Ge Tan
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/TFBSTools |
| Branch: RELEASE_3_8 |
| Last Commit: 74035fc |
| Last Changed Date: 2018-10-30 11:41:52 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:50:17 -0400 (Tue, 16 Apr 2019).
| Package 1555/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| TFBSTools 1.20.0 Ge Tan
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: TFBSTools |
| Version: 1.20.0 |
| Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:TFBSTools.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings TFBSTools_1.20.0.tar.gz |
| StartedAt: 2019-04-16 03:23:25 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 03:29:26 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 360.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: TFBSTools.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:TFBSTools.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings TFBSTools_1.20.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/TFBSTools.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (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 ‘1.20.0’
* 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 61.484 0.032 61.569
searchAln-methods 9.596 0.008 9.619
SiteSet-class 8.632 0.060 8.705
toGRangesList-methods 6.708 0.000 6.743
* 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
‘/home/biocbuild/bbs-3.8-bioc/meat/TFBSTools.Rcheck/00check.log’
for details.
TFBSTools.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL TFBSTools
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘TFBSTools’ ...
** libs
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c matrixAlignerDynamic.c -o matrixAlignerDynamic.o
matrixAlignerDynamic.c: In function ‘score’:
matrixAlignerDynamic.c:235:22: warning: ‘best_pntr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
while (current_pntr->father != NULL){ // while the father of the current pointer exists, walk through the best posible alignment
^
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c R_init_TFBSTools.c -o R_init_TFBSTools.o
gcc -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o TFBSTools.so matrixAlignerDynamic.o R_init_TFBSTools.o -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/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)
TFBSTools.Rcheck/tests/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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
12.780 0.416 13.207
TFBSTools.Rcheck/TFBSTools-Ex.timings
| name | user | system | elapsed | |
| IUPAC2Matrix | 0 | 0 | 0 | |
| MA0004.1 | 0.000 | 0.008 | 0.006 | |
| MotifSet-class | 0 | 0 | 0 | |
| PFMSimilarity-methods | 0.368 | 0.020 | 0.511 | |
| PWMSimilarity-methods | 0.016 | 0.000 | 0.013 | |
| SiteSet-class | 8.632 | 0.060 | 8.705 | |
| SiteSetList-class | 61.484 | 0.032 | 61.569 | |
| TFFM-class | 0.028 | 0.000 | 0.037 | |
| XMatrix-class | 0.004 | 0.004 | 0.009 | |
| XMatrixList-class | 0.004 | 0.000 | 0.002 | |
| deleteMatrixHavingID-methods | 0.064 | 0.004 | 0.068 | |
| dmmEM-methods | 0 | 0 | 0 | |
| getEmissionProb | 0.256 | 0.000 | 0.256 | |
| getMatrixByID-methods | 0.164 | 0.008 | 0.190 | |
| getMatrixSet-methods | 0 | 0 | 0 | |
| getPosProb | 0.196 | 0.000 | 0.196 | |
| makeFlatFileDir | 0.000 | 0.000 | 0.001 | |
| parseMEMEOutput | 0.140 | 0.004 | 0.144 | |
| permuteMatrix-methods | 0.100 | 0.000 | 0.101 | |
| rPWMDmm-methods | 0.000 | 0.000 | 0.001 | |
| readJASPARMatrix | 0.012 | 0.004 | 0.035 | |
| readXMLTFFM | 0.040 | 0.000 | 0.037 | |
| runMEME-methods | 0.000 | 0.000 | 0.001 | |
| sampleRanges | 0.372 | 0.000 | 0.375 | |
| searchAln-methods | 9.596 | 0.008 | 9.619 | |
| searchPairBSgenome-methods | 0 | 0 | 0 | |
| searchSeq-methods | 0.828 | 0.000 | 0.827 | |
| seqLogo | 1.404 | 0.000 | 1.403 | |
| shannon.entropy | 0 | 0 | 0 | |
| toGRangesList-methods | 6.708 | 0.000 | 6.743 | |
| toICM-methods | 0.016 | 0.000 | 0.015 | |
| toPWM-methods | 0.012 | 0.000 | 0.012 | |