BioC 3.1: CHECK report for TFBSTools on petty

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TFBSTools_1.6.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/TFBSTools.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 ‘TFBSTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TFBSTools’ version ‘1.6.1’
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘TFBSTools’ can be installed ... [25s/26s] 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
Unexported object imported by a ':::' call: ‘S4Vectors:::new_SimpleList_from_list’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... 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 ... [138s/121s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
SiteSetList-class     70.008  2.768  72.820
searchAln-methods     18.452  1.789  11.912
toGRangesList-methods 10.028  1.066  11.052
SiteSet-class          9.548  0.276   9.830
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [11s/11s]
 [11s/11s] 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-3.1-bioc/meat/TFBSTools.Rcheck/00check.log’
for details.

* installing *source* package ‘TFBSTools’ ...
** 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 matrixAlignerDynamic.c -o matrixAlignerDynamic.o
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_TFBSTools.c -o R_init_TFBSTools.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -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 TFBSTools.so matrixAlignerDynamic.o R_init_TFBSTools.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.1-bioc/meat/TFBSTools.Rcheck/TFBSTools/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Creating a new generic function for ‘seqLogo’ in package ‘TFBSTools’
Creating a generic function for ‘colSums’ from package ‘base’ in package ‘TFBSTools’
Creating a generic function for ‘rowSums’ from package ‘base’ in package ‘TFBSTools’
Creating a generic function for ‘update’ from package ‘stats’ in package ‘TFBSTools’
Creating a generic function for ‘as.matrix’ from package ‘base’ in package ‘TFBSTools’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (TFBSTools)

name	user	system	elapsed
MA0004.1	0.007	0.001	0.008
MotifSet-class	0.000	0.000	0.001
PFMSimilarity-methods	0.562	0.030	0.668
PWMSimilarity-methods	0.026	0.005	0.030
SiteSet-class	9.548	0.276	9.830
SiteSetList-class	70.008	2.768	72.820
XMatrix-class	0.018	0.001	0.019
XMatrixList-class	0.006	0.001	0.007
deleteMatrixHavingID-methods	0.002	0.000	0.002
dmmEM-methods	0.001	0.000	0.002
getMatrixByID-methods	0.002	0.000	0.002
getMatrixSet-methods	0.002	0.000	0.001
permuteMatrix-methods	0.019	0.001	0.020
rPWMDmm-methods	0.001	0.000	0.001
runMEME-methods	0.001	0.000	0.002
searchAln-methods	18.452	1.789	11.912
searchPairBSgenome-methods	0.001	0.001	0.001
searchSeq-methods	1.759	0.017	1.779
seqLogo	0.155	0.022	0.177
shannon.entropy	0.001	0.000	0.001
toGRangesList-methods	10.028	1.066	11.052
toICM-methods	0.009	0.000	0.009
toPWM-methods	0.009	0.000	0.010

BioC 3.1: CHECK report for TFBSTools on petty

Summary

Command output