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CHECK report for MotIV on tokay1

This page was generated on 2021-05-06 12:32:21 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the MotIV package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1147/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MotIV 1.46.0  (landing page)
Eloi Mercier , Raphael Gottardo
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/MotIV
Branch: RELEASE_3_12
Last Commit: 05f7b55
Last Changed Date: 2020-10-27 10:37:48 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    ERROR  
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    ERROR    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: MotIV
Version: 1.46.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MotIV.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings MotIV_1.46.0.tar.gz
StartedAt: 2021-05-06 04:49:16 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 04:54:45 -0400 (Thu, 06 May 2021)
EllapsedTime: 328.3 seconds
RetCode: 1
Status:   ERROR   
CheckDir: MotIV.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MotIV.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings MotIV_1.46.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/MotIV.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MotIV/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MotIV' version '1.46.0'
* 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 'MotIV' can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'MotIV' is deprecated and will be removed from Bioconductor
See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/MotIV.Rcheck/00install.out' for details.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
motifDistances: no visible binding for global variable 'jaspar.scores'
motifMatch: no visible binding for global variable 'jaspar'
motifMatch: no visible binding for global variable 'jaspar.scores'
Undefined global functions or variables:
  jaspar jaspar.scores
* 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 shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... NOTE
Package has both 'src/Makevars.in' and 'src/Makevars'.
Installation with --no-configure' is unlikely to work.  If you intended
'src/Makevars' to be used on Windows, rename it to 'src/Makevars.win'
otherwise remove it.  If 'configure' created 'src/Makevars', you need a
'cleanup' script.
* 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-3.12-bioc/R/library/MotIV/libs/i386/MotIV.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  Found 'rand', possibly from 'rand' (C)
File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/MotIV/libs/x64/MotIV.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  Found 'rand', possibly from 'rand' (C)

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' ... ERROR
Running examples in 'MotIV-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: motifDistances
> ### Title: Clustering PWMs Computation
> ### Aliases: motifDistances motifHclust motifCutree
> ### Keywords: misc
> 
> ### ** Examples
> 
> #####Database and Scores#####
> path <- system.file(package="MotIV")
> jaspar <- readPWMfile(paste(path,"/extdata/jaspar2010.txt",sep=""))
> jaspar.scores <- readDBScores(paste(path,"/extdata/jaspar2010_PCC_SWU.scores",sep=""))
> 
> #####Input#####
> data(FOXA1_rGADEM)
> motifs <- getPWM(gadem)
> motifs.trimed <- lapply(motifs,trimPWMedge, threshold=1)
> 
> #####Analysis#####
> foxa1.analysis.jaspar <- motifMatch(inputPWM=motifs,align="SWU",cc="PCC",database=jaspar,DBscores=jaspar.scores,top=5)

	Ungapped Alignment
	Scores read
	Database read
	Motif matches : 5
> 
> #####Clustering#####
> d <- motifDistances(getPWM(foxa1.analysis.jaspar))
> hc <- motifHclust(d)
> plot(hc)
> f <- motifCutree(hc, k=2)
 ----------- FAILURE REPORT -------------- 
 --- failure: length > 1 in coercion to logical ---
 --- srcref --- 
: 
 --- package (from environment) --- 
MotIV
 --- call from context --- 
setFilter(name = names(cut[cut == i]))
 --- call from argument --- 
name == "" && tfname == ""
 --- R stacktrace ---
where 1: setFilter(name = names(cut[cut == i]))
where 2: motifCutree(hc, k = 2)

 --- value of length: 3 type: logical ---
[1] FALSE FALSE FALSE
 --- function from context --- 
function (name = "", tfname = "", evalueMax = 1, top = 10, lengthMax = 100, 
    valid = NULL) 
{
    if (name == "" && tfname == "" && evalueMax >= 1 && top >= 
        10 && lengthMax >= 100) {
        warning("Filter does not contain condition.")
    }
    fit <- new("filter", name = list(name), tfname = list(tfname), 
        evalueMax = list(evalueMax), top = list(top), lengthMax = list(lengthMax), 
        valid = list(valid))
    filters <- new("filters", filters = list(fit))
    return(filters)
}
<bytecode: 0x238fdec8>
<environment: namespace:MotIV>
 --- function search by body ---
Function setFilter in namespace MotIV has this body.
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: length > 1 in coercion to logical

** running examples for arch 'x64' ... ERROR
Running examples in 'MotIV-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: motifDistances
> ### Title: Clustering PWMs Computation
> ### Aliases: motifDistances motifHclust motifCutree
> ### Keywords: misc
> 
> ### ** Examples
> 
> #####Database and Scores#####
> path <- system.file(package="MotIV")
> jaspar <- readPWMfile(paste(path,"/extdata/jaspar2010.txt",sep=""))
> jaspar.scores <- readDBScores(paste(path,"/extdata/jaspar2010_PCC_SWU.scores",sep=""))
> 
> #####Input#####
> data(FOXA1_rGADEM)
> motifs <- getPWM(gadem)
> motifs.trimed <- lapply(motifs,trimPWMedge, threshold=1)
> 
> #####Analysis#####
> foxa1.analysis.jaspar <- motifMatch(inputPWM=motifs,align="SWU",cc="PCC",database=jaspar,DBscores=jaspar.scores,top=5)

	Ungapped Alignment
	Scores read
	Database read
	Motif matches : 5
> 
> #####Clustering#####
> d <- motifDistances(getPWM(foxa1.analysis.jaspar))
> hc <- motifHclust(d)
> plot(hc)
> f <- motifCutree(hc, k=2)
 ----------- FAILURE REPORT -------------- 
 --- failure: length > 1 in coercion to logical ---
 --- srcref --- 
: 
 --- package (from environment) --- 
MotIV
 --- call from context --- 
setFilter(name = names(cut[cut == i]))
 --- call from argument --- 
name == "" && tfname == ""
 --- R stacktrace ---
where 1: setFilter(name = names(cut[cut == i]))
where 2: motifCutree(hc, k = 2)

 --- value of length: 3 type: logical ---
[1] FALSE FALSE FALSE
 --- function from context --- 
function (name = "", tfname = "", evalueMax = 1, top = 10, lengthMax = 100, 
    valid = NULL) 
{
    if (name == "" && tfname == "" && evalueMax >= 1 && top >= 
        10 && lengthMax >= 100) {
        warning("Filter does not contain condition.")
    }
    fit <- new("filter", name = list(name), tfname = list(tfname), 
        evalueMax = list(evalueMax), top = list(top), lengthMax = list(lengthMax), 
        valid = list(valid))
    filters <- new("filters", filters = list(fit))
    return(filters)
}
<bytecode: 0x00000000364bae50>
<environment: namespace:MotIV>
 --- function search by body ---
Function setFilter in namespace MotIV has this body.
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: length > 1 in coercion to logical

* 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 ERRORs, 1 WARNING, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/MotIV.Rcheck/00check.log'
for details.

Installation output

MotIV.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/MotIV_1.46.0.tar.gz && rm -rf MotIV.buildbin-libdir && mkdir MotIV.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MotIV.buildbin-libdir MotIV_1.46.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL MotIV_1.46.0.zip && rm MotIV_1.46.0.tar.gz MotIV_1.46.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  274k  100  274k    0     0  18.7M      0 --:--:-- --:--:-- --:--:-- 20.6M

install for i386

* installing *source* package 'MotIV' ...
** using staged installation

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c Alignment.cpp -o Alignment.o
Alignment.cpp: In member function 'double Alignment::AlignMotifs2D(Motif*, Motif*, int&, int&, int&, bool&, bool&)':
Alignment.cpp:176:17: warning: unused variable 'score2' [-Wunused-variable]
  double score1, score2, bestScore=0;
                 ^~~~~~
Alignment.cpp:177:18: warning: unused variable 'i1_B' [-Wunused-variable]
  int i1_A, i2_A, i1_B, i2_B;
                  ^~~~
Alignment.cpp:177:24: warning: unused variable 'i2_B' [-Wunused-variable]
  int i1_A, i2_A, i1_B, i2_B;
                        ^~~~
Alignment.cpp:178:12: warning: unused variable 'aL_B' [-Wunused-variable]
  int aL_A, aL_B;
            ^~~~
Alignment.cpp:179:14: warning: unused variable 'for_B' [-Wunused-variable]
  bool for_A, for_B;
              ^~~~~
Alignment.cpp:184:9: warning: variable 'currOne' set but not used [-Wunused-but-set-variable]
  Motif* currOne = one;
         ^~~~~~~
Alignment.cpp:185:9: warning: unused variable 'currTwo' [-Wunused-variable]
  Motif* currTwo = two;
         ^~~~~~~
Alignment.cpp: In member function 'virtual double SmithWatermanUngappedExtended::AlignMotifs(Motif*, Motif*, int&, int&, int&, bool&)':
Alignment.cpp:423:9: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
  double tmp;
         ^~~
Alignment.cpp: In member function 'virtual double SmithWaterman::AlignMotifs(Motif*, Motif*, int&, int&, int&, bool&)':
Alignment.cpp:319:2: warning: 'revScore' may be used uninitialized in this function [-Wmaybe-uninitialized]
  if(forScore>revScore){
  ^~
Alignment.cpp:319:2: warning: 'forScore' may be used uninitialized in this function [-Wmaybe-uninitialized]
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c ColumnComp.cpp -o ColumnComp.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c DeclareAll.cpp -o DeclareAll.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c Motif.cpp -o Motif.o
Motif.cpp: In member function 'char Motif::ColConsensus(int)':
Motif.cpp:148:7: warning: variable 'three_base_l' set but not used [-Wunused-but-set-variable]
  char three_base_l[4]; //three base consensus
       ^~~~~~~~~~~~
Motif.cpp:149:9: warning: variable 'three_base_c' set but not used [-Wunused-but-set-variable]
  double three_base_c[4];
         ^~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c MotifDistances.cpp -o MotifDistances.o
MotifDistances.cpp: In function 'SEXPREC* motifDistances(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
MotifDistances.cpp:115:11: warning: deleting object of abstract class type 'ColumnComp' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor]
  delete(CC);
           ^
MotifDistances.cpp:50:10: warning: variable 'colChosen' set but not used [-Wunused-but-set-variable]
     bool colChosen=false, alignChosen=false;
          ^~~~~~~~~
MotifDistances.cpp:50:27: warning: variable 'alignChosen' set but not used [-Wunused-but-set-variable]
     bool colChosen=false, alignChosen=false;
                           ^~~~~~~~~~~
MotifDistances.cpp:51:6: warning: variable 'matchTopX' set but not used [-Wunused-but-set-variable]
  int matchTopX = TOP_MATCH;
      ^~~~~~~~~
MotifDistances.cpp:58:7: warning: variable 'ungapped' set but not used [-Wunused-but-set-variable]
  bool ungapped=false;
       ^~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c MotifMatch.cpp -o MotifMatch.o
MotifMatch.cpp: In function 'SEXPREC* motifMatch(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
MotifMatch.cpp:120:11: warning: deleting object of abstract class type 'ColumnComp' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor]
  delete(CC);
           ^
MotifMatch.cpp:50:10: warning: variable 'colChosen' set but not used [-Wunused-but-set-variable]
     bool colChosen=false, alignChosen=false;
          ^~~~~~~~~
MotifMatch.cpp:50:27: warning: variable 'alignChosen' set but not used [-Wunused-but-set-variable]
     bool colChosen=false, alignChosen=false;
                           ^~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c PlatformSupport.cpp -o PlatformSupport.o
PlatformSupport.cpp: In member function 'void PlatformSupport::PreAlign(Alignment*)':
PlatformSupport.cpp:412:47: warning: variable 'max_score' set but not used [-Wunused-but-set-variable]
  double curr_score, curr_z_score, curr_p_val, max_score;
                                               ^~~~~~~~~
In file included from Motif.h:39,
                 from PlatformSupport.h:41,
                 from PlatformSupport.cpp:33:
C:/Users/BIOCBU~1/BBS-3~1.12-/R/include/Rinternals.h: In member function 'int PlatformSupport::ReadTransfacFile(SEXP, SEXP)':
C:/Users/BIOCBU~1/BBS-3~1.12-/R/include/Rinternals.h:1629:29: warning: 'input' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define length(x)  Rf_length(x)
                             ^
PlatformSupport.cpp:103:18: note: 'input' was declared here
  SEXP inputName, input;
                  ^~~~~
PlatformSupport.cpp:102:10: warning: 'currMotifs' may be used uninitialized in this function [-Wmaybe-uninitialized]
  Motif** currMotifs; int currCnt;
          ^~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RandPSSMGen.cpp -o RandPSSMGen.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c generateScoresDB.cpp -o generateScoresDB.o
generateScoresDB.cpp: In function 'SEXPREC* generateScoresDB(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
generateScoresDB.cpp:127:11: warning: deleting object of abstract class type 'ColumnComp' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor]
  delete(CC);
           ^
generateScoresDB.cpp:54:10: warning: variable 'colChosen' set but not used [-Wunused-but-set-variable]
     bool colChosen=false, alignChosen=false;
          ^~~~~~~~~
generateScoresDB.cpp:54:27: warning: variable 'alignChosen' set but not used [-Wunused-but-set-variable]
     bool colChosen=false, alignChosen=false;
                           ^~~~~~~~~~~
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o MotIV.dll tmp.def Alignment.o ColumnComp.o DeclareAll.o Motif.o MotifDistances.o MotifMatch.o PlatformSupport.o RandPSSMGen.o generateScoresDB.o -lws2_32 -L/i386/lib -lgsl -lgslcblas -lm -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/MotIV.buildbin-libdir/00LOCK-MotIV/00new/MotIV/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'filter' in package 'MotIV'
** help
*** installing help indices
  converting help for package 'MotIV'
    finding HTML links ... done
    FOXA_rGADEM                             html  
    aligns-class                            html  
    as.data.frame                           html  
    combineMotifs                           html  
    exportAsGRanges                         html  
    exportAsRangedData                      html  
    exportAsTransfacFile                    html  
    filter-class                            html  
    filter-methods                          html  
    filter                                  html  
    generateDBScores                        html  
    getGademPWM                             html  
    getPWM                                  html  
    jaspar                                  html  
    makePWM                                 html  
    matches-class                           html  
    motifDistance                           html  
    motifMatch                              html  
    motifOccurences                         html  
    motiv-class                             html  
    motiv-methods                           html  
    plot                                    html  
    readGademPWMFile                        html  
    readPWMfile                             html  
    seqLogo2                                html  
    setFilter                               html  
    split                                   html  
    tf-class                                html  
    trimPWMedge                             html  
    viewAlignment                           html  
    viewMotifs                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'MotIV' is deprecated and will be removed from Bioconductor
  version 3.13
** testing if installed package can be loaded from final location
Warning: Package 'MotIV' is deprecated and will be removed from Bioconductor
  version 3.13
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'MotIV' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c Alignment.cpp -o Alignment.o
Alignment.cpp: In member function 'double Alignment::AlignMotifs2D(Motif*, Motif*, int&, int&, int&, bool&, bool&)':
Alignment.cpp:176:17: warning: unused variable 'score2' [-Wunused-variable]
  double score1, score2, bestScore=0;
                 ^~~~~~
Alignment.cpp:177:18: warning: unused variable 'i1_B' [-Wunused-variable]
  int i1_A, i2_A, i1_B, i2_B;
                  ^~~~
Alignment.cpp:177:24: warning: unused variable 'i2_B' [-Wunused-variable]
  int i1_A, i2_A, i1_B, i2_B;
                        ^~~~
Alignment.cpp:178:12: warning: unused variable 'aL_B' [-Wunused-variable]
  int aL_A, aL_B;
            ^~~~
Alignment.cpp:179:14: warning: unused variable 'for_B' [-Wunused-variable]
  bool for_A, for_B;
              ^~~~~
Alignment.cpp:184:9: warning: variable 'currOne' set but not used [-Wunused-but-set-variable]
  Motif* currOne = one;
         ^~~~~~~
Alignment.cpp:185:9: warning: unused variable 'currTwo' [-Wunused-variable]
  Motif* currTwo = two;
         ^~~~~~~
Alignment.cpp: In member function 'virtual double SmithWatermanUngappedExtended::AlignMotifs(Motif*, Motif*, int&, int&, int&, bool&)':
Alignment.cpp:423:9: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
  double tmp;
         ^~~
Alignment.cpp: In member function 'virtual double SmithWaterman::AlignMotifs(Motif*, Motif*, int&, int&, int&, bool&)':
Alignment.cpp:319:2: warning: 'revScore' may be used uninitialized in this function [-Wmaybe-uninitialized]
  if(forScore>revScore){
  ^~
Alignment.cpp:319:2: warning: 'forScore' may be used uninitialized in this function [-Wmaybe-uninitialized]
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c ColumnComp.cpp -o ColumnComp.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c DeclareAll.cpp -o DeclareAll.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c Motif.cpp -o Motif.o
Motif.cpp: In member function 'char Motif::ColConsensus(int)':
Motif.cpp:148:7: warning: variable 'three_base_l' set but not used [-Wunused-but-set-variable]
  char three_base_l[4]; //three base consensus
       ^~~~~~~~~~~~
Motif.cpp:149:9: warning: variable 'three_base_c' set but not used [-Wunused-but-set-variable]
  double three_base_c[4];
         ^~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c MotifDistances.cpp -o MotifDistances.o
MotifDistances.cpp: In function 'SEXPREC* motifDistances(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
MotifDistances.cpp:115:11: warning: deleting object of abstract class type 'ColumnComp' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor]
  delete(CC);
           ^
MotifDistances.cpp:50:10: warning: variable 'colChosen' set but not used [-Wunused-but-set-variable]
     bool colChosen=false, alignChosen=false;
          ^~~~~~~~~
MotifDistances.cpp:50:27: warning: variable 'alignChosen' set but not used [-Wunused-but-set-variable]
     bool colChosen=false, alignChosen=false;
                           ^~~~~~~~~~~
MotifDistances.cpp:51:6: warning: variable 'matchTopX' set but not used [-Wunused-but-set-variable]
  int matchTopX = TOP_MATCH;
      ^~~~~~~~~
MotifDistances.cpp:58:7: warning: variable 'ungapped' set but not used [-Wunused-but-set-variable]
  bool ungapped=false;
       ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c MotifMatch.cpp -o MotifMatch.o
MotifMatch.cpp: In function 'SEXPREC* motifMatch(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
MotifMatch.cpp:120:11: warning: deleting object of abstract class type 'ColumnComp' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor]
  delete(CC);
           ^
MotifMatch.cpp:50:10: warning: variable 'colChosen' set but not used [-Wunused-but-set-variable]
     bool colChosen=false, alignChosen=false;
          ^~~~~~~~~
MotifMatch.cpp:50:27: warning: variable 'alignChosen' set but not used [-Wunused-but-set-variable]
     bool colChosen=false, alignChosen=false;
                           ^~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c PlatformSupport.cpp -o PlatformSupport.o
PlatformSupport.cpp: In member function 'void PlatformSupport::PreAlign(Alignment*)':
PlatformSupport.cpp:412:47: warning: variable 'max_score' set but not used [-Wunused-but-set-variable]
  double curr_score, curr_z_score, curr_p_val, max_score;
                                               ^~~~~~~~~
In file included from Motif.h:39,
                 from PlatformSupport.h:41,
                 from PlatformSupport.cpp:33:
C:/Users/BIOCBU~1/BBS-3~1.12-/R/include/Rinternals.h: In member function 'int PlatformSupport::ReadTransfacFile(SEXP, SEXP)':
C:/Users/BIOCBU~1/BBS-3~1.12-/R/include/Rinternals.h:1629:29: warning: 'input' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define length(x)  Rf_length(x)
                             ^
PlatformSupport.cpp:103:18: note: 'input' was declared here
  SEXP inputName, input;
                  ^~~~~
PlatformSupport.cpp:102:10: warning: 'currMotifs' may be used uninitialized in this function [-Wmaybe-uninitialized]
  Motif** currMotifs; int currCnt;
          ^~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RandPSSMGen.cpp -o RandPSSMGen.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c generateScoresDB.cpp -o generateScoresDB.o
generateScoresDB.cpp: In function 'SEXPREC* generateScoresDB(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
generateScoresDB.cpp:127:11: warning: deleting object of abstract class type 'ColumnComp' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor]
  delete(CC);
           ^
generateScoresDB.cpp:54:10: warning: variable 'colChosen' set but not used [-Wunused-but-set-variable]
     bool colChosen=false, alignChosen=false;
          ^~~~~~~~~
generateScoresDB.cpp:54:27: warning: variable 'alignChosen' set but not used [-Wunused-but-set-variable]
     bool colChosen=false, alignChosen=false;
                           ^~~~~~~~~~~
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o MotIV.dll tmp.def Alignment.o ColumnComp.o DeclareAll.o Motif.o MotifDistances.o MotifMatch.o PlatformSupport.o RandPSSMGen.o generateScoresDB.o -lws2_32 -L/x64/lib -lgsl -lgslcblas -lm -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/MotIV.buildbin-libdir/MotIV/libs/x64
** testing if installed package can be loaded
Warning: Package 'MotIV' is deprecated and will be removed from Bioconductor
  version 3.13
* MD5 sums
packaged installation of 'MotIV' as MotIV_1.46.0.zip
* DONE (MotIV)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'MotIV' successfully unpacked and MD5 sums checked

Tests output

Example timings

MotIV.Rcheck/examples_i386/MotIV-Ex.timings

nameusersystemelapsed
FOXA_rGADEM0.310.120.44
as.data.frame0.420.050.47
combineMotifs0.470.080.54
exportAsGRanges0.930.151.10
exportAsRangedData0.540.030.56
exportAsTransfacFile0.560.000.56
filter-class000
filter-methods000
filter0.440.020.45
generateDBScores0.020.000.02
getGademPWM0.250.020.26
jaspar0.270.170.43
makePWM000
matches-class000

MotIV.Rcheck/examples_x64/MotIV-Ex.timings

nameusersystemelapsed
FOXA_rGADEM0.500.030.55
as.data.frame0.590.020.61
combineMotifs0.450.050.50
exportAsGRanges0.930.040.97
exportAsRangedData0.390.000.39
exportAsTransfacFile0.430.020.46
filter-class000
filter-methods000
filter1.440.001.43
generateDBScores0.020.000.02
getGademPWM0.290.010.31
jaspar0.430.000.42
makePWM000
matches-class000