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CHECK report for TFBSTools on tokay2

This page was generated on 2020-10-17 11:57:55 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE TFBSTools PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1793/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TFBSTools 1.26.0
Ge Tan
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/TFBSTools
Branch: RELEASE_3_11
Last Commit: 1466c2e
Last Changed Date: 2020-04-27 14:37:11 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] NA 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: TFBSTools
Version: 1.26.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TFBSTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings TFBSTools_1.26.0.tar.gz
StartedAt: 2020-10-17 08:49:57 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 08:59:43 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 586.4 seconds
RetCode: 0
Status:  OK  
CheckDir: TFBSTools.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TFBSTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings TFBSTools_1.26.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/TFBSTools.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'TFBSTools/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TFBSTools' version '1.26.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.11-bioc/R/library/TFBSTools/libs/i386/TFBSTools.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.11-bioc/R/library/TFBSTools/libs/x64/TFBSTools.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
SiteSetList-class     51.64   1.56   53.24
toGRangesList-methods 10.12   0.00   10.20
searchAln-methods      9.58   0.03    9.67
SiteSet-class          7.33   0.55    7.87
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
SiteSetList-class     49.47   2.10   51.60
toGRangesList-methods 10.37   0.00   10.37
searchAln-methods      9.85   0.00    9.87
SiteSet-class          6.56   0.23    6.79
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/TFBSTools.Rcheck/00check.log'
for details.



Installation output

TFBSTools.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/TFBSTools_1.26.0.tar.gz && rm -rf TFBSTools.buildbin-libdir && mkdir TFBSTools.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TFBSTools.buildbin-libdir TFBSTools_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL TFBSTools_1.26.0.zip && rm TFBSTools_1.26.0.tar.gz TFBSTools_1.26.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0  151k    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  151k  100  151k    0     0  1728k      0 --:--:-- --:--:-- --:--:-- 1849k

install for i386

* installing *source* package 'TFBSTools' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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
          ~~~~~~~~~~~~^~~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_TFBSTools.c -o R_init_TFBSTools.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o TFBSTools.dll tmp.def matrixAlignerDynamic.o R_init_TFBSTools.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/TFBSTools.buildbin-libdir/00LOCK-TFBSTools/00new/TFBSTools/libs/i386
** 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
  converting help for package 'TFBSTools'
    finding HTML links ... done
    IUPAC2Matrix                            html  
    MA0004.1                                html  
    MotifSet-class                          html  
    PFMSimilarity-methods                   html  
    PWMSimilarity-methods                   html  
    SitePairSet-class                       html  
    SitePairSetList-class                   html  
    SiteSet-class                           html  
    SiteSetList-class                       html  
    TFBSTools-package                       html  
    TFFM-class                              html  
    XMatrix-class                           html  
    XMatrixList-class                       html  
    calConservation-methods                 html  
    deleteMatrixHavingID-methods            html  
    dmmEM-methods                           html  
    getEmissionProb                         html  
    getMatrixByID-methods                   html  
    getMatrixSet-methods                    html  
    getPosProb                              html  
    makeFlatFileDir                         html  
    parseMEMEOutput                         html  
    permuteMatrix-methods                   html  
    rPWMDmm-methods                         html  
    readJASPARMatrix                        html  
    readXMLTFFM                             html  
    runMEME-methods                         html  
    sampleRanges                            html  
    searchAln-methods                       html  
    searchPairBSgenome-methods              html  
    searchSeq-methods                       html  
    seqLogo                                 html  
    shannon.entropy                         html  
    toGRangesList-methods                   html  
    toICM-methods                           html  
    finding level-2 HTML links ... done

    toPWM-methods                           html  
    writeGFF3-methods                       html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'TFBSTools' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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
          ~~~~~~~~~~~~^~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_TFBSTools.c -o R_init_TFBSTools.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o TFBSTools.dll tmp.def matrixAlignerDynamic.o R_init_TFBSTools.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/TFBSTools.buildbin-libdir/TFBSTools/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TFBSTools' as TFBSTools_1.26.0.zip
* DONE (TFBSTools)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'TFBSTools' successfully unpacked and MD5 sums checked

Tests output

TFBSTools.Rcheck/tests_i386/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  13.98    1.37   15.34 

TFBSTools.Rcheck/tests_x64/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  14.59    0.68   15.26 

Example timings

TFBSTools.Rcheck/examples_i386/TFBSTools-Ex.timings

nameusersystemelapsed
IUPAC2Matrix000
MA0004.1000
MotifSet-class000
PFMSimilarity-methods0.390.070.69
PWMSimilarity-methods0.030.000.03
SiteSet-class7.330.557.87
SiteSetList-class51.64 1.5653.24
TFFM-class0.040.000.04
XMatrix-class0.020.000.02
XMatrixList-class0.020.000.01
deleteMatrixHavingID-methods0.070.060.15
dmmEM-methods000
getEmissionProb0.330.000.32
getMatrixByID-methods0.280.030.32
getMatrixSet-methods000
getPosProb0.300.000.29
makeFlatFileDir000
parseMEMEOutput0.230.010.25
permuteMatrix-methods0.050.050.09
rPWMDmm-methods000
readJASPARMatrix0.020.020.03
readXMLTFFM0.030.000.03
runMEME-methods000
sampleRanges0.280.080.36
searchAln-methods9.580.039.67
searchPairBSgenome-methods000
searchSeq-methods1.250.011.26
seqLogo2.140.172.32
shannon.entropy000
toGRangesList-methods10.12 0.0010.20
toICM-methods0.020.000.01
toPWM-methods000

TFBSTools.Rcheck/examples_x64/TFBSTools-Ex.timings

nameusersystemelapsed
IUPAC2Matrix000
MA0004.10.010.000.01
MotifSet-class000
PFMSimilarity-methods0.360.050.41
PWMSimilarity-methods0.020.000.02
SiteSet-class6.560.236.79
SiteSetList-class49.47 2.1051.60
TFFM-class0.030.000.03
XMatrix-class0.010.000.01
XMatrixList-class0.000.010.02
deleteMatrixHavingID-methods0.080.070.14
dmmEM-methods000
getEmissionProb0.220.010.23
getMatrixByID-methods0.240.030.27
getMatrixSet-methods000
getPosProb0.220.000.22
makeFlatFileDir000
parseMEMEOutput0.220.000.22
permuteMatrix-methods0.060.000.06
rPWMDmm-methods000
readJASPARMatrix0.020.000.02
readXMLTFFM0.010.020.03
runMEME-methods000
sampleRanges0.280.010.30
searchAln-methods9.850.009.87
searchPairBSgenome-methods000
searchSeq-methods0.930.020.96
seqLogo1.930.142.06
shannon.entropy000
toGRangesList-methods10.37 0.0010.37
toICM-methods0.020.000.02
toPWM-methods0.010.000.02