Julius Muller
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/TransView |
| Branch: RELEASE_3_10 |
| Last Commit: 8f39927 |
| Last Changed Date: 2019-10-29 13:08:35 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:21:03 -0400 (Wed, 15 Apr 2020).
| Package 1748/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| TransView 1.30.0 Julius Muller
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | WARNINGS | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: TransView |
| Version: 1.30.0 |
| Command: C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/TransView_1.30.0.tar.gz && rm -rf TransView.buildbin-libdir && mkdir TransView.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TransView.buildbin-libdir TransView_1.30.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL TransView_1.30.0.zip && rm TransView_1.30.0.tar.gz TransView_1.30.0.zip |
| StartedAt: 2020-04-14 19:29:51 -0400 (Tue, 14 Apr 2020) |
| EndedAt: 2020-04-14 19:31:07 -0400 (Tue, 14 Apr 2020) |
| EllapsedTime: 75.6 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/TransView_1.30.0.tar.gz && rm -rf TransView.buildbin-libdir && mkdir TransView.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TransView.buildbin-libdir TransView_1.30.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL TransView_1.30.0.zip && rm TransView_1.30.0.tar.gz TransView_1.30.0.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
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install for i386
* installing *source* package 'TransView' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c R_init_TransView.c -o R_init_TransView.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c bam_plbuf.c -o bam_plbuf.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c bin_density.c -o bin_density.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c construct_dc.c -o construct_dc.o
In file included from C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include/htslib/hts.h:35:0,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include/htslib/sam.h:31,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include/sam.h:28,
from parse_sam.h:4,
from construct_dc.c:23:
C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include/htslib/hts_log.h:72:1: warning: 'Rprintf' is an unrecognized format function type [-Wformat=]
HTS_FORMAT(printf, 3, 4);
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c parse_sam.c -o parse_sam.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c sam.c -o sam.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c slice_dc.c -o slice_dc.o
slice_dc.c: In function 'slice_dc':
slice_dc.c:179:5: warning: 'slicep' may be used uninitialized in this function [-Wmaybe-uninitialized]
shrink(slicep,new_vecp,rebuildc,wsize,summarizep);
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c visuals.c -o visuals.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o TransView.dll tmp.def R_init_TransView.o bam_plbuf.o bin_density.o construct_dc.o parse_sam.o sam.o slice_dc.o visuals.o C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/usrlib/i386/libhts.a -LC:/extsoft/lib/i386 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -lidn -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/TransView.buildbin-libdir/00LOCK-TransView/00new/TransView/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'TransView'
finding HTML links ... done
DensityContainer-class html
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpMP2iqM/R.INSTALL156c6f4331f/TransView/man/DensityContainer-class.Rd:137: file link 'slice1-methods' in package 'TransView' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpMP2iqM/R.INSTALL156c6f4331f/TransView/man/DensityContainer-class.Rd:138: file link 'sliceN-methods' in package 'TransView' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpMP2iqM/R.INSTALL156c6f4331f/TransView/man/DensityContainer-class.Rd:140: file link 'rmTV-methods' in package 'TransView' does not exist and so has been treated as a topic
TVResults-class html
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpMP2iqM/R.INSTALL156c6f4331f/TransView/man/TVResults-class.Rd:57: file link 'plotTVData-methods' in package 'TransView' does not exist and so has been treated as a topic
TransView-package html
annotatePeaks html
finding level-2 HTML links ... done
gtf2gr html
histogram-methods html
macs2gr html
meltPeak html
parseReads html
peak2tss html
plotTV html
plotTVData html
rmTV html
slice1 html
slice1T html
tvStats-methods 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 'TransView' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c R_init_TransView.c -o R_init_TransView.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c bam_plbuf.c -o bam_plbuf.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c bin_density.c -o bin_density.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c construct_dc.c -o construct_dc.o
In file included from C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include/htslib/hts.h:35:0,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include/htslib/sam.h:31,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include/sam.h:28,
from parse_sam.h:4,
from construct_dc.c:23:
C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include/htslib/hts_log.h:72:1: warning: 'Rprintf' is an unrecognized format function type [-Wformat=]
HTS_FORMAT(printf, 3, 4);
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c parse_sam.c -o parse_sam.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c sam.c -o sam.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c slice_dc.c -o slice_dc.o
slice_dc.c: In function 'slice_dc':
slice_dc.c:179:5: warning: 'slicep' may be used uninitialized in this function [-Wmaybe-uninitialized]
shrink(slicep,new_vecp,rebuildc,wsize,summarizep);
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c visuals.c -o visuals.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o TransView.dll tmp.def R_init_TransView.o bam_plbuf.o bin_density.o construct_dc.o parse_sam.o sam.o slice_dc.o visuals.o C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -LC:/extsoft/lib/x64 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/TransView.buildbin-libdir/TransView/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TransView' as TransView_1.30.0.zip
* DONE (TransView)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'TransView' successfully unpacked and MD5 sums checked