Package: MotIV

Version: 1.38.0

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:MotIV.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings MotIV_1.38.0.tar.gz

StartedAt: 2019-04-16 01:34:37 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 01:38:17 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 220.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: MotIV.Rcheck

Warnings: 1

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:MotIV.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings MotIV_1.38.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/MotIV.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MotIV/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MotIV’ version ‘1.38.0’
* 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 ‘MotIV’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... 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’
motifDistances: no visible global function definition for ‘as.dist’
motifMatch: no visible binding for global variable ‘jaspar’
motifMatch: no visible binding for global variable ‘jaspar.scores’
plotDistanceHistogram: no visible global function definition for ‘hist’
plotDistributionHistogram: no visible global function definition for
  ‘hist’
[,motiv-ANY-ANY-ANY: no visible binding for global variable ‘ANY’
Undefined global functions or variables:
  ANY as.dist hist jaspar jaspar.scores
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "as.dist")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'motiv,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.8-bioc/R/library/MotIV/libs/MotIV.so’:
  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 ... 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: 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.8-bioc/meat/MotIV.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL MotIV
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘MotIV’ ...
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for gsl-config... /usr/bin/gsl-config
checking for GSL - version >= 1.6... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -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]
Alignment.cpp: In member function ‘virtual double NeedlemanWunsch::AlignMotifs(Motif*, Motif*, int&, int&, int&, bool&)’:
Alignment.cpp:713:2: warning: ‘forScore’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  if(forScore>revScore){
  ^
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c ColumnComp.cpp -o ColumnComp.o
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c DeclareAll.cpp -o DeclareAll.o
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -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];
         ^
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -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 behaviour [-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; 
       ^
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -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 behaviour [-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;
                           ^
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -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:41:0,
                 from PlatformSupport.h:41,
                 from PlatformSupport.cpp:33:
/home/biocbuild/bbs-3.8-bioc/R/include/Rdefines.h: In member function ‘int PlatformSupport::ReadTransfacFile(SEXP, SEXP)’:
/home/biocbuild/bbs-3.8-bioc/R/include/Rdefines.h:122:31: warning: ‘input’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define NUMERIC_DATA(x)  (REAL(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; 
          ^
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c RandPSSMGen.cpp -o RandPSSMGen.o
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -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 behaviour [-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;
                           ^
g++ -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o MotIV.so Alignment.o ColumnComp.o DeclareAll.o Motif.o MotifDistances.o MotifMatch.o PlatformSupport.o RandPSSMGen.o generateScoresDB.o -lgsl -lgslcblas -lm -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/MotIV/libs
** 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
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MotIV)

name	user	system	elapsed
FOXA_rGADEM	0.456	0.028	0.486
as.data.frame	0.532	0.020	0.571
combineMotifs	0.452	0.032	0.483
exportAsRangedData	2.088	0.048	2.139
exportAsTransfacFile	0.456	0.008	0.466
filter-class	0	0	0
filter-methods	0	0	0
filter	0.292	0.000	0.294
generateDBScores	0.012	0.000	0.010
getGademPWM	0.228	0.008	0.235
jaspar	0.468	0.012	0.480
makePWM	0	0	0
matches-class	0.000	0.000	0.001
motifDistance	0.496	0.004	0.499
motifMatch	0.496	0.004	0.499
motifOccurences	0.912	0.008	0.922
motiv-class	0.004	0.000	0.001
motiv-methods	0.000	0.000	0.001
plot	3.404	0.000	3.409
readGademPWMFile	0.168	0.000	0.168
readPWMfile	0.020	0.000	0.018
seqLogo2	0.000	0.000	0.001
setFilter	0.464	0.012	0.479
split	0.508	0.004	0.512
tf-class	0	0	0
trimPWMedge	0.280	0.000	0.281
viewAlignment	0.424	0.000	0.530
viewMotifs	0.432	0.000	0.434