Package: TFBSTools

Version: 1.16.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TFBSTools_1.16.0.tar.gz

StartedAt: 2018-04-12 10:17:54 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 10:23:13 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 319.6 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_1.16.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/TFBSTools.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.16.0’
* 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 ... 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     44.464  1.787  46.940
searchAln-methods      8.790  0.032   8.970
toGRangesList-methods  6.261  0.017   6.354
SiteSet-class          5.369  0.204   5.618
* 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-3.6-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   -fPIC  -Wall -g -O2  -c matrixAlignerDynamic.c -o matrixAlignerDynamic.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -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-3.6-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)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(TFBSTools)

> 
> test_check("TFBSTools")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 34 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 12.498   0.368  13.062 

name	user	system	elapsed
IUPAC2Matrix	0.001	0.000	0.001
MA0004.1	0.004	0.002	0.005
MotifSet-class	0.001	0.000	0.000
PFMSimilarity-methods	0.266	0.019	0.298
PWMSimilarity-methods	0.016	0.001	0.018
SiteSet-class	5.369	0.204	5.618
SiteSetList-class	44.464	1.787	46.940
TFFM-class	0.035	0.001	0.035
XMatrix-class	0.012	0.001	0.013
XMatrixList-class	0.004	0.001	0.005
deleteMatrixHavingID-methods	0.071	0.024	0.095
dmmEM-methods	0.001	0.000	0.000
getEmissionProb	0.402	0.031	0.442
getMatrixByID-methods	0.280	0.010	0.302
getMatrixSet-methods	0.000	0.000	0.001
getPosProb	0.292	0.002	0.300
makeFlatFileDir	0	0	0
parseMEMEOutput	0.159	0.001	0.161
permuteMatrix-methods	0.030	0.002	0.031
rPWMDmm-methods	0.001	0.000	0.000
readJASPARMatrix	0.027	0.000	0.028
readXMLTFFM	0.031	0.000	0.031
runMEME-methods	0.001	0.000	0.001
sampleRanges	0.366	0.005	0.378
searchAln-methods	8.790	0.032	8.970
searchPairBSgenome-methods	0.000	0.000	0.001
searchSeq-methods	0.852	0.008	0.875
seqLogo	1.431	0.241	1.691
shannon.entropy	0.001	0.000	0.001
toGRangesList-methods	6.261	0.017	6.354
toICM-methods	0.045	0.001	0.048
toPWM-methods	0.007	0.001	0.008