Mark Robinson
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/Repitools |
| Branch: RELEASE_3_9 |
| Last Commit: c9e099c |
| Last Changed Date: 2019-05-02 11:53:26 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:25:16 -0400 (Wed, 16 Oct 2019).
| Package 1355/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Repitools 1.30.0 Mark Robinson
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: Repitools |
| Version: 1.30.0 |
| Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/Repitools_1.30.0.tar.gz && rm -rf Repitools.buildbin-libdir && mkdir Repitools.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Repitools.buildbin-libdir Repitools_1.30.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL Repitools_1.30.0.zip && rm Repitools_1.30.0.tar.gz Repitools_1.30.0.zip |
| StartedAt: 2019-10-15 20:36:56 -0400 (Tue, 15 Oct 2019) |
| EndedAt: 2019-10-15 20:39:24 -0400 (Tue, 15 Oct 2019) |
| EllapsedTime: 148.2 seconds |
| RetCode: 0 |
| Status: OK |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/Repitools_1.30.0.tar.gz && rm -rf Repitools.buildbin-libdir && mkdir Repitools.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Repitools.buildbin-libdir Repitools_1.30.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL Repitools_1.30.0.zip && rm Repitools_1.30.0.tar.gz Repitools_1.30.0.zip
###
##############################################################################
##############################################################################
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 1420k 100 1420k 0 0 15.3M 0 --:--:-- --:--:-- --:--:-- 16.7M
install for i386
* installing *source* package 'Repitools' ...
** 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" -D R_NO_REMAP -I. -O3 -Wall -std=gnu99 -mtune=generic -c const.c -o const.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -D R_NO_REMAP -I. -O3 -Wall -std=gnu99 -mtune=generic -c hyp2f1.c -o hyp2f1.o
In file included from hyp2f1.c:81:0:
./mconf.h:100:0: warning: "DOMAIN" redefined
#define DOMAIN 1 /* argument domain error */
^
In file included from C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include/Rmath.h:45:0,
from hyp2f1.c:80:
C:/Rtools/mingw_32/i686-w64-mingw32/include/math.h:29:0: note: this is the location of the previous definition
#define DOMAIN _DOMAIN
^
In file included from hyp2f1.c:81:0:
./mconf.h:101:0: warning: "SING" redefined
#define SING 2 /* argument singularity */
^
In file included from C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include/Rmath.h:45:0,
from hyp2f1.c:80:
C:/Rtools/mingw_32/i686-w64-mingw32/include/math.h:30:0: note: this is the location of the previous definition
#define SING _SING
^
In file included from hyp2f1.c:81:0:
./mconf.h:102:0: warning: "OVERFLOW" redefined
#define OVERFLOW 3 /* overflow range error */
^
In file included from C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include/Rmath.h:45:0,
from hyp2f1.c:80:
C:/Rtools/mingw_32/i686-w64-mingw32/include/math.h:31:0: note: this is the location of the previous definition
#define OVERFLOW _OVERFLOW
^
In file included from hyp2f1.c:81:0:
./mconf.h:103:0: warning: "UNDERFLOW" redefined
#define UNDERFLOW 4 /* underflow range error */
^
In file included from C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include/Rmath.h:45:0,
from hyp2f1.c:80:
C:/Rtools/mingw_32/i686-w64-mingw32/include/math.h:32:0: note: this is the location of the previous definition
#define UNDERFLOW _UNDERFLOW
^
In file included from hyp2f1.c:81:0:
./mconf.h:104:0: warning: "TLOSS" redefined
#define TLOSS 5 /* total loss of precision */
^
In file included from C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include/Rmath.h:45:0,
from hyp2f1.c:80:
C:/Rtools/mingw_32/i686-w64-mingw32/include/math.h:33:0: note: this is the location of the previous definition
#define TLOSS _TLOSS
^
In file included from hyp2f1.c:81:0:
./mconf.h:105:0: warning: "PLOSS" redefined
#define PLOSS 6 /* partial loss of precision */
^
In file included from C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include/Rmath.h:45:0,
from hyp2f1.c:80:
C:/Rtools/mingw_32/i686-w64-mingw32/include/math.h:34:0: note: this is the location of the previous definition
#define PLOSS _PLOSS
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -D R_NO_REMAP -I. -O3 -Wall -std=gnu99 -mtune=generic -c mtherr.c -o mtherr.o
In file included from mtherr.c:58:0:
./mconf.h:100:0: warning: "DOMAIN" redefined
#define DOMAIN 1 /* argument domain error */
^
In file included from C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include/R.h:58:0,
from mtherr.c:56:
C:/Rtools/mingw_32/i686-w64-mingw32/include/math.h:29:0: note: this is the location of the previous definition
#define DOMAIN _DOMAIN
^
In file included from mtherr.c:58:0:
./mconf.h:101:0: warning: "SING" redefined
#define SING 2 /* argument singularity */
^
In file included from C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include/R.h:58:0,
from mtherr.c:56:
C:/Rtools/mingw_32/i686-w64-mingw32/include/math.h:30:0: note: this is the location of the previous definition
#define SING _SING
^
In file included from mtherr.c:58:0:
./mconf.h:102:0: warning: "OVERFLOW" redefined
#define OVERFLOW 3 /* overflow range error */
^
In file included from C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include/R.h:58:0,
from mtherr.c:56:
C:/Rtools/mingw_32/i686-w64-mingw32/include/math.h:31:0: note: this is the location of the previous definition
#define OVERFLOW _OVERFLOW
^
In file included from mtherr.c:58:0:
./mconf.h:103:0: warning: "UNDERFLOW" redefined
#define UNDERFLOW 4 /* underflow range error */
^
In file included from C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include/R.h:58:0,
from mtherr.c:56:
C:/Rtools/mingw_32/i686-w64-mingw32/include/math.h:32:0: note: this is the location of the previous definition
#define UNDERFLOW _UNDERFLOW
^
In file included from mtherr.c:58:0:
./mconf.h:104:0: warning: "TLOSS" redefined
#define TLOSS 5 /* total loss of precision */
^
In file included from C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include/R.h:58:0,
from mtherr.c:56:
C:/Rtools/mingw_32/i686-w64-mingw32/include/math.h:33:0: note: this is the location of the previous definition
#define TLOSS _TLOSS
^
In file included from mtherr.c:58:0:
./mconf.h:105:0: warning: "PLOSS" redefined
#define PLOSS 6 /* partial loss of precision */
^
In file included from C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include/R.h:58:0,
from mtherr.c:56:
C:/Rtools/mingw_32/i686-w64-mingw32/include/math.h:34:0: note: this is the location of the previous definition
#define PLOSS _PLOSS
^
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o Repitools.dll tmp.def const.o hyp2f1.o mtherr.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/Repitools.buildbin-libdir/00LOCK-Repitools/00new/Repitools/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'Repitools'
finding HTML links ... done
AdjustedCopyEstimate-class html
finding level-2 HTML links ... done
AffymetrixCdfFile-class html
AffymetrixCelSet-class html
BAM2GRanges html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpsxfwWa/R.INSTALL118873b97612/Repitools/man/BAM2GRanges.Rd:27: file link 'ScanBamParam' in package 'Rsamtools' does not exist and so has been treated as a topic
BayMethList-class html
ChromaBlocks html
ChromaResults-class html
ClusteredScoresList-class html
CopyEstimate-class html
FastQC-class html
GCAdjustParams-class html
GCadjustCopy html
GCbiasPlots html
MappabilitySource-class html
QdnaData html
ScoresList-class html
abcdDNA html
absoluteCN html
annoDF2GR html
annoGR2DF html
annotationBlocksCounts html
annotationBlocksLookup html
annotationCounts html
annotationLookup html
binPlots html
blocksStats html
checkProbes html
chr21genes html
chromosomeCNplots html
clusterPlots html
cpgBoxPlots html
cpgDensityCalc html
cpgDensityPlot html
determineOffset html
empBayes html
enrichmentCalc html
enrichmentPlot html
expr html
featureBlocks html
featureScores html
findClusters html
gcContentCalc html
genQC html
genomeBlocks html
getProbePositionsDf html
getSampleOffsets html
hcRegions html
hyper html
loadPairFile html
loadSampleDirectory html
makeWindowLookupTable html
mappabilityCalc html
maskOut html
mergeReplicates html
methylEst html
multiHeatmap html
plotClusters html
plotQdnaByCN html
processNDF html
profilePlots html
regionStats html
relativeCN html
samplesList html
sequenceCalc html
setCNVOffsets html
summarizeScores html
writeWig 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 'Repitools' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -D R_NO_REMAP -I. -O2 -Wall -std=gnu99 -mtune=generic -c const.c -o const.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -D R_NO_REMAP -I. -O2 -Wall -std=gnu99 -mtune=generic -c hyp2f1.c -o hyp2f1.o
In file included from hyp2f1.c:81:0:
./mconf.h:100:0: warning: "DOMAIN" redefined
#define DOMAIN 1 /* argument domain error */
^
In file included from C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include/Rmath.h:45:0,
from hyp2f1.c:80:
C:/Rtools/mingw_64/x86_64-w64-mingw32/include/math.h:29:0: note: this is the location of the previous definition
#define DOMAIN _DOMAIN
^
In file included from hyp2f1.c:81:0:
./mconf.h:101:0: warning: "SING" redefined
#define SING 2 /* argument singularity */
^
In file included from C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include/Rmath.h:45:0,
from hyp2f1.c:80:
C:/Rtools/mingw_64/x86_64-w64-mingw32/include/math.h:30:0: note: this is the location of the previous definition
#define SING _SING
^
In file included from hyp2f1.c:81:0:
./mconf.h:102:0: warning: "OVERFLOW" redefined
#define OVERFLOW 3 /* overflow range error */
^
In file included from C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include/Rmath.h:45:0,
from hyp2f1.c:80:
C:/Rtools/mingw_64/x86_64-w64-mingw32/include/math.h:31:0: note: this is the location of the previous definition
#define OVERFLOW _OVERFLOW
^
In file included from hyp2f1.c:81:0:
./mconf.h:103:0: warning: "UNDERFLOW" redefined
#define UNDERFLOW 4 /* underflow range error */
^
In file included from C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include/Rmath.h:45:0,
from hyp2f1.c:80:
C:/Rtools/mingw_64/x86_64-w64-mingw32/include/math.h:32:0: note: this is the location of the previous definition
#define UNDERFLOW _UNDERFLOW
^
In file included from hyp2f1.c:81:0:
./mconf.h:104:0: warning: "TLOSS" redefined
#define TLOSS 5 /* total loss of precision */
^
In file included from C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include/Rmath.h:45:0,
from hyp2f1.c:80:
C:/Rtools/mingw_64/x86_64-w64-mingw32/include/math.h:33:0: note: this is the location of the previous definition
#define TLOSS _TLOSS
^
In file included from hyp2f1.c:81:0:
./mconf.h:105:0: warning: "PLOSS" redefined
#define PLOSS 6 /* partial loss of precision */
^
In file included from C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include/Rmath.h:45:0,
from hyp2f1.c:80:
C:/Rtools/mingw_64/x86_64-w64-mingw32/include/math.h:34:0: note: this is the location of the previous definition
#define PLOSS _PLOSS
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -D R_NO_REMAP -I. -O2 -Wall -std=gnu99 -mtune=generic -c mtherr.c -o mtherr.o
In file included from mtherr.c:58:0:
./mconf.h:100:0: warning: "DOMAIN" redefined
#define DOMAIN 1 /* argument domain error */
^
In file included from C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include/R.h:58:0,
from mtherr.c:56:
C:/Rtools/mingw_64/x86_64-w64-mingw32/include/math.h:29:0: note: this is the location of the previous definition
#define DOMAIN _DOMAIN
^
In file included from mtherr.c:58:0:
./mconf.h:101:0: warning: "SING" redefined
#define SING 2 /* argument singularity */
^
In file included from C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include/R.h:58:0,
from mtherr.c:56:
C:/Rtools/mingw_64/x86_64-w64-mingw32/include/math.h:30:0: note: this is the location of the previous definition
#define SING _SING
^
In file included from mtherr.c:58:0:
./mconf.h:102:0: warning: "OVERFLOW" redefined
#define OVERFLOW 3 /* overflow range error */
^
In file included from C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include/R.h:58:0,
from mtherr.c:56:
C:/Rtools/mingw_64/x86_64-w64-mingw32/include/math.h:31:0: note: this is the location of the previous definition
#define OVERFLOW _OVERFLOW
^
In file included from mtherr.c:58:0:
./mconf.h:103:0: warning: "UNDERFLOW" redefined
#define UNDERFLOW 4 /* underflow range error */
^
In file included from C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include/R.h:58:0,
from mtherr.c:56:
C:/Rtools/mingw_64/x86_64-w64-mingw32/include/math.h:32:0: note: this is the location of the previous definition
#define UNDERFLOW _UNDERFLOW
^
In file included from mtherr.c:58:0:
./mconf.h:104:0: warning: "TLOSS" redefined
#define TLOSS 5 /* total loss of precision */
^
In file included from C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include/R.h:58:0,
from mtherr.c:56:
C:/Rtools/mingw_64/x86_64-w64-mingw32/include/math.h:33:0: note: this is the location of the previous definition
#define TLOSS _TLOSS
^
In file included from mtherr.c:58:0:
./mconf.h:105:0: warning: "PLOSS" redefined
#define PLOSS 6 /* partial loss of precision */
^
In file included from C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include/R.h:58:0,
from mtherr.c:56:
C:/Rtools/mingw_64/x86_64-w64-mingw32/include/math.h:34:0: note: this is the location of the previous definition
#define PLOSS _PLOSS
^
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o Repitools.dll tmp.def const.o hyp2f1.o mtherr.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/Repitools.buildbin-libdir/Repitools/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Repitools' as Repitools_1.30.0.zip
* DONE (Repitools)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'Repitools' successfully unpacked and MD5 sums checked