Moritz Gerstung
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/deepSNV |
| Branch: RELEASE_3_11 |
| Last Commit: 80be4e4 |
| Last Changed Date: 2020-05-15 11:41:35 -0400 (Fri, 15 May 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:56:25 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE deepSNV PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 440/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| deepSNV 1.34.1 Moritz Gerstung
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | OK | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: deepSNV |
| Version: 1.34.1 |
| Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/deepSNV_1.34.1.tar.gz && rm -rf deepSNV.buildbin-libdir && mkdir deepSNV.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=deepSNV.buildbin-libdir deepSNV_1.34.1.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL deepSNV_1.34.1.zip && rm deepSNV_1.34.1.tar.gz deepSNV_1.34.1.zip |
| StartedAt: 2020-10-16 19:16:04 -0400 (Fri, 16 Oct 2020) |
| EndedAt: 2020-10-16 19:19:37 -0400 (Fri, 16 Oct 2020) |
| EllapsedTime: 213.1 seconds |
| RetCode: 0 |
| Status: OK |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/deepSNV_1.34.1.tar.gz && rm -rf deepSNV.buildbin-libdir && mkdir deepSNV.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=deepSNV.buildbin-libdir deepSNV_1.34.1.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL deepSNV_1.34.1.zip && rm deepSNV_1.34.1.tar.gz deepSNV_1.34.1.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 1241k 100 1241k 0 0 12.1M 0 --:--:-- --:--:-- --:--:-- 12.8M
install for i386
* installing *source* package 'deepSNV' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c bam2R.cpp -o bam2R.o
bam2R.cpp: In function 'int bam2R(char**, char**, int*, int*, int*, int*, int*, int*, int*, int*, int*, int*, int*, int*)':
bam2R.cpp:97:13: warning: unused variable 'iter' [-Wunused-variable]
hts_itr_t *iter = NULL;
^~~~
bam2R.cpp:100:6: warning: unused variable 'c' [-Wunused-variable]
int c = 0;
^
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c betabinom.c -o betabinom.o
betabinom.c: In function 'pbb':
betabinom.c:27:9: warning: unused variable 'log' [-Wunused-variable]
int i, log=0;
^~~
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o deepSNV.dll tmp.def bam2R.o betabinom.o C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/deepSNV.buildbin-libdir/00LOCK-deepSNV/00new/deepSNV/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'deepSNV'
finding HTML links ... done
Extract-methods html
RCC html
RF html
bam2R html
betabinLRT html
bf2Vcf html
finding level-2 HTML links ... done
consensusSequence-methods html
control-methods html
coordinates-methods html
counts html
dbetabinom html
deepSNV-class html
deepSNV-methods html
deepSNV-package html
estimateDirichlet-methods html
estimateDispersion-methods html
estimateRho html
loadAllData html
makePrior html
manhattanPlot html
mcChunk html
normalize-methods html
p.combine html
p.val-methods html
pbetabinom html
phiX html
pi html
plot.deepSNV html
qvals2Vcf html
repeatMask-methods html
shearwater html
show-deepSNV-method html
summary-methods html
test-methods html
trueSNVs 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 'deepSNV' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c bam2R.cpp -o bam2R.o
bam2R.cpp: In function 'int bam2R(char**, char**, int*, int*, int*, int*, int*, int*, int*, int*, int*, int*, int*, int*)':
bam2R.cpp:97:13: warning: unused variable 'iter' [-Wunused-variable]
hts_itr_t *iter = NULL;
^~~~
bam2R.cpp:100:6: warning: unused variable 'c' [-Wunused-variable]
int c = 0;
^
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c betabinom.c -o betabinom.o
betabinom.c: In function 'pbb':
betabinom.c:27:9: warning: unused variable 'log' [-Wunused-variable]
int i, log=0;
^~~
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o deepSNV.dll tmp.def bam2R.o betabinom.o C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/deepSNV.buildbin-libdir/deepSNV/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'deepSNV' as deepSNV_1.34.1.zip
* DONE (deepSNV)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'deepSNV' successfully unpacked and MD5 sums checked