| Back to Multiple platform build/check report for BioC 3.11 |
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This page was generated on 2020-10-17 11:57:44 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE SANTA PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1573/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
Alex J. Cornish
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | ERROR | skipped | |||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | ERROR | skipped | skipped | |||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | ERROR | skipped | skipped |
| Package: SANTA |
| Version: 2.26.0 |
| Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/SANTA_2.26.0.tar.gz && rm -rf SANTA.buildbin-libdir && mkdir SANTA.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SANTA.buildbin-libdir SANTA_2.26.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL SANTA_2.26.0.zip && rm SANTA_2.26.0.tar.gz SANTA_2.26.0.zip |
| StartedAt: 2020-10-16 17:30:31 -0400 (Fri, 16 Oct 2020) |
| EndedAt: 2020-10-16 17:31:32 -0400 (Fri, 16 Oct 2020) |
| EllapsedTime: 61.1 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/3.11/bioc/src/contrib/SANTA_2.26.0.tar.gz && rm -rf SANTA.buildbin-libdir && mkdir SANTA.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SANTA.buildbin-libdir SANTA_2.26.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL SANTA_2.26.0.zip && rm SANTA_2.26.0.tar.gz SANTA_2.26.0.zip
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100 3759k 100 3759k 0 0 33.2M 0 --:--:-- --:--:-- --:--:-- 35.3M
install for i386
* installing *source* package 'SANTA' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c computenetK_fewzeros.c -o computenetK_fewzeros.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c computenetK_manyzeros.c -o computenetK_manyzeros.o
computenetK_manyzeros.c: In function 'computenetK_manyzeros':
computenetK_manyzeros.c:29:24: warning: assignment to 'int *' from incompatible pointer type 'char *' [-Wincompatible-pointer-types]
p_which_vw_nonzero = R_alloc(n_nonzero_vertices, sizeof(int));
^
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c computenodeAUK.c -o computenodeAUK.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c computeweights.c -o computeweights.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o SANTA.dll tmp.def computenetK_fewzeros.o computenetK_manyzeros.o computenodeAUK.o computeweights.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/SANTA.buildbin-libdir/00LOCK-SANTA/00new/SANTA/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'SANTA'
finding HTML links ... done
BinGraph html
Compactness html
CreateGrid html
DistGraph html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpIxTpeN/R.INSTALL1850676731c7/SANTA/man/DistGraph.Rd:53: file link 'shortest.paths' in package 'igraph' does not exist and so has been treated as a topic
GraphDiffusion html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpIxTpeN/R.INSTALL1850676731c7/SANTA/man/GraphDiffusion.Rd:45: file link 'shortest.paths' in package 'igraph' does not exist and so has been treated as a topic
GraphMFPT html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpIxTpeN/R.INSTALL1850676731c7/SANTA/man/GraphMFPT.Rd:46: file link 'shortest.paths' in package 'igraph' does not exist and so has been treated as a topic
Knet html
Knode html
SANTA.data html
SpreadHits html
plot.Knet html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'SANTA' is deprecated and will be removed from Bioconductor
version 3.12
** testing if installed package can be loaded from final location
Warning: Package 'SANTA' is deprecated and will be removed from Bioconductor
version 3.12
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'SANTA' ...
** libs
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c computenetK_fewzeros.c -o computenetK_fewzeros.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c computenetK_manyzeros.c -o computenetK_manyzeros.o
computenetK_manyzeros.c: In function 'computenetK_manyzeros':
computenetK_manyzeros.c:29:24: warning: assignment to 'int *' from incompatible pointer type 'char *' [-Wincompatible-pointer-types]
p_which_vw_nonzero = R_alloc(n_nonzero_vertices, sizeof(int));
^
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c computenodeAUK.c -o computenodeAUK.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c computeweights.c -o computeweights.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o SANTA.dll tmp.def computenetK_fewzeros.o computenetK_manyzeros.o computenodeAUK.o computeweights.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/SANTA.buildbin-libdir/SANTA/libs/x64
** testing if installed package can be loaded
Warning: Package 'SANTA' is deprecated and will be removed from Bioconductor
version 3.12
* MD5 sums
packaged installation of 'SANTA' as SANTA_2.26.0.zip
* DONE (SANTA)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'SANTA' successfully unpacked and MD5 sums checked