BioC 3.2: CHECK report for cn.farms on perceval

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings cn.farms_1.17.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/cn.farms.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cn.farms/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cn.farms’ version ‘1.17.0’
* 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 ‘cn.farms’ can be installed ... [19s/19s] 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
initializeBigMatrix: no visible global function definition for
  ‘isPackageLoaded’
* 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 R/sysdata.rda ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [22s/22s] 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/cn.farms.Rcheck/00check.log’
for details.

* installing *source* package ‘cn.farms’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c R_init_cnfarms.c -o R_init_cnfarms.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c laplace.cpp -o laplace.o
laplace.cpp: In function ‘SEXPREC* momentsGauss(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)’:
laplace.cpp:442: warning: unused variable ‘method’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c sparse_farms.c -o sparse_farms.o
llvm-g++-4.2 -arch x86_64 -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 -L/usr/local/lib -o cn.farms.so R_init_cnfarms.o laplace.o sparse_farms.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.2-bioc/meat/cn.farms.Rcheck/cn.farms/libs
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (cn.farms)

name	user	system	elapsed
cn.farms	0.001	0.000	0.001
combineData	1.138	0.076	1.218
createAnnotation	0.000	0.000	0.001
distributionDistance	0.590	0.018	0.612
dnaCopySf	0.151	0.002	0.153
fragLengCorr	2.638	0.075	2.718
mlSummarization	3.488	0.167	3.664
normalizeAverage	0.001	0.001	0.003
normalizeCels	0.000	0.000	0.001
normalizeNpData	0.001	0.001	0.001
plotDendrogram	0.140	0.008	0.147
plotDensity	0.796	0.013	0.814
plotEvalIc	0.439	0.018	0.462
plotRegions	0.150	0.008	0.159
plotSmoothScatter	0.786	0.026	0.819
plotViolines	0.145	0.005	0.150
slSummarization	3.063	0.047	3.115
sparseFarmsC	0.002	0.000	0.002
summarizeFarmsExact	0.006	0.002	0.009
summarizeFarmsExact2	0.006	0.002	0.008
summarizeFarmsExact3	0.006	0.002	0.008
summarizeFarmsGaussian	0.003	0.001	0.004
summarizeFarmsMethods	0.003	0.000	0.004
summarizeFarmsVariational	0.003	0.001	0.004
summarizeWindowBps	0.008	0.001	0.008
summarizeWindowMethods	0.002	0.000	0.003
summarizeWindowStd	0.003	0.001	0.004

BioC 3.2: CHECK report for cn.farms on perceval

Summary

Command output