MotIV 1.16.0
Eloi Mercier , Raphael Gottardo
| Snapshot Date: 2013-04-30 17:01:37 -0700 (Tue, 30 Apr 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/MotIV | | Last Changed Rev: 75263 / Revision: 76155 | | Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013) |
| george2 | Linux (Ubuntu 12.04.1 LTS) / x86_64 | OK | OK | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK |
| pelham | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | [ WARNINGS ] | OK |
* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/MotIV.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'MotIV/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MotIV' version '1.16.0'
* 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 ... [24s/58s] WARNING
Found the following significant warnings:
PlatformSupport.cpp:112:11: warning: variable 'input' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
See '/Users/biocbuild/bbs-2.12-bioc/meat/MotIV.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package 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 for unstated 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
plot,motiv-ANY: no visible binding for global variable 'y'
* 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 for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [43s/57s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
plot 7.640 0.088 12.954
motifOccurences 6.732 0.130 7.882
exportAsRangedData 5.803 0.076 7.829
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK
WARNING: There was 1 warning.
NOTE: There was 1 note.
See
'/Users/biocbuild/bbs-2.12-bioc/meat/MotIV.Rcheck/00check.log'
for details.
* installing *source* package 'MotIV' ...
checking for gcc... clang
checking for C compiler default output file name... rm: a.out.dSYM: is a directory
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 -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c Alignment.cpp -o Alignment.o
Alignment.cpp:185:9: warning: unused variable 'currTwo' [-Wunused-variable]
Motif* currTwo = two;
^
Alignment.cpp:176:17: warning: unused variable 'score2' [-Wunused-variable]
double score1, score2, bestScore=0;
^
Alignment.cpp:178:12: warning: unused variable 'aL_B' [-Wunused-variable]
int aL_A, aL_B;
^
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:179:14: warning: unused variable 'for_B' [-Wunused-variable]
bool for_A, for_B;
^
Alignment.cpp:968:6: warning: implicit conversion turns floating-point number into integer: 'double' to 'bool' [-Wconversion]
if(col[b]) {
˜˜ ^˜˜˜˜˜
7 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c ColumnComp.cpp -o ColumnComp.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c DeclareAll.cpp -o DeclareAll.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c Motif.cpp -o Motif.o
Motif.cpp:188:10: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
curr = tolower(curr);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -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 -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -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 -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c PlatformSupport.cpp -o PlatformSupport.o
PlatformSupport.cpp:57:30: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
markov[j]=(double*)malloc(((int)pow(B,j))*sizeof(double));
^˜˜˜˜˜˜˜˜˜˜˜˜ ˜
PlatformSupport.cpp:58:30: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
charMap[j]=(char**)malloc(((int)pow(B,j))*sizeof(char*));
^˜˜˜˜˜˜˜˜˜˜˜˜ ˜
PlatformSupport.cpp:60:34: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
charMap[j][i]=(char*)malloc((j+1)*sizeof(char));
˜^˜ ˜
PlatformSupport.cpp:79:6: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
j=strlen(xmer);
˜^˜˜˜˜˜˜˜˜˜˜˜
PlatformSupport.cpp:156:10: warning: explicitly assigning a 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:129:33: note: expanded from macro 'GET_NAMES'
#define GET_NAMES(x) 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
PlatformSupport.cpp:314:5: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
x=REAL(inputScores)[k] ;
˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
PlatformSupport.cpp:315:5: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
y=REAL(inputScores)[k+400] ;
˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
PlatformSupport.cpp:682:7: warning: implicit conversion turns floating-point number into integer: 'double' to 'bool' [-Wconversion]
if(m->f[j][b]) {
˜˜ ^˜˜˜˜˜˜˜˜˜
9 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c RandPSSMGen.cpp -o RandPSSMGen.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -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/usr/local/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 /Users/biocbuild/bbs-2.12-bioc/meat/MotIV.Rcheck/MotIV/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for 'filter' in package 'MotIV'
Creating a generic function for 'plot' from package 'graphics' in package 'MotIV'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MotIV)