Anusha Nagari
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/groHMM |
| Branch: RELEASE_3_9 |
| Last Commit: 991c027 |
| Last Changed Date: 2019-05-02 11:53:50 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:31:40 -0400 (Wed, 16 Oct 2019).
| Package 720/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| groHMM 1.18.0 Anusha Nagari
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: groHMM |
| Version: 1.18.0 |
| Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/groHMM_1.18.0.tar.gz && rm -rf groHMM.buildbin-libdir && mkdir groHMM.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=groHMM.buildbin-libdir groHMM_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL groHMM_1.18.0.zip && rm groHMM_1.18.0.tar.gz groHMM_1.18.0.zip |
| StartedAt: 2019-10-15 20:21:35 -0400 (Tue, 15 Oct 2019) |
| EndedAt: 2019-10-15 20:23:00 -0400 (Tue, 15 Oct 2019) |
| EllapsedTime: 84.9 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/groHMM_1.18.0.tar.gz && rm -rf groHMM.buildbin-libdir && mkdir groHMM.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=groHMM.buildbin-libdir groHMM_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL groHMM_1.18.0.zip && rm groHMM_1.18.0.tar.gz groHMM_1.18.0.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
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100 3956k 100 3956k 0 0 35.7M 0 --:--:-- --:--:-- --:--:-- 38.2M
install for i386
* installing *source* package 'groHMM' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c AnnotateProbes.c -o AnnotateProbes.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c DecayAlgorithm.c -o DecayAlgorithm.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c MLEfit.c -o MLEfit.o
In file included from MLEfit.c:44:0:
hmmHeader.h:281:16: warning: 'MargainalizeSumLogProbOver' defined but not used [-Wunused-function]
static double MargainalizeSumLogProbOver(int state, int position,
^
hmmHeader.h:301:16: warning: 'expSum' defined but not used [-Wunused-function]
static double expSum(double *logValues, int length) {
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c RegisterRRoutines.c -o RegisterRRoutines.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c Windowing.c -o Windowing.o
Windowing.c: In function 'WindowAnalysis':
Windowing.c:147:6: warning: unused variable 'II' [-Wunused-variable]
int II = 0;
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c hmmEM.c -o hmmEM.o
In file included from hmmHeader.h:36:0,
from hmmEM.c:51:
UsefulValues.h:39:15: warning: 'VERY_LARGE_DOUBLE_VALUE' defined but not used [-Wunused-variable]
static double VERY_LARGE_DOUBLE_VALUE = 1e20;
^
In file included from hmmEM.c:51:0:
hmmHeader.h:281:16: warning: 'MargainalizeSumLogProbOver' defined but not used [-Wunused-function]
static double MargainalizeSumLogProbOver(int state, int position,
^
hmmHeader.h:301:16: warning: 'expSum' defined but not used [-Wunused-function]
static double expSum(double *logValues, int length) {
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c hmmFwBw.c -o hmmFwBw.o
In file included from hmmHeader.h:36:0,
from hmmFwBw.c:46:
UsefulValues.h:39:15: warning: 'VERY_LARGE_DOUBLE_VALUE' defined but not used [-Wunused-variable]
static double VERY_LARGE_DOUBLE_VALUE = 1e20;
^
In file included from hmmFwBw.c:46:0:
hmmHeader.h:281:16: warning: 'MargainalizeSumLogProbOver' defined but not used [-Wunused-function]
static double MargainalizeSumLogProbOver(int state, int position,
^
hmmHeader.h:301:16: warning: 'expSum' defined but not used [-Wunused-function]
static double expSum(double *logValues, int length) {
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c hmmMiscFunctions.c -o hmmMiscFunctions.o
hmmMiscFunctions.c: In function 'SStatsNormExp':
hmmMiscFunctions.c:385:10: warning: unused variable 'wi' [-Wunused-variable]
double wi, *newEx;
^
hmmMiscFunctions.c: In function 'UpdateNormExp':
hmmMiscFunctions.c:418:10: warning: unused variable 'epsilon' [-Wunused-variable]
double epsilon=0.00001;
^
In file included from hmmHeader.h:36:0,
from hmmMiscFunctions.c:44:
hmmMiscFunctions.c: At top level:
UsefulValues.h:39:15: warning: 'VERY_LARGE_DOUBLE_VALUE' defined but not used [-Wunused-variable]
static double VERY_LARGE_DOUBLE_VALUE = 1e20;
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c hmmViterbi.c -o hmmViterbi.o
In file included from hmmHeader.h:36:0,
from hmmViterbi.c:49:
UsefulValues.h:39:15: warning: 'VERY_LARGE_DOUBLE_VALUE' defined but not used [-Wunused-variable]
static double VERY_LARGE_DOUBLE_VALUE = 1e20;
^
In file included from hmmViterbi.c:49:0:
hmmHeader.h:281:16: warning: 'MargainalizeSumLogProbOver' defined but not used [-Wunused-function]
static double MargainalizeSumLogProbOver(int state, int position,
^
hmmHeader.h:301:16: warning: 'expSum' defined but not used [-Wunused-function]
static double expSum(double *logValues, int length) {
^
C:/Rtools/mingw_32/bin/gcc -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 -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/groHMM.buildbin-libdir/00LOCK-groHMM/00new/groHMM/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'groHMM'
finding HTML links ... done
RgammaMLE html
Rnorm html
Rnorm.exp html
averagePlot html
breakTranscriptsOnGenes html
combineTranscripts html
countMappableReadsInInterval html
detectTranscripts html
evaluateHMMInAnnotations html
expressedGenes html
getCores html
getTxDensity html
groHMM-package html
limitToXkb html
makeConsensusAnnotations html
metaGene html
metaGeneMatrix html
metaGene_nL html
pausingIndex html
polymeraseWave html
readBed html
runMetaGene html
tlsDeming html
tlsLoess html
tlsSvd html
windowAnalysis html
writeWiggle html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'groHMM' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c AnnotateProbes.c -o AnnotateProbes.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c DecayAlgorithm.c -o DecayAlgorithm.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c MLEfit.c -o MLEfit.o
In file included from MLEfit.c:44:0:
hmmHeader.h:281:16: warning: 'MargainalizeSumLogProbOver' defined but not used [-Wunused-function]
static double MargainalizeSumLogProbOver(int state, int position,
^
hmmHeader.h:301:16: warning: 'expSum' defined but not used [-Wunused-function]
static double expSum(double *logValues, int length) {
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c RegisterRRoutines.c -o RegisterRRoutines.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c Windowing.c -o Windowing.o
Windowing.c: In function 'WindowAnalysis':
Windowing.c:147:6: warning: unused variable 'II' [-Wunused-variable]
int II = 0;
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c hmmEM.c -o hmmEM.o
In file included from hmmHeader.h:36:0,
from hmmEM.c:51:
UsefulValues.h:39:15: warning: 'VERY_LARGE_DOUBLE_VALUE' defined but not used [-Wunused-variable]
static double VERY_LARGE_DOUBLE_VALUE = 1e20;
^
In file included from hmmEM.c:51:0:
hmmHeader.h:281:16: warning: 'MargainalizeSumLogProbOver' defined but not used [-Wunused-function]
static double MargainalizeSumLogProbOver(int state, int position,
^
hmmHeader.h:301:16: warning: 'expSum' defined but not used [-Wunused-function]
static double expSum(double *logValues, int length) {
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c hmmFwBw.c -o hmmFwBw.o
In file included from hmmHeader.h:36:0,
from hmmFwBw.c:46:
UsefulValues.h:39:15: warning: 'VERY_LARGE_DOUBLE_VALUE' defined but not used [-Wunused-variable]
static double VERY_LARGE_DOUBLE_VALUE = 1e20;
^
In file included from hmmFwBw.c:46:0:
hmmHeader.h:281:16: warning: 'MargainalizeSumLogProbOver' defined but not used [-Wunused-function]
static double MargainalizeSumLogProbOver(int state, int position,
^
hmmHeader.h:301:16: warning: 'expSum' defined but not used [-Wunused-function]
static double expSum(double *logValues, int length) {
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c hmmMiscFunctions.c -o hmmMiscFunctions.o
hmmMiscFunctions.c: In function 'SStatsNormExp':
hmmMiscFunctions.c:385:10: warning: unused variable 'wi' [-Wunused-variable]
double wi, *newEx;
^
hmmMiscFunctions.c: In function 'UpdateNormExp':
hmmMiscFunctions.c:418:10: warning: unused variable 'epsilon' [-Wunused-variable]
double epsilon=0.00001;
^
In file included from hmmHeader.h:36:0,
from hmmMiscFunctions.c:44:
hmmMiscFunctions.c: At top level:
UsefulValues.h:39:15: warning: 'VERY_LARGE_DOUBLE_VALUE' defined but not used [-Wunused-variable]
static double VERY_LARGE_DOUBLE_VALUE = 1e20;
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c hmmViterbi.c -o hmmViterbi.o
In file included from hmmHeader.h:36:0,
from hmmViterbi.c:49:
UsefulValues.h:39:15: warning: 'VERY_LARGE_DOUBLE_VALUE' defined but not used [-Wunused-variable]
static double VERY_LARGE_DOUBLE_VALUE = 1e20;
^
In file included from hmmViterbi.c:49:0:
hmmHeader.h:281:16: warning: 'MargainalizeSumLogProbOver' defined but not used [-Wunused-function]
static double MargainalizeSumLogProbOver(int state, int position,
^
hmmHeader.h:301:16: warning: 'expSum' defined but not used [-Wunused-function]
static double expSum(double *logValues, int length) {
^
C:/Rtools/mingw_64/bin/gcc -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 -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/groHMM.buildbin-libdir/groHMM/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'groHMM' as groHMM_1.18.0.zip
* DONE (groHMM)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'groHMM' successfully unpacked and MD5 sums checked