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CHECK report for TFBSTools on machv2

This page was generated on 2020-10-17 11:59:47 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE TFBSTools PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1793/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TFBSTools 1.26.0
Ge Tan
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/TFBSTools
Branch: RELEASE_3_11
Last Commit: 1466c2e
Last Changed Date: 2020-04-27 14:37:11 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  NA 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: TFBSTools
Version: 1.26.0
Command: /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_1.26.0.tar.gz
StartedAt: 2020-10-17 05:52:02 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 06:00:18 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 496.3 seconds
RetCode: 0
Status:  OK 
CheckDir: TFBSTools.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /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_1.26.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/TFBSTools.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.26.0’
* 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 use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
SiteSetList-class     63.157  2.145  65.368
searchAln-methods     15.172  0.102  15.291
toGRangesList-methods 11.381  0.041  11.428
SiteSet-class          9.850  0.451  10.310
* 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-3.11-bioc/meat/TFBSTools.Rcheck/00check.log’
for details.



Installation output

TFBSTools.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL TFBSTools
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘TFBSTools’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c matrixAlignerDynamic.c -o matrixAlignerDynamic.o
clang -mmacosx-version-min=10.13 -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 -mmacosx-version-min=10.13 -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/4.0/Resources/library/00LOCK-TFBSTools/00new/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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (TFBSTools)

Tests output

TFBSTools.Rcheck/tests/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 20.734   0.865  21.596 

Example timings

TFBSTools.Rcheck/TFBSTools-Ex.timings

nameusersystemelapsed
IUPAC2Matrix0.0020.0010.001
MA0004.10.0070.0060.013
MotifSet-class0.0010.0010.001
PFMSimilarity-methods0.3620.0220.395
PWMSimilarity-methods0.0120.0040.016
SiteSet-class 9.850 0.45110.310
SiteSetList-class63.157 2.14565.368
TFFM-class0.0460.0010.047
XMatrix-class0.0240.0040.027
XMatrixList-class0.0050.0030.008
deleteMatrixHavingID-methods0.1140.0610.176
dmmEM-methods0.0000.0010.001
getEmissionProb0.3970.0070.406
getMatrixByID-methods0.2740.0190.300
getMatrixSet-methods0.0000.0000.001
getPosProb0.2880.0020.310
makeFlatFileDir0.0000.0010.000
parseMEMEOutput0.3420.0020.344
permuteMatrix-methods0.0990.0020.101
rPWMDmm-methods0.0000.0000.001
readJASPARMatrix0.0170.0010.018
readXMLTFFM0.0450.0010.046
runMEME-methods0.0000.0010.001
sampleRanges0.4030.0080.412
searchAln-methods15.172 0.10215.291
searchPairBSgenome-methods0.0000.0010.001
searchSeq-methods1.4840.0241.509
seqLogo1.8240.2132.038
shannon.entropy0.0000.0010.001
toGRangesList-methods11.381 0.04111.428
toICM-methods0.0160.0030.020
toPWM-methods0.0110.0040.015