Multiple platform build/check report for BioC 3.7 - CHECK report for TFBSTools on merida2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:TFBSTools.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TFBSTools_1.18.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/TFBSTools.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.18.0’
* 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 ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
SiteSetList-class     51.781  1.879  54.229
searchAln-methods     10.029  0.028  10.159
SiteSet-class          7.153  0.410   7.641
toGRangesList-methods  7.121  0.017   7.202
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/TFBSTools.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL TFBSTools
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* 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 /Library/Frameworks/R.framework/Versions/3.5/Resources/library/TFBSTools/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare 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)

Tests output


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
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 
 14.349   0.816  15.269

Example timings

name	user	system	elapsed
IUPAC2Matrix	0.002	0.000	0.002
MA0004.1	0.007	0.004	0.011
MotifSet-class	0.002	0.000	0.001
PFMSimilarity-methods	0.295	0.014	0.323
PWMSimilarity-methods	0.017	0.004	0.020
SiteSet-class	7.153	0.410	7.641
SiteSetList-class	51.781	1.879	54.229
TFFM-class	0.049	0.000	0.051
XMatrix-class	0.023	0.001	0.025
XMatrixList-class	0.005	0.001	0.006
deleteMatrixHavingID-methods	0.093	0.027	0.122
dmmEM-methods	0.001	0.000	0.001
getEmissionProb	0.285	0.003	0.291
getMatrixByID-methods	0.218	0.011	0.237
getMatrixSet-methods	0.001	0.000	0.002
getPosProb	0.360	0.011	0.375
makeFlatFileDir	0.002	0.000	0.001
parseMEMEOutput	0.113	0.001	0.115
permuteMatrix-methods	0.076	0.002	0.078
rPWMDmm-methods	0.001	0.000	0.001
readJASPARMatrix	0.018	0.001	0.019
readXMLTFFM	0.044	0.001	0.046
runMEME-methods	0.002	0.000	0.003
sampleRanges	0.350	0.010	0.362
searchAln-methods	10.029	0.028	10.159
searchPairBSgenome-methods	0.003	0.001	0.004
searchSeq-methods	1.152	0.010	1.170
seqLogo	1.680	0.300	1.996
shannon.entropy	0.002	0.000	0.002
toGRangesList-methods	7.121	0.017	7.202
toICM-methods	0.019	0.002	0.021
toPWM-methods	0.013	0.002	0.014

CHECK report for TFBSTools on merida2

Summary

Command output

Installation output

Tests output

Example timings