groHMM 1.3.1
Anusha Nagari, W. Lee Kraus
| Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/groHMM | | Last Changed Rev: 106614 / Revision: 109384 | | Last Changed Date: 2015-07-21 07:39:34 -0700 (Tue, 21 Jul 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ OK ] | OK | |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### rm -rf groHMM.buildbin-libdir groHMM.Rcheck && mkdir groHMM.buildbin-libdir groHMM.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=groHMM.buildbin-libdir groHMM_1.3.1.tar.gz >groHMM.Rcheck\00install.out 2>&1 && cp groHMM.Rcheck\00install.out groHMM-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=groHMM.buildbin-libdir --install="check:groHMM-install.out" --force-multiarch --no-vignettes --timings groHMM_1.3.1.tar.gz
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* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/groHMM.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'groHMM/DESCRIPTION' ... OK
* this is package 'groHMM' version '1.3.1'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'MASS' 'S4Vectors' 'IRanges' 'GenomicRanges' 'GenomicAlignments'
'rtracklayer' 'parallel'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'groHMM' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
It is recommended to use 'given' instead of 'middle'.
It is recommended to use 'given' instead of 'middle'.
Authors@R field gives more than one person with maintainer role:
Minho Chae <minho.chae@gmail.com> [aut, cre]
W Lee Kraus <lee.kraus@utsouthwestern.edu> [aut, cre]
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: 'S4Vectors'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
combineTranscripts: no visible global function definition for 'Rle'
combineTranscripts: no visible global function definition for
'seqlevels<-'
combineTranscripts: no visible global function definition for
'seqlevels'
detectTranscripts: no visible global function definition for 'Rle'
getLIValues: no visible global function definition for 'Rle'
getTxDensity : <anonymous>: no visible global function definition for
'Rle'
metaGene: no visible global function definition for 'seqlevels<-'
metaGene: no visible global function definition for 'seqlevels'
metaGene: no visible global function definition for 'Rle'
metaGene_foreachChrom: no visible global function definition for 'Rle'
readBed: no visible global function definition for 'Rle'
samplingMetaGene : <anonymous>: no visible global function definition
for 'Rle'
samplingMetaGene: no visible global function definition for 'Rle'
windowAnalysis : <anonymous>: no visible global function definition for
'seqlevels<-'
windowAnalysis : <anonymous>: no visible global function definition for
'Rle'
* 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 line endings in C/C++/Fortran sources/headers ... 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 'E:/biocbld/bbs-3.1-bioc/meat/groHMM.buildbin-libdir/groHMM/libs/i386/groHMM.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'E:/biocbld/bbs-3.1-bioc/meat/groHMM.buildbin-libdir/groHMM/libs/x64/groHMM.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
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.
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [12s] OK
** running examples for arch 'x64' ... [12s] 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: 5 NOTEs
See
'E:/biocbld/bbs-3.1-bioc/meat/groHMM.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'groHMM' ...
It is recommended to use 'given' instead of 'middle'.
It is recommended to use 'given' instead of 'middle'.
** libs
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c AnnotateProbes.c -o AnnotateProbes.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c DecayAlgorithm.c -o DecayAlgorithm.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c MLEfit.c -o MLEfit.o
hmmHeader.h:281:16: warning: 'MargainalizeSumLogProbOver' defined but not used [-Wunused-function]
hmmHeader.h:301:16: warning: 'expSum' defined but not used [-Wunused-function]
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c RegisterRRoutines.c -o RegisterRRoutines.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c Windowing.c -o Windowing.o
Windowing.c: In function 'WindowAnalysis':
Windowing.c:147:6: warning: unused variable 'II' [-Wunused-variable]
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c hmmEM.c -o hmmEM.o
UsefulValues.h:39:15: warning: 'VERY_LARGE_DOUBLE_VALUE' defined but not used [-Wunused-variable]
hmmHeader.h:281:16: warning: 'MargainalizeSumLogProbOver' defined but not used [-Wunused-function]
hmmHeader.h:301:16: warning: 'expSum' defined but not used [-Wunused-function]
hmmEM.c: In function 'getEMReturnRTypes':
hmmEM.c:191:33: warning: 'posteriors' may be used uninitialized in this function [-Wuninitialized]
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c hmmFwBw.c -o hmmFwBw.o
UsefulValues.h:39:15: warning: 'VERY_LARGE_DOUBLE_VALUE' defined but not used [-Wunused-variable]
hmmHeader.h:281:16: warning: 'MargainalizeSumLogProbOver' defined but not used [-Wunused-function]
hmmHeader.h:301:16: warning: 'expSum' defined but not used [-Wunused-function]
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c hmmMiscFunctions.c -o hmmMiscFunctions.o
hmmMiscFunctions.c: In function 'SStatsNormExp':
hmmMiscFunctions.c:385:10: warning: unused variable 'wi' [-Wunused-variable]
hmmMiscFunctions.c: In function 'UpdateNormExp':
hmmMiscFunctions.c:418:10: warning: unused variable 'epsilon' [-Wunused-variable]
hmmMiscFunctions.c: At top level:
UsefulValues.h:39:15: warning: 'VERY_LARGE_DOUBLE_VALUE' defined but not used [-Wunused-variable]
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c hmmViterbi.c -o hmmViterbi.o
UsefulValues.h:39:15: warning: 'VERY_LARGE_DOUBLE_VALUE' defined but not used [-Wunused-variable]
hmmHeader.h:281:16: warning: 'MargainalizeSumLogProbOver' defined but not used [-Wunused-function]
hmmHeader.h:301:16: warning: 'expSum' defined but not used [-Wunused-function]
gcc -m32 -shared -s -static-libgcc -o groHMM.dll tmp.def AnnotateProbes.o DecayAlgorithm.o MLEfit.o RegisterRRoutines.o Windowing.o hmmEM.o hmmFwBw.o hmmMiscFunctions.o hmmViterbi.o -Ld:/RCompile/r-compiling/local/local320/lib/i386 -Ld:/RCompile/r-compiling/local/local320/lib -LE:/biocbld/BBS-3˜1.1-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-3.1-bioc/meat/groHMM.buildbin-libdir/groHMM/libs/i386
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
install for x64
* installing *source* package 'groHMM' ...
** libs
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c AnnotateProbes.c -o AnnotateProbes.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c DecayAlgorithm.c -o DecayAlgorithm.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c MLEfit.c -o MLEfit.o
hmmHeader.h:281:16: warning: 'MargainalizeSumLogProbOver' defined but not used [-Wunused-function]
hmmHeader.h:301:16: warning: 'expSum' defined but not used [-Wunused-function]
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c RegisterRRoutines.c -o RegisterRRoutines.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c Windowing.c -o Windowing.o
Windowing.c: In function 'WindowAnalysis':
Windowing.c:147:6: warning: unused variable 'II' [-Wunused-variable]
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c hmmEM.c -o hmmEM.o
UsefulValues.h:39:15: warning: 'VERY_LARGE_DOUBLE_VALUE' defined but not used [-Wunused-variable]
hmmHeader.h:281:16: warning: 'MargainalizeSumLogProbOver' defined but not used [-Wunused-function]
hmmHeader.h:301:16: warning: 'expSum' defined but not used [-Wunused-function]
hmmEM.c: In function 'getEMReturnRTypes':
hmmEM.c:191:33: warning: 'posteriors' may be used uninitialized in this function [-Wuninitialized]
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c hmmFwBw.c -o hmmFwBw.o
UsefulValues.h:39:15: warning: 'VERY_LARGE_DOUBLE_VALUE' defined but not used [-Wunused-variable]
hmmHeader.h:281:16: warning: 'MargainalizeSumLogProbOver' defined but not used [-Wunused-function]
hmmHeader.h:301:16: warning: 'expSum' defined but not used [-Wunused-function]
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c hmmMiscFunctions.c -o hmmMiscFunctions.o
hmmMiscFunctions.c: In function 'SStatsNormExp':
hmmMiscFunctions.c:385:10: warning: unused variable 'wi' [-Wunused-variable]
hmmMiscFunctions.c: In function 'UpdateNormExp':
hmmMiscFunctions.c:418:10: warning: unused variable 'epsilon' [-Wunused-variable]
hmmMiscFunctions.c: At top level:
UsefulValues.h:39:15: warning: 'VERY_LARGE_DOUBLE_VALUE' defined but not used [-Wunused-variable]
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c hmmViterbi.c -o hmmViterbi.o
UsefulValues.h:39:15: warning: 'VERY_LARGE_DOUBLE_VALUE' defined but not used [-Wunused-variable]
hmmHeader.h:281:16: warning: 'MargainalizeSumLogProbOver' defined but not used [-Wunused-function]
hmmHeader.h:301:16: warning: 'expSum' defined but not used [-Wunused-function]
gcc -m64 -shared -s -static-libgcc -o groHMM.dll tmp.def AnnotateProbes.o DecayAlgorithm.o MLEfit.o RegisterRRoutines.o Windowing.o hmmEM.o hmmFwBw.o hmmMiscFunctions.o hmmViterbi.o -Ld:/RCompile/r-compiling/local/local320/lib/x64 -Ld:/RCompile/r-compiling/local/local320/lib -LE:/biocbld/BBS-3˜1.1-B/R/bin/x64 -lR
installing to E:/biocbld/bbs-3.1-bioc/meat/groHMM.buildbin-libdir/groHMM/libs/x64
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* MD5 sums
packaged installation of 'groHMM' as groHMM_1.3.1.zip
* DONE (groHMM)