Package: MotIV

Version: 1.38.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MotIV.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MotIV_1.38.0.tar.gz

StartedAt: 2019-04-16 01:25:18 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 01:29:34 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 256.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: MotIV.Rcheck

Warnings: 2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MotIV.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MotIV_1.38.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/MotIV.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (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 ... WARNING
Found the following significant warnings:
  PlatformSupport.cpp:156:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/Users/biocbuild/bbs-3.8-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
* 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 ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/MotIV/libs/MotIV.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
  Found ‘_abort’, possibly from ‘abort’ (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 sizes of PDF files under ‘inst/doc’ ... OK
* 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: 2 WARNINGs, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/MotIV.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL MotIV
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘MotIV’ ...
checking for gcc... clang
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 clang accepts -g... yes
checking for clang option to accept ISO C89... none needed
checking for gsl-config... /usr/local/bin/gsl-config
checking for GSL - version >= 1.6... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c Alignment.cpp -o Alignment.o
Alignment.cpp:177:24: warning: unused variable 'i2_B' [-Wunused-variable]
        int i1_A, i2_A, i1_B, i2_B;
                              ^
Alignment.cpp:179:14: warning: unused variable 'for_B' [-Wunused-variable]
        bool for_A, for_B;
                    ^
Alignment.cpp:185:9: warning: unused variable 'currTwo' [-Wunused-variable]
        Motif* currTwo = two;
               ^
Alignment.cpp:178:12: warning: unused variable 'aL_B' [-Wunused-variable]
        int aL_A, aL_B; 
                  ^
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;
                        ^
6 warnings generated.
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c ColumnComp.cpp -o ColumnComp.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c DeclareAll.cpp -o DeclareAll.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c Motif.cpp -o Motif.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c MotifDistances.cpp -o MotifDistances.o
MotifDistances.cpp:115:2: warning: delete called on 'ColumnComp' that is abstract but has non-virtual destructor [-Wdelete-non-virtual-dtor]
        delete(CC);
        ^
1 warning generated.
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c MotifMatch.cpp -o MotifMatch.o
MotifMatch.cpp:120:2: warning: delete called on 'ColumnComp' that is abstract but has non-virtual destructor [-Wdelete-non-virtual-dtor]
        delete(CC);
        ^
1 warning generated.
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c PlatformSupport.cpp -o PlatformSupport.o
PlatformSupport.cpp:156:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
                currCnt=currCnt;
                ˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
PlatformSupport.cpp:112:11: warning: variable 'input' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
        else if (inputDB!=0)
                 ^˜˜˜˜˜˜˜˜˜
PlatformSupport.cpp:126:22: note: uninitialized use occurs here
        inputName=GET_NAMES(input);
                            ^˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rdefines.h:149:36: note: expanded from macro 'GET_NAMES'
#define GET_NAMES(x)            Rf_getAttrib(x, R_NamesSymbol)
                                             ^
PlatformSupport.cpp:112:7: note: remove the 'if' if its condition is always true
        else if (inputDB!=0)
             ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
PlatformSupport.cpp:103:23: note: initialize the variable 'input' to silence this warning
        SEXP inputName, input;
                             ^
                              = NULL
2 warnings generated.
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c RandPSSMGen.cpp -o RandPSSMGen.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c generateScoresDB.cpp -o generateScoresDB.o
generateScoresDB.cpp:127:2: warning: delete called on 'ColumnComp' that is abstract but has non-virtual destructor [-Wdelete-non-virtual-dtor]
        delete(CC);
        ^
1 warning generated.
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/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	0.472	0.018	0.498
as.data.frame	0.504	0.028	0.535
combineMotifs	0.485	0.049	0.536
exportAsRangedData	1.878	0.111	1.997
exportAsTransfacFile	0.422	0.007	0.432
filter-class	0.000	0.000	0.001
filter-methods	0.000	0.001	0.001
filter	0.490	0.007	0.501
generateDBScores	0.025	0.001	0.025
getGademPWM	0.233	0.005	0.238
jaspar	0.408	0.012	0.423
makePWM	0.001	0.000	0.000
matches-class	0.001	0.000	0.001
motifDistance	0.469	0.016	0.492
motifMatch	0.520	0.010	0.532
motifOccurences	1.408	0.274	1.701
motiv-class	0	0	0
motiv-methods	0.001	0.000	0.000
plot	3.239	0.147	3.431
readGademPWMFile	0.241	0.006	0.248
readPWMfile	0.024	0.000	0.025
seqLogo2	0.000	0.000	0.001
setFilter	0.491	0.009	0.505
split	0.441	0.009	0.453
tf-class	0.001	0.000	0.000
trimPWMedge	0.195	0.006	0.201
viewAlignment	0.412	0.011	0.430
viewMotifs	0.389	0.010	0.405