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.
|
| 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) |
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | ERROR | | | |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | | |
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | ERROR | OK | | |
Summary
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
###
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* 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
###
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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
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
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MotIV.Rcheck/examples_x64/MotIV-Ex.timings
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