BioC 3.5: CHECK report for TFBSTools on oaxaca

Package: TFBSTools

Version: 1.13.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TFBSTools_1.13.2.tar.gz

StartedAt: 2017-03-04 10:02:29 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 10:08:09 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 340.2 seconds

RetCode: 0

Status:  OK

CheckDir: TFBSTools.Rcheck

Warnings: 0

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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_1.13.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/TFBSTools.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* 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 ‘1.13.2’
* 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 ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
SiteSetList-class     51.294  2.157  53.472
searchAln-methods      9.288  0.035   9.372
SiteSet-class          7.541  0.305   7.848
toGRangesList-methods  7.090  0.024   7.118
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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-3.5-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-3.5-bioc/meat/TFBSTools.Rcheck/TFBSTools/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a new generic function for ‘seqLogo’ 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
IUPAC2Matrix	0.001	0.000	0.001
MA0004.1	0.006	0.002	0.008
MotifSet-class	0.001	0.000	0.001
PFMSimilarity-methods	0.458	0.016	0.561
PWMSimilarity-methods	0.027	0.001	0.028
SiteSet-class	7.541	0.305	7.848
SiteSetList-class	51.294	2.157	53.472
TFFM-class	0.034	0.000	0.035
XMatrix-class	0.012	0.001	0.013
XMatrixList-class	0.004	0.001	0.006
deleteMatrixHavingID-methods	0.078	0.025	0.113
dmmEM-methods	0.001	0.000	0.000
getEmissionProb	0.525	0.007	0.533
getMatrixByID-methods	0.323	0.029	0.565
getMatrixSet-methods	0	0	0
getPosProb	0.376	0.019	0.396
makeFlatFileDir	0	0	0
parseMEMEOutput	0.152	0.001	0.153
permuteMatrix-methods	0.028	0.001	0.030
rPWMDmm-methods	0.001	0.000	0.001
readJASPARMatrix	0.035	0.001	0.037
readXMLTFFM	0.036	0.000	0.037
runMEME-methods	0.001	0.000	0.001
sampleRanges	0.519	0.005	0.524
searchAln-methods	9.288	0.035	9.372
searchPairBSgenome-methods	0.001	0.000	0.002
searchSeq-methods	0.743	0.007	0.751
seqLogo	1.633	0.269	1.903
shannon.entropy	0.002	0.000	0.001
toGRangesList-methods	7.090	0.024	7.118
toICM-methods	0.082	0.002	0.083
toPWM-methods	0.012	0.002	0.014