BioC 3.2: CHECK report for TFBSTools on oaxaca

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TFBSTools_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/TFBSTools.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.8.0’
* 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 ‘TFBSTools’ can be installed ... [20s/21s] 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 objects imported by ':::' calls:
  ‘S4Vectors:::new_SimpleList_from_list’ ‘seqLogo:::pwm2ic’
  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 ... [98s/87s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
SiteSetList-class     49.372  1.781  51.210
searchAln-methods     13.992  0.982   9.264
SiteSet-class          6.829  0.312   7.158
toGRangesList-methods  6.111  0.550   6.616
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [10s/10s]
 [10s/10s] 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/TFBSTools.Rcheck/00check.log’
for details.

* installing *source* package ‘TFBSTools’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c matrixAlignerDynamic.c -o matrixAlignerDynamic.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c R_init_TFBSTools.c -o R_init_TFBSTools.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 TFBSTools.so matrixAlignerDynamic.o R_init_TFBSTools.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.2-bioc/meat/TFBSTools.Rcheck/TFBSTools/libs
** R
** data
** inst
** preparing package for lazy loading
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
* DONE (TFBSTools)

name	user	system	elapsed
MA0004.1	0.005	0.004	0.010
MotifSet-class	0.001	0.000	0.001
PFMSimilarity-methods	0.531	0.012	0.577
PWMSimilarity-methods	0.014	0.000	0.015
SiteSet-class	6.829	0.312	7.158
SiteSetList-class	49.372	1.781	51.210
TFFM-class	0.027	0.000	0.028
XMatrix-class	0.008	0.001	0.008
XMatrixList-class	0.004	0.001	0.005
deleteMatrixHavingID-methods	0.059	0.025	0.214
dmmEM-methods	0.001	0.000	0.000
getEmissionProb	0.230	0.001	0.231
getMatrixByID-methods	0	0	0
getMatrixSet-methods	0.000	0.000	0.001
getPosProb	0.340	0.001	0.341
permuteMatrix-methods	0.006	0.002	0.009
rPWMDmm-methods	0	0	0
readXMLTFFM	0.032	0.001	0.032
runMEME-methods	0.001	0.000	0.000
searchAln-methods	13.992	0.982	9.264
searchPairBSgenome-methods	0.001	0.000	0.001
searchSeq-methods	1.124	0.009	1.133
seqLogo	1.792	0.271	2.068
shannon.entropy	0.001	0.000	0.001
toGRangesList-methods	6.111	0.550	6.616
toICM-methods	0.007	0.001	0.008
toPWM-methods	0.005	0.000	0.007

BioC 3.2: CHECK report for TFBSTools on oaxaca

Summary

Command output