no visible global
  function definition for ‘callGeneric’
Undefined global functions or variables:
  abline callGeneric exprs fisher.test median p.adjust plot var
Consider adding
  importFrom("graphics", "abline", "plot")
  importFrom("methods", "callGeneric")
  importFrom("stats", "fisher.test", "median", "p.adjust", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ‘birta/libs/birta.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Objects: ‘BayesNetwork.o’, ‘BayesNetworkNC.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Objects: ‘BayesNetwork.o’, ‘BayesNetworkNC.o’

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.

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 ... 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/birta.Rcheck/00check.log’
for details.

* installing *source* package ‘birta’ ...
** libs
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c BayesNetwork.cpp -o BayesNetwork.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c BayesNetworkNC.cpp -o BayesNetworkNC.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c getStates.cpp -o getStates.o
getStates.cpp:259:13: warning: variable 'nreps' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
                                else if(c == 1) {
                                        ^˜˜˜˜˜
getStates.cpp:262:49: note: uninitialized use occurs here
                                Otf[c][i] = (double*) malloc(sizeof(double)*nreps);
                                                                            ^˜˜˜˜
getStates.cpp:259:10: note: remove the 'if' if its condition is always true
                                else if(c == 1) {
                                     ^˜˜˜˜˜˜˜˜˜˜
getStates.cpp:255:14: note: initialize the variable 'nreps' to silence this warning
                                int nreps;
                                         ^
                                          = 0
getStates.cpp:228:12: warning: variable 'nreps' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
                        else if(c == 1) {
                                ^˜˜˜˜˜
getStates.cpp:231:46: note: uninitialized use occurs here
                        O[c][i] = (double*) malloc(sizeof(double)*nreps);
                                                                  ^˜˜˜˜
getStates.cpp:228:9: note: remove the 'if' if its condition is always true
                        else if(c == 1) {
                             ^˜˜˜˜˜˜˜˜˜˜
getStates.cpp:224:13: note: initialize the variable 'nreps' to silence this warning
                        int nreps;
                                 ^
                                  = 0
getStates.cpp:201:13: warning: variable 'nreps' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
                                else if(c == 1) {
                                        ^˜˜˜˜˜
getStates.cpp:204:47: note: uninitialized use occurs here
                                A[c][i] = (double*) malloc(sizeof(double)*nreps);
                                                                          ^˜˜˜˜
getStates.cpp:201:10: note: remove the 'if' if its condition is always true
                                else if(c == 1) {
                                     ^˜˜˜˜˜˜˜˜˜˜
getStates.cpp:197:14: note: initialize the variable 'nreps' to silence this warning
                                int nreps;
                                         ^
                                          = 0
3 warnings generated.
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 birta.so BayesNetwork.o BayesNetworkNC.o getStates.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.6-bioc/meat/birta.Rcheck/birta/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 (birta)

name	user	system	elapsed
birta.run	1.670	0.034	1.761
get_potential_swaps	0.002	0.001	0.002
limmaAnalysis	0.063	0.005	0.069
plotConvergence	1.396	0.027	1.449

CHECK report for birta on veracruz1

Summary

Command output

Installation output

Tests output

Example timings