Ge Tan
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/TFBSTools |
| Branch: RELEASE_3_10 |
| Last Commit: 952afaa |
| Last Changed Date: 2019-10-29 13:08:50 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:08:11 -0400 (Wed, 15 Apr 2020).
| Package 1717/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| TFBSTools 1.24.0 Ge Tan
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: TFBSTools |
| Version: 1.24.0 |
| Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:TFBSTools.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings TFBSTools_1.24.0.tar.gz |
| StartedAt: 2020-04-15 01:56:42 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 02:03:45 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 423.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: TFBSTools.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:TFBSTools.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings TFBSTools_1.24.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/TFBSTools.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.24.0’
* 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 71.020 0.044 71.457
searchAln-methods 12.012 0.004 12.108
toGRangesList-methods 9.116 0.000 9.160
SiteSet-class 8.344 0.028 8.406
* 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-3.10-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-3.10-bioc/R/bin/R CMD INSTALL TFBSTools
###
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘TFBSTools’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.10-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-3.10-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-3.10-bioc/R/lib -L/usr/local/lib -o TFBSTools.so matrixAlignerDynamic.o R_init_TFBSTools.o -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.10-bioc/R/library/00LOCK-TFBSTools/00new/TFBSTools/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
No methods found in package ‘IRanges’ for request: ‘score’ when loading ‘TFBSTools’
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
No methods found in package ‘IRanges’ for request: ‘score’ when loading ‘TFBSTools’
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
No methods found in package ‘IRanges’ for request: ‘score’ when loading ‘TFBSTools’
** testing if installed package keeps a record of temporary installation path
* DONE (TFBSTools)
TFBSTools.Rcheck/tests/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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)
No methods found in package 'IRanges' for request: 'score' when loading 'TFBSTools'
>
> test_check("TFBSTools")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 34 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
17.128 0.560 17.833
TFBSTools.Rcheck/TFBSTools-Ex.timings
| name | user | system | elapsed | |
| IUPAC2Matrix | 0.004 | 0.000 | 0.001 | |
| MA0004.1 | 0.008 | 0.000 | 0.007 | |
| MotifSet-class | 0 | 0 | 0 | |
| PFMSimilarity-methods | 0.388 | 0.000 | 1.021 | |
| PWMSimilarity-methods | 0.012 | 0.000 | 0.011 | |
| SiteSet-class | 8.344 | 0.028 | 8.406 | |
| SiteSetList-class | 71.020 | 0.044 | 71.457 | |
| TFFM-class | 0.040 | 0.000 | 0.051 | |
| XMatrix-class | 0.016 | 0.000 | 0.018 | |
| XMatrixList-class | 0.004 | 0.000 | 0.005 | |
| deleteMatrixHavingID-methods | 0.072 | 0.024 | 0.096 | |
| dmmEM-methods | 0 | 0 | 0 | |
| getEmissionProb | 0.280 | 0.000 | 0.291 | |
| getMatrixByID-methods | 0.252 | 0.016 | 0.358 | |
| getMatrixSet-methods | 0 | 0 | 0 | |
| getPosProb | 0.284 | 0.004 | 0.287 | |
| makeFlatFileDir | 0 | 0 | 0 | |
| parseMEMEOutput | 0.284 | 0.000 | 0.285 | |
| permuteMatrix-methods | 0.076 | 0.000 | 0.077 | |
| rPWMDmm-methods | 0.000 | 0.000 | 0.001 | |
| readJASPARMatrix | 0.016 | 0.000 | 0.029 | |
| readXMLTFFM | 0.032 | 0.000 | 0.032 | |
| runMEME-methods | 0 | 0 | 0 | |
| sampleRanges | 0.368 | 0.000 | 0.369 | |
| searchAln-methods | 12.012 | 0.004 | 12.108 | |
| searchPairBSgenome-methods | 0 | 0 | 0 | |
| searchSeq-methods | 1.036 | 0.016 | 1.055 | |
| seqLogo | 1.020 | 0.064 | 1.085 | |
| shannon.entropy | 0.004 | 0.000 | 0.000 | |
| toGRangesList-methods | 9.116 | 0.000 | 9.160 | |
| toICM-methods | 0.016 | 0.000 | 0.014 | |
| toPWM-methods | 0.008 | 0.000 | 0.009 | |