Ge Tan
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/TFBSTools |
| Branch: master |
| Last Commit: 0e44f9e |
| Last Changed Date: 2018-11-16 09:48:49 -0400 (Fri, 16 Nov 2018) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 13:09:07 -0400 (Tue, 09 Apr 2019).
| Package 1605/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| TFBSTools 1.21.2 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 | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: TFBSTools |
| Version: 1.21.2 |
| 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_1.21.2.tar.gz |
| StartedAt: 2019-04-09 05:55:53 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 06:04:04 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 491.4 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_1.21.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/TFBSTools.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.21.2’
* 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 ... 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 57.261 4.557 61.819
searchAln-methods 10.170 0.037 10.209
toGRangesList-methods 9.741 0.144 9.885
SiteSet-class 8.156 0.851 9.008
* 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 -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/3.6/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 Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
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 FAILED: 0
>
> proc.time()
user system elapsed
19.114 1.597 20.657
TFBSTools.Rcheck/TFBSTools-Ex.timings
| name | user | system | elapsed | |
| IUPAC2Matrix | 0.001 | 0.000 | 0.001 | |
| MA0004.1 | 0.010 | 0.007 | 0.018 | |
| MotifSet-class | 0.001 | 0.000 | 0.001 | |
| PFMSimilarity-methods | 0.483 | 0.039 | 0.553 | |
| PWMSimilarity-methods | 0.016 | 0.004 | 0.020 | |
| SiteSet-class | 8.156 | 0.851 | 9.008 | |
| SiteSetList-class | 57.261 | 4.557 | 61.819 | |
| TFFM-class | 0.051 | 0.001 | 0.053 | |
| XMatrix-class | 0.025 | 0.002 | 0.027 | |
| XMatrixList-class | 0.006 | 0.004 | 0.009 | |
| deleteMatrixHavingID-methods | 0.156 | 0.063 | 0.236 | |
| dmmEM-methods | 0 | 0 | 0 | |
| getEmissionProb | 0.384 | 0.004 | 0.389 | |
| getMatrixByID-methods | 0.287 | 0.021 | 0.351 | |
| getMatrixSet-methods | 0.000 | 0.000 | 0.001 | |
| getPosProb | 0.428 | 0.010 | 0.439 | |
| makeFlatFileDir | 0 | 0 | 0 | |
| parseMEMEOutput | 0.226 | 0.002 | 0.229 | |
| permuteMatrix-methods | 0.057 | 0.002 | 0.059 | |
| rPWMDmm-methods | 0 | 0 | 0 | |
| readJASPARMatrix | 0.017 | 0.001 | 0.019 | |
| readXMLTFFM | 0.033 | 0.001 | 0.034 | |
| runMEME-methods | 0 | 0 | 0 | |
| sampleRanges | 0.259 | 0.005 | 0.266 | |
| searchAln-methods | 10.170 | 0.037 | 10.209 | |
| searchPairBSgenome-methods | 0 | 0 | 0 | |
| searchSeq-methods | 1.183 | 0.016 | 1.200 | |
| seqLogo | 2.011 | 0.562 | 2.575 | |
| shannon.entropy | 0.001 | 0.000 | 0.001 | |
| toGRangesList-methods | 9.741 | 0.144 | 9.885 | |
| toICM-methods | 0.017 | 0.003 | 0.019 | |
| toPWM-methods | 0.014 | 0.004 | 0.017 | |