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This page was generated on 2023-02-08 01:15:32 -0000 (Wed, 08 Feb 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng1Linux (Ubuntu 22.04.1 LTS)aarch64R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" 4164
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CHECK results for TFBSTools on kunpeng1


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? 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 2024/2164HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TFBSTools 1.37.0  (landing page)
Ge Tan
Snapshot Date: 2023-02-06 00:12:45 -0000 (Mon, 06 Feb 2023)
git_url: https://git.bioconductor.org/packages/TFBSTools
git_branch: master
git_last_commit: 57c24b2
git_last_commit_date: 2022-11-01 15:08:54 -0000 (Tue, 01 Nov 2022)
kunpeng1Linux (Ubuntu 22.04.1 LTS) / aarch64  OK    OK    ERROR  

Summary

Package: TFBSTools
Version: 1.37.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:TFBSTools.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings TFBSTools_1.37.0.tar.gz
StartedAt: 2023-02-07 17:29:49 -0000 (Tue, 07 Feb 2023)
EndedAt: 2023-02-07 17:36:52 -0000 (Tue, 07 Feb 2023)
EllapsedTime: 422.7 seconds
RetCode: 1
Status:   ERROR  
CheckDir: TFBSTools.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:TFBSTools.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings TFBSTools_1.37.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/TFBSTools.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘TFBSTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TFBSTools’ version ‘1.37.0’
* 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
* used C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* 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 ... ERROR
Running examples in ‘TFBSTools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: SiteSetList
> ### Title: Class '"SiteSetList"'
> ### Aliases: SiteSetList SiteSetList-class as.data.frame,SiteSetList-method
> ###   relScore,SiteSetList-method pvalues,SiteSetList-method
> ### Keywords: classes
> 
> ### ** Examples
> 
>   data(MA0003.2)
>   data(MA0004.1)
>   pwmList <- PWMatrixList(MA0003.2=toPWM(MA0003.2), MA0004.1=toPWM(MA0004.1))
>   sitesetList <- searchSeq(pwmList, "GAATTCTCTCTTGTTGTAGTCTCTTGACAAAATG", 
+                            min.score="50%")
> 
>   ## elementNROWS of each pwm hits
>   library(S4Vectors)
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min


Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:base’:

    I, expand.grid, unname

>   elementNROWS(sitesetList)
MA0003.2 MA0004.1 
      13        7 
> 
>   ## Output of SiteSetList                         
>   writeGFF3(sitesetList, scoreType="absolute")
            seqname source feature start end      score strand frame
MA0003.2.1  Unknown   TFBS    TFBS     2  16 -27.623703      +     .
MA0003.2.2  Unknown   TFBS    TFBS     3  17 -24.560384      +     .
MA0003.2.3  Unknown   TFBS    TFBS     5  19 -24.037513      +     .
MA0003.2.4  Unknown   TFBS    TFBS     8  22 -19.709791      +     .
MA0003.2.5  Unknown   TFBS    TFBS    15  29 -20.516907      +     .
MA0003.2.6  Unknown   TFBS    TFBS    16  30 -20.207857      +     .
MA0003.2.7  Unknown   TFBS    TFBS     4  18 -25.859889      -     .
MA0003.2.8  Unknown   TFBS    TFBS     5  19 -26.980302      -     .
MA0003.2.9  Unknown   TFBS    TFBS     7  21 -18.813417      -     .
MA0003.2.10 Unknown   TFBS    TFBS    11  25 -25.701717      -     .
MA0003.2.11 Unknown   TFBS    TFBS    17  31 -26.900540      -     .
MA0003.2.12 Unknown   TFBS    TFBS    18  32 -16.437682      -     .
MA0003.2.13 Unknown   TFBS    TFBS    20  34 -25.203202      -     .
MA0004.1.1  Unknown   TFBS    TFBS     8  13  -1.888154      +     .
MA0004.1.2  Unknown   TFBS    TFBS    21  26  -1.888154      +     .
MA0004.1.3  Unknown   TFBS    TFBS    29  34  -3.908935      +     .
MA0004.1.4  Unknown   TFBS    TFBS     6  11  -7.908935      -     .
MA0004.1.5  Unknown   TFBS    TFBS     8  13  -1.961403      -     .
MA0004.1.6  Unknown   TFBS    TFBS    10  15  -3.908935      -     .
MA0004.1.7  Unknown   TFBS    TFBS    21  26  -1.961403      -     .
                                                      attributes
MA0003.2.1  TF=TFAP2A;class=Zipper-Type;sequence=AATTCTCTCTTGTTG
MA0003.2.2  TF=TFAP2A;class=Zipper-Type;sequence=ATTCTCTCTTGTTGT
MA0003.2.3  TF=TFAP2A;class=Zipper-Type;sequence=TCTCTCTTGTTGTAG
MA0003.2.4  TF=TFAP2A;class=Zipper-Type;sequence=CTCTTGTTGTAGTCT
MA0003.2.5  TF=TFAP2A;class=Zipper-Type;sequence=TGTAGTCTCTTGACA
MA0003.2.6  TF=TFAP2A;class=Zipper-Type;sequence=GTAGTCTCTTGACAA
MA0003.2.7  TF=TFAP2A;class=Zipper-Type;sequence=TACAACAAGAGAGAA
MA0003.2.8  TF=TFAP2A;class=Zipper-Type;sequence=CTACAACAAGAGAGA
MA0003.2.9  TF=TFAP2A;class=Zipper-Type;sequence=GACTACAACAAGAGA
MA0003.2.10 TF=TFAP2A;class=Zipper-Type;sequence=AAGAGACTACAACAA
MA0003.2.11 TF=TFAP2A;class=Zipper-Type;sequence=TTTGTCAAGAGACTA
MA0003.2.12 TF=TFAP2A;class=Zipper-Type;sequence=TTTTGTCAAGAGACT
MA0003.2.13 TF=TFAP2A;class=Zipper-Type;sequence=CATTTTGTCAAGAGA
MA0004.1.1             TF=Arnt;class=Zipper-Type;sequence=CTCTTG
MA0004.1.2             TF=Arnt;class=Zipper-Type;sequence=CTCTTG
MA0004.1.3             TF=Arnt;class=Zipper-Type;sequence=AAAATG
MA0004.1.4             TF=Arnt;class=Zipper-Type;sequence=AGAGAG
MA0004.1.5             TF=Arnt;class=Zipper-Type;sequence=CAAGAG
MA0004.1.6             TF=Arnt;class=Zipper-Type;sequence=AACAAG
MA0004.1.7             TF=Arnt;class=Zipper-Type;sequence=CAAGAG
>   as(sitesetList, "DataFrame")
DataFrame with 20 rows and 12 columns
    seqnames source feature     start       end  absScore  relScore strand
       <Rle>  <Rle>   <Rle> <integer> <integer> <numeric> <numeric>  <Rle>
1    Unknown   TFBS    TFBS         2        16  -27.6237  0.502950      +
2    Unknown   TFBS    TFBS         3        17  -24.5604  0.534919      +
3    Unknown   TFBS    TFBS         5        19  -24.0375  0.540376      +
4    Unknown   TFBS    TFBS         8        22  -19.7098  0.585540      +
5    Unknown   TFBS    TFBS        15        29  -20.5169  0.577117      +
...      ...    ...     ...       ...       ...       ...       ...    ...
16   Unknown   TFBS    TFBS        29        34  -3.90894  0.614134      +
17   Unknown   TFBS    TFBS         6        11  -7.90894  0.513016      -
18   Unknown   TFBS    TFBS         8        13  -1.96140  0.663367      -
19   Unknown   TFBS    TFBS        10        15  -3.90894  0.614134      -
20   Unknown   TFBS    TFBS        21        26  -1.96140  0.663367      -
          ID     TF       class        siteSeqs
       <Rle>  <Rle>       <Rle>  <DNAStringSet>
1   MA0003.2 TFAP2A Zipper-Type AATTCTCTCTTGTTG
2   MA0003.2 TFAP2A Zipper-Type ATTCTCTCTTGTTGT
3   MA0003.2 TFAP2A Zipper-Type TCTCTCTTGTTGTAG
4   MA0003.2 TFAP2A Zipper-Type CTCTTGTTGTAGTCT
5   MA0003.2 TFAP2A Zipper-Type TGTAGTCTCTTGACA
...      ...    ...         ...             ...
16  MA0004.1   Arnt Zipper-Type          AAAATG
17  MA0004.1   Arnt Zipper-Type          AGAGAG
18  MA0004.1   Arnt Zipper-Type          CAAGAG
19  MA0004.1   Arnt Zipper-Type          AACAAG
20  MA0004.1   Arnt Zipper-Type          CAAGAG
>   as(sitesetList, "data.frame")
   seqnames source feature start end   absScore  relScore strand       ID
1   Unknown   TFBS    TFBS     2  16 -27.623703 0.5029502      + MA0003.2
2   Unknown   TFBS    TFBS     3  17 -24.560384 0.5349192      + MA0003.2
3   Unknown   TFBS    TFBS     5  19 -24.037513 0.5403760      + MA0003.2
4   Unknown   TFBS    TFBS     8  22 -19.709791 0.5855404      + MA0003.2
5   Unknown   TFBS    TFBS    15  29 -20.516907 0.5771173      + MA0003.2
6   Unknown   TFBS    TFBS    16  30 -20.207857 0.5803426      + MA0003.2
7   Unknown   TFBS    TFBS     4  18 -25.859889 0.5213575      - MA0003.2
8   Unknown   TFBS    TFBS     5  19 -26.980302 0.5096648      - MA0003.2
9   Unknown   TFBS    TFBS     7  21 -18.813417 0.5948950      - MA0003.2
10  Unknown   TFBS    TFBS    11  25 -25.701717 0.5230082      - MA0003.2
11  Unknown   TFBS    TFBS    17  31 -26.900540 0.5104972      - MA0003.2
12  Unknown   TFBS    TFBS    18  32 -16.437682 0.6196884      - MA0003.2
13  Unknown   TFBS    TFBS    20  34 -25.203202 0.5282107      - MA0003.2
14  Unknown   TFBS    TFBS     8  13  -1.888154 0.6652185      + MA0004.1
15  Unknown   TFBS    TFBS    21  26  -1.888154 0.6652185      + MA0004.1
16  Unknown   TFBS    TFBS    29  34  -3.908935 0.6141340      + MA0004.1
17  Unknown   TFBS    TFBS     6  11  -7.908935 0.5130158      - MA0004.1
18  Unknown   TFBS    TFBS     8  13  -1.961403 0.6633668      - MA0004.1
19  Unknown   TFBS    TFBS    10  15  -3.908935 0.6141340      - MA0004.1
20  Unknown   TFBS    TFBS    21  26  -1.961403 0.6633668      - MA0004.1
       TF       class        siteSeqs
1  TFAP2A Zipper-Type AATTCTCTCTTGTTG
2  TFAP2A Zipper-Type ATTCTCTCTTGTTGT
3  TFAP2A Zipper-Type TCTCTCTTGTTGTAG
4  TFAP2A Zipper-Type CTCTTGTTGTAGTCT
5  TFAP2A Zipper-Type TGTAGTCTCTTGACA
6  TFAP2A Zipper-Type GTAGTCTCTTGACAA
7  TFAP2A Zipper-Type TACAACAAGAGAGAA
8  TFAP2A Zipper-Type CTACAACAAGAGAGA
9  TFAP2A Zipper-Type GACTACAACAAGAGA
10 TFAP2A Zipper-Type AAGAGACTACAACAA
11 TFAP2A Zipper-Type TTTGTCAAGAGACTA
12 TFAP2A Zipper-Type TTTTGTCAAGAGACT
13 TFAP2A Zipper-Type CATTTTGTCAAGAGA
14   Arnt Zipper-Type          CTCTTG
15   Arnt Zipper-Type          CTCTTG
16   Arnt Zipper-Type          AAAATG
17   Arnt Zipper-Type          AGAGAG
18   Arnt Zipper-Type          CAAGAG
19   Arnt Zipper-Type          AACAAG
20   Arnt Zipper-Type          CAAGAG
>   as.data.frame(sitesetList)
   seqnames source feature start end   absScore  relScore strand       ID
1   Unknown   TFBS    TFBS     2  16 -27.623703 0.5029502      + MA0003.2
2   Unknown   TFBS    TFBS     3  17 -24.560384 0.5349192      + MA0003.2
3   Unknown   TFBS    TFBS     5  19 -24.037513 0.5403760      + MA0003.2
4   Unknown   TFBS    TFBS     8  22 -19.709791 0.5855404      + MA0003.2
5   Unknown   TFBS    TFBS    15  29 -20.516907 0.5771173      + MA0003.2
6   Unknown   TFBS    TFBS    16  30 -20.207857 0.5803426      + MA0003.2
7   Unknown   TFBS    TFBS     4  18 -25.859889 0.5213575      - MA0003.2
8   Unknown   TFBS    TFBS     5  19 -26.980302 0.5096648      - MA0003.2
9   Unknown   TFBS    TFBS     7  21 -18.813417 0.5948950      - MA0003.2
10  Unknown   TFBS    TFBS    11  25 -25.701717 0.5230082      - MA0003.2
11  Unknown   TFBS    TFBS    17  31 -26.900540 0.5104972      - MA0003.2
12  Unknown   TFBS    TFBS    18  32 -16.437682 0.6196884      - MA0003.2
13  Unknown   TFBS    TFBS    20  34 -25.203202 0.5282107      - MA0003.2
14  Unknown   TFBS    TFBS     8  13  -1.888154 0.6652185      + MA0004.1
15  Unknown   TFBS    TFBS    21  26  -1.888154 0.6652185      + MA0004.1
16  Unknown   TFBS    TFBS    29  34  -3.908935 0.6141340      + MA0004.1
17  Unknown   TFBS    TFBS     6  11  -7.908935 0.5130158      - MA0004.1
18  Unknown   TFBS    TFBS     8  13  -1.961403 0.6633668      - MA0004.1
19  Unknown   TFBS    TFBS    10  15  -3.908935 0.6141340      - MA0004.1
20  Unknown   TFBS    TFBS    21  26  -1.961403 0.6633668      - MA0004.1
       TF       class        siteSeqs
1  TFAP2A Zipper-Type AATTCTCTCTTGTTG
2  TFAP2A Zipper-Type ATTCTCTCTTGTTGT
3  TFAP2A Zipper-Type TCTCTCTTGTTGTAG
4  TFAP2A Zipper-Type CTCTTGTTGTAGTCT
5  TFAP2A Zipper-Type TGTAGTCTCTTGACA
6  TFAP2A Zipper-Type GTAGTCTCTTGACAA
7  TFAP2A Zipper-Type TACAACAAGAGAGAA
8  TFAP2A Zipper-Type CTACAACAAGAGAGA
9  TFAP2A Zipper-Type GACTACAACAAGAGA
10 TFAP2A Zipper-Type AAGAGACTACAACAA
11 TFAP2A Zipper-Type TTTGTCAAGAGACTA
12 TFAP2A Zipper-Type TTTTGTCAAGAGACT
13 TFAP2A Zipper-Type CATTTTGTCAAGAGA
14   Arnt Zipper-Type          CTCTTG
15   Arnt Zipper-Type          CTCTTG
16   Arnt Zipper-Type          AAAATG
17   Arnt Zipper-Type          AGAGAG
18   Arnt Zipper-Type          CAAGAG
19   Arnt Zipper-Type          AACAAG
20   Arnt Zipper-Type          CAAGAG
>   as(sitesetList, "GRanges")
GRanges object with 20 ranges and 8 metadata columns:
       seqnames    ranges strand | source feature  absScore  relScore       ID
          <Rle> <IRanges>  <Rle> |  <Rle>   <Rle> <numeric> <numeric>    <Rle>
   [1]  Unknown      2-16      + |   TFBS    TFBS  -27.6237  0.502950 MA0003.2
   [2]  Unknown      3-17      + |   TFBS    TFBS  -24.5604  0.534919 MA0003.2
   [3]  Unknown      5-19      + |   TFBS    TFBS  -24.0375  0.540376 MA0003.2
   [4]  Unknown      8-22      + |   TFBS    TFBS  -19.7098  0.585540 MA0003.2
   [5]  Unknown     15-29      + |   TFBS    TFBS  -20.5169  0.577117 MA0003.2
   ...      ...       ...    ... .    ...     ...       ...       ...      ...
  [16]  Unknown     29-34      + |   TFBS    TFBS  -3.90894  0.614134 MA0004.1
  [17]  Unknown      6-11      - |   TFBS    TFBS  -7.90894  0.513016 MA0004.1
  [18]  Unknown      8-13      - |   TFBS    TFBS  -1.96140  0.663367 MA0004.1
  [19]  Unknown     10-15      - |   TFBS    TFBS  -3.90894  0.614134 MA0004.1
  [20]  Unknown     21-26      - |   TFBS    TFBS  -1.96140  0.663367 MA0004.1
           TF       class        siteSeqs
        <Rle>       <Rle>  <DNAStringSet>
   [1] TFAP2A Zipper-Type AATTCTCTCTTGTTG
   [2] TFAP2A Zipper-Type ATTCTCTCTTGTTGT
   [3] TFAP2A Zipper-Type TCTCTCTTGTTGTAG
   [4] TFAP2A Zipper-Type CTCTTGTTGTAGTCT
   [5] TFAP2A Zipper-Type TGTAGTCTCTTGACA
   ...    ...         ...             ...
  [16]   Arnt Zipper-Type          AAAATG
  [17]   Arnt Zipper-Type          AGAGAG
  [18]   Arnt Zipper-Type          CAAGAG
  [19]   Arnt Zipper-Type          AACAAG
  [20]   Arnt Zipper-Type          CAAGAG
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths
> 
>   ## Calculate the p-values
>   pvalues(sitesetList, type="TFMPvalue")
Killed
* 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 ...
  ‘TFBSTools.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘TFBSTools.Rmd’ using rmarkdown
Killed

* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/TFBSTools.Rcheck/00check.log’
for details.

Installation output

TFBSTools.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL TFBSTools
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘TFBSTools’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
gcc -I"/home/biocbuild/bbs-3.17-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-3.17-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-3.17-bioc/R/lib -L/usr/local/lib -o TFBSTools.so matrixAlignerDynamic.o R_init_TFBSTools.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-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 Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 
 18.023   0.644  19.017

Example timings

TFBSTools.Rcheck/TFBSTools-Ex.timings

nameusersystemelapsed
IUPAC2Matrix0.0020.0000.001
MA0004.10.0030.0020.005
MotifSet-class000
PFMSimilarity-methods0.3370.0120.381
PWMSimilarity-methods0.0110.0000.012
SiteSet-class9.5560.0729.636