BioC 2.13: CHECK report for BGmix on perceval

Package: BGmix

Version: 1.22.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch BGmix_1.22.0.tar.gz

StartedAt: 2014-04-04 23:41:03 -0700 (Fri, 04 Apr 2014)

EndedAt: 2014-04-04 23:42:21 -0700 (Fri, 04 Apr 2014)

EllapsedTime: 78.3 seconds

RetCode: 0

Status:  OK

CheckDir: BGmix.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/BGmix.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BGmix/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BGmix’ 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BGmix’ can be installed ... [7s/8s] 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 ... NOTE
‘library’ or ‘require’ call to ‘KernSmooth’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘KernSmooth’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ccSummary: warning in agrep("genes", summ, max = 0): partial argument
  match of 'max' to 'max.distance'
ccSummary: warning in agrep("conds", summ, max = 0): partial argument
  match of 'max' to 'max.distance'
ccSummary: warning in agrep("effects", summ, max = 0): partial argument
  match of 'max' to 'max.distance'
ccSummary: warning in agrep("mix comps", summ, max = 0): partial
  argument match of 'max' to 'max.distance'
ccSummary: warning in agrep("variance", summ, max = 0): partial
  argument match of 'max' to 'max.distance'
ccSummary: warning in agrep("mix prior", summ, max = 0): partial
  argument match of 'max' to 'max.distance'
ccSummary: warning in agrep("niter", summ, max = 0): partial argument
  match of 'max' to 'max.distance'
ccSummary: warning in agrep("nburn", summ, max = 0): partial argument
  match of 'max' to 'max.distance'
ccSummary: warning in agrep("nthin", summ, max = 0): partial argument
  match of 'max' to 'max.distance'
ccSummary: warning in agrep("seed", summ, max = 0): partial argument
  match of 'max' to 'max.distance'
ccSummary: warning in agrep("move", summ, max = 0): partial argument
  match of 'max' to 'max.distance'
ccSummary: warning in agrep("fullBayes", summ, max = 0): partial
  argument match of 'max' to 'max.distance'
ccSummary: warning in agrep("aa updated", summ, max = 0): partial
  argument match of 'max' to 'max.distance'
ccSummary: warning in agrep("eta updated", summ, max = 0): partial
  argument match of 'max' to 'max.distance'
ccSummary: warning in agrep("lambdas updated", summ, max = 0): partial
  argument match of 'max' to 'max.distance'
ccSummary: warning in agrep("tau's", summ, max = 0): partial argument
  match of 'max' to 'max.distance'
ccSummary: warning in agrep("t-dist", summ, max = 0): partial argument
  match of 'max' to 'max.distance'
ccSummary: warning in agrep("(params)", summ, max = 0): partial
  argument match of 'max' to 'max.distance'
ccSummary: warning in agrep("(predictive)", summ, max = 0): partial
  argument match of 'max' to 'max.distance'
ccSummary: warning in agrep("eta_up", summ, max = 0): partial argument
  match of 'max' to 'max.distance'
ccSummary: warning in agrep("eta_down", summ, max = 0): partial
  argument match of 'max' to 'max.distance'
ccSummary: warning in agrep("lambda+ for", summ, max = 0): partial
  argument match of 'max' to 'max.distance'
ccSummary: warning in agrep("lambda- for", summ, max = 0): partial
  argument match of 'max' to 'max.distance'
plotFDR: warning in legend(xx, yy, leg = c("FDR=5%", "FDR=10%"), col =
  c("red", "blue"), lty = c(1, 1), bg = "white"): partial argument
  match of 'leg' to 'legend'
* 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 compilation flags in Makevars ... NOTE
Package has both ‘src/Makevars.in’ and ‘src/Makevars’.
Installation with --no-configure' is unlikely to work.  If you intended
‘src/Makevars’ to be used on Windows, rename it to ‘src/Makevars.win’
otherwise remove it.  If ‘configure’ created ‘src/Makevars’, you need a
‘cleanup’ script.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘/Users/biocbuild/bbs-2.13-bioc/meat/BGmix.Rcheck/BGmix/libs/BGmix.so’:
  Found ‘__ZSt4cerr’, possibly from ‘std::cerr’ (C++)
    Object: ‘updates_BGmix.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console.

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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘BGmix.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [44s/46s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
FDRforTailPP 7.706  1.410   9.555
BGmix        5.681  0.358   6.365
* 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

NOTE: There were 6 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/BGmix.Rcheck/00check.log’
for details.

* installing *source* package ‘BGmix’ ...
checking for gcc... llvm-gcc-4.2 -arch x86_64 -std=gnu99
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether llvm-gcc-4.2 -arch x86_64 -std=gnu99 accepts -g... yes
checking for llvm-gcc-4.2 -arch x86_64 -std=gnu99 option to accept ISO C89... none needed
checking for llvm-gcc-4.2 -arch x86_64 -std=gnu99 option to accept ISO C99... none needed
checking for cos in -lm... yes
Untarring Boost header files...
checking for an ANSI C-conforming const... yes
checking for inline... inline
configure: creating ./config.status
config.status: creating src/Makevars
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I ../boostIncl -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -DUSING_R -c BGmix_main.cpp -o BGmix_main.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I ../boostIncl -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -DUSING_R -c rundir.cpp -o rundir.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I ../boostIncl -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -DUSING_R -c updates_BGmix.cpp -o updates_BGmix.o
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o BGmix.so BGmix_main.o rundir.o updates_BGmix.o -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
rm -r ../boostIncl 
installing to /Users/biocbuild/bbs-2.13-bioc/meat/BGmix.Rcheck/BGmix/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 (BGmix)

name	user	system	elapsed
BGmix-package	2.986	0.232	3.478
BGmix	5.681	0.358	6.365
EstimatePi0	3.630	0.452	4.464
FDRforTailPP	7.706	1.410	9.555
FDRplotTailPP	2.955	0.861	3.970
TailPP	3.005	0.366	3.596
calcFDR	0.659	0.063	0.785
ccParams	0.657	0.089	0.815
ccPred	0.636	0.053	0.758
ccSummary	0.634	0.052	0.749
ccTrace	0.889	0.090	1.073
histTailPP	3.055	0.382	3.570
plotBasic	0.664	0.059	0.769
plotCompare	0.015	0.007	0.022
plotFDR	0.658	0.114	0.796
plotMixDensity	2.262	0.251	2.611
plotPredChecks	0.653	0.089	0.791
plotTrace	0.973	0.103	1.479