MotIV 1.32.0
Eloi Mercier , Raphael Gottardo
| Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/MotIV | | Last Changed Rev: 129126 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MotIV_1.32.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/MotIV.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.32.0’
* 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 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
File ‘MotIV/libs/MotIV.so’:
Found ‘_rand’, possibly from ‘rand’ (C)
Object: ‘RandPSSMGen.o’
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘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: 1 WARNING, 3 NOTEs
See
‘/Users/biocbuild/bbs-3.5-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 -Wall -g -O2 -c Alignment.cpp -o Alignment.o
Alignment.cpp:178:12: warning: unused variable 'aL_B' [-Wunused-variable]
int aL_A, aL_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:177:18: warning: unused variable 'i1_B' [-Wunused-variable]
int i1_A, i2_A, i1_B, i2_B;
^
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;
^
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 /Users/biocbuild/bbs-3.5-bioc/meat/MotIV.Rcheck/MotIV/libs
** R
** data
** inst
** preparing 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)