Michael Lawrence
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/biovizBase |
| Branch: RELEASE_3_9 |
| Last Commit: de044bf |
| Last Changed Date: 2019-05-02 11:53:30 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:25:43 -0400 (Wed, 16 Oct 2019).
| Package 172/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| biovizBase 1.32.0 Michael Lawrence
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: biovizBase |
| Version: 1.32.0 |
| Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/biovizBase_1.32.0.tar.gz && rm -rf biovizBase.buildbin-libdir && mkdir biovizBase.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=biovizBase.buildbin-libdir biovizBase_1.32.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL biovizBase_1.32.0.zip && rm biovizBase_1.32.0.tar.gz biovizBase_1.32.0.zip |
| StartedAt: 2019-10-15 20:45:00 -0400 (Tue, 15 Oct 2019) |
| EndedAt: 2019-10-15 20:46:57 -0400 (Tue, 15 Oct 2019) |
| EllapsedTime: 117.1 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/biovizBase_1.32.0.tar.gz && rm -rf biovizBase.buildbin-libdir && mkdir biovizBase.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=biovizBase.buildbin-libdir biovizBase_1.32.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL biovizBase_1.32.0.zip && rm biovizBase_1.32.0.tar.gz biovizBase_1.32.0.zip
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install for i386
* installing *source* package 'biovizBase' ...
** 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 R_init_biovizBase.c -o R_init_biovizBase.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 bin_offsets.c -o bin_offsets.o
bin_offsets.c: In function 'scan_bam_bin_offsets':
bin_offsets.c:57:15: warning: pointer targets in passing argument 1 of 'strncmp' differ in signedness [-Wpointer-sign]
if (strncmp(b, "BAI\1", 4))
^
In file included from C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include/R_ext/RS.h:34:0,
from C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include/Rdefines.h:37,
from bin_offsets.h:1,
from bin_offsets.c:3:
C:/Rtools/mingw_32/i686-w64-mingw32/include/string.h:76:15: note: expected 'const char *' but argument is of type 'Rbyte *'
int __cdecl strncmp(const char *_Str1,const char *_Str2,size_t _MaxCount);
^
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o biovizBase.dll tmp.def R_init_biovizBase.o bin_offsets.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/biovizBase.buildbin-libdir/00LOCK-biovizBase/00new/biovizBase/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'biovizBase'
finding HTML links ... done
CRC html
GCcontent html
addStepping-method html
aes-utils html
biovizBase-package html
colorBlindSafePal html
containLetters html
crc1.GeRL html
crunch-method html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4mivJT/R.INSTALL1868463b7e23/biovizBase/man/crunch-method.Rd:31: file link 'AnnotationFilter-class' in package 'AnnotationFilter' does not exist and so has been treated as a topic
darned_hg19_subset500 html
estimateCoverage-method html
flatGrl html
genesymbol html
getBioColor html
getFormalNames html
getGaps html
getIdeoGR html
getIdeogram html
getScale html
hg19Ideogram html
hg19IdeogramCyto html
ideo html
ideoCyto html
isIdeogram html
isMatchedWithModel html
isSimpleIdeogram html
labs html
maxGap-method html
mold-method html
finding level-2 HTML links ... done
pileupAsGRanges html
pileupGRangesAsVariantTable html
plotColorLegend html
scale html
showColor html
shrinkageFun-method html
splitByFacets-method html
strip_formula_dots html
subsetArgsByFormals html
transform html
transformGRangesForEvenSpace 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 'biovizBase' ...
** 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 R_init_biovizBase.c -o R_init_biovizBase.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 bin_offsets.c -o bin_offsets.o
bin_offsets.c: In function 'scan_bam_bin_offsets':
bin_offsets.c:57:15: warning: pointer targets in passing argument 1 of 'strncmp' differ in signedness [-Wpointer-sign]
if (strncmp(b, "BAI\1", 4))
^
In file included from C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include/R_ext/RS.h:34:0,
from C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include/Rdefines.h:37,
from bin_offsets.h:1,
from bin_offsets.c:3:
C:/Rtools/mingw_64/x86_64-w64-mingw32/include/string.h:76:15: note: expected 'const char *' but argument is of type 'Rbyte *'
int __cdecl strncmp(const char *_Str1,const char *_Str2,size_t _MaxCount);
^
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o biovizBase.dll tmp.def R_init_biovizBase.o bin_offsets.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/biovizBase.buildbin-libdir/biovizBase/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'biovizBase' as biovizBase_1.32.0.zip
* DONE (biovizBase)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'biovizBase' successfully unpacked and MD5 sums checked