Ge Tan
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/TFBSTools |
| Branch: RELEASE_3_9 |
| Last Commit: 613d356 |
| Last Changed Date: 2019-05-02 11:53:46 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:52:16 -0400 (Wed, 16 Oct 2019).
| Package 1640/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| TFBSTools 1.22.0 Ge Tan
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: TFBSTools |
| Version: 1.22.0 |
| 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_1.22.0.tar.gz |
| StartedAt: 2019-10-16 07:20:05 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 07:28:31 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 506.1 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 --install=check:TFBSTools.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TFBSTools_1.22.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/TFBSTools.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.22.0’
* 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 57.272 4.413 61.684
searchAln-methods 13.004 0.072 13.082
toGRangesList-methods 10.165 0.032 10.197
SiteSet-class 8.465 0.733 9.200
* 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-3.9-bioc/meat/TFBSTools.Rcheck/00check.log’
for details.
TFBSTools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL TFBSTools ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘TFBSTools’ ... ** using staged installation ** libs clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c matrixAlignerDynamic.c -o matrixAlignerDynamic.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/3.6/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)
TFBSTools.Rcheck/tests/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
19.793 1.746 21.493
TFBSTools.Rcheck/TFBSTools-Ex.timings
| name | user | system | elapsed | |
| IUPAC2Matrix | 0.001 | 0.000 | 0.001 | |
| MA0004.1 | 0.005 | 0.004 | 0.010 | |
| MotifSet-class | 0 | 0 | 0 | |
| PFMSimilarity-methods | 0.484 | 0.037 | 0.551 | |
| PWMSimilarity-methods | 0.014 | 0.005 | 0.019 | |
| SiteSet-class | 8.465 | 0.733 | 9.200 | |
| SiteSetList-class | 57.272 | 4.413 | 61.684 | |
| TFFM-class | 0.056 | 0.001 | 0.058 | |
| XMatrix-class | 0.021 | 0.002 | 0.023 | |
| XMatrixList-class | 0.005 | 0.003 | 0.009 | |
| deleteMatrixHavingID-methods | 0.138 | 0.055 | 0.209 | |
| dmmEM-methods | 0.000 | 0.001 | 0.001 | |
| getEmissionProb | 0.295 | 0.006 | 0.303 | |
| getMatrixByID-methods | 0.349 | 0.023 | 0.389 | |
| getMatrixSet-methods | 0 | 0 | 0 | |
| getPosProb | 0.356 | 0.022 | 0.378 | |
| makeFlatFileDir | 0 | 0 | 0 | |
| parseMEMEOutput | 0.267 | 0.002 | 0.271 | |
| permuteMatrix-methods | 0.106 | 0.003 | 0.109 | |
| rPWMDmm-methods | 0 | 0 | 0 | |
| readJASPARMatrix | 0.023 | 0.001 | 0.024 | |
| readXMLTFFM | 0.045 | 0.000 | 0.045 | |
| runMEME-methods | 0.000 | 0.000 | 0.001 | |
| sampleRanges | 0.481 | 0.010 | 0.491 | |
| searchAln-methods | 13.004 | 0.072 | 13.082 | |
| searchPairBSgenome-methods | 0.000 | 0.000 | 0.001 | |
| searchSeq-methods | 1.210 | 0.015 | 1.224 | |
| seqLogo | 1.275 | 0.739 | 2.016 | |
| shannon.entropy | 0.000 | 0.000 | 0.001 | |
| toGRangesList-methods | 10.165 | 0.032 | 10.197 | |
| toICM-methods | 0.022 | 0.004 | 0.026 | |
| toPWM-methods | 0.015 | 0.004 | 0.018 | |