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This page was generated on 2021-10-15 15:05:55 -0400 (Fri, 15 Oct 2021).

CHECK results for TFBSTools on nebbiolo1

To the developers/maintainers of the TFBSTools package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TFBSTools.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1908/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TFBSTools 1.30.0  (landing page)
Ge Tan
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/TFBSTools
git_branch: RELEASE_3_13
git_last_commit: a8d5eba
git_last_commit_date: 2021-05-19 12:01:28 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: TFBSTools
Version: 1.30.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:TFBSTools.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings TFBSTools_1.30.0.tar.gz
StartedAt: 2021-10-14 11:50:50 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 11:56:28 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 338.1 seconds
RetCode: 0
Status:   OK  
CheckDir: TFBSTools.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:TFBSTools.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings TFBSTools_1.30.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/TFBSTools.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.30.0’
* 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 LazyData ... 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     56.856  0.504  57.363
searchAln-methods      9.470  0.766  10.238
toGRangesList-methods  6.932  0.020   6.952
SiteSet-class          5.877  0.128   6.005
* 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-3.13-bioc/meat/TFBSTools.Rcheck/00check.log’
for details.



Installation output

TFBSTools.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL TFBSTools
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘TFBSTools’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.13-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]
  235 |   while (current_pntr->father != NULL){ // while the father of the current pointer exists, walk through the best posible alignment
      |          ~~~~~~~~~~~~^~~~~~~~
gcc -I"/home/biocbuild/bbs-3.13-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-3.13-bioc/R/lib -L/usr/local/lib -o TFBSTools.so matrixAlignerDynamic.o R_init_TFBSTools.o -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.13-bioc/R/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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 34 ]
> 
> proc.time()
   user  system elapsed 
 13.100   0.643  13.724 

Example timings

TFBSTools.Rcheck/TFBSTools-Ex.timings

nameusersystemelapsed
IUPAC2Matrix0.0020.0000.001
MA0004.10.0000.0040.003
MotifSet-class0.0000.0000.001
PFMSimilarity-methods0.2200.0100.243
PWMSimilarity-methods0.0040.0040.009
SiteSet-class5.8770.1286.005
SiteSetList-class56.856 0.50457.363
TFFM-class0.0190.0060.025
XMatrix-class0.0120.0040.017
XMatrixList-class0.0030.0000.003
deleteMatrixHavingID-methods0.0780.0080.085
dmmEM-methods000
getEmissionProb0.1500.0080.158
getMatrixByID-methods0.2610.0050.273
getMatrixSet-methods000
getPosProb0.1460.0040.149
makeFlatFileDir0.0010.0000.000
parseMEMEOutput0.2140.0240.238
permuteMatrix-methods0.0660.0040.070
rPWMDmm-methods000
readJASPARMatrix0.0090.0040.014
readXMLTFFM0.0210.0000.021
runMEME-methods0.0000.0000.001
sampleRanges0.4070.0160.423
searchAln-methods 9.470 0.76610.238
searchPairBSgenome-methods0.0010.0000.000
searchSeq-methods0.8480.0120.859
seqLogo1.7250.5682.292
shannon.entropy0.0010.0000.001
toGRangesList-methods6.9320.0206.952
toICM-methods0.0090.0000.010
toPWM-methods0.0020.0040.007