Till Soerensen
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/immunoClust |
| Branch: RELEASE_3_7 |
| Last Commit: c0ecf5a |
| Last Changed Date: 2018-04-30 10:35:36 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:40:06 -0400 (Wed, 17 Oct 2018).
| Package 729/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| immunoClust 1.12.0 Till Soerensen
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: immunoClust |
| Version: 1.12.0 |
| Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:immunoClust.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings immunoClust_1.12.0.tar.gz |
| StartedAt: 2018-10-17 02:47:25 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 02:54:59 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 453.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: immunoClust.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:immunoClust.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings immunoClust_1.12.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/immunoClust.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'immunoClust/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'immunoClust' version '1.12.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'immunoClust' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/immunoClust/libs/i386/immunoClust.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
dat.fcs 73.16 0.14 73.30
cell.process 66.79 0.03 66.84
cell.SubClustering 16.77 0.03 16.80
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
dat.fcs 78.70 0.11 78.84
cell.process 68.14 0.04 68.22
cell.SubClustering 19.10 0.00 19.09
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.7-bioc/meat/immunoClust.Rcheck/00check.log'
for details.
immunoClust.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/immunoClust_1.12.0.tar.gz && rm -rf immunoClust.buildbin-libdir && mkdir immunoClust.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=immunoClust.buildbin-libdir immunoClust_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL immunoClust_1.12.0.zip && rm immunoClust_1.12.0.tar.gz immunoClust_1.12.0.zip
###
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% 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 421k 100 421k 0 0 3083k 0 --:--:-- --:--:-- --:--:-- 3244k
install for i386
* installing *source* package 'immunoClust' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/i386/include -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c R_meta.cpp -o R_meta.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/i386/include -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c R_model.cpp -o R_model.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/i386/include -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c dist_mvn.cpp -o dist_mvn.o
dist_mvn.cpp: In member function 'int dist_mvn::hellinger(double*)':
dist_mvn.cpp:56:14: warning: variable 'det_k' set but not used [-Wunused-but-set-variable]
double det, det_k, det_l, logD;
^
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/i386/include -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c em_meta.cpp -o em_meta.o
em_meta.cpp: In member function 'double em_meta::bt_step()':
em_meta.cpp:438:10: warning: variable 'sndLike' set but not used [-Wunused-but-set-variable]
double sndLike = 0.0;
^
em_meta.cpp: In member function 'int em_meta::wt_step()':
em_meta.cpp:539:9: warning: variable 'minNk' set but not used [-Wunused-but-set-variable]
double minNk = T_sum;
^
em_meta.cpp:541:9: warning: variable 'minDelta' set but not used [-Wunused-but-set-variable]
double minDelta = FLTMAX;
^
em_meta.cpp: In member function 'int em_meta::st_step()':
em_meta.cpp:609:9: warning: variable 'minNk' set but not used [-Wunused-but-set-variable]
double minNk = T_sum;
^
em_meta.cpp:611:9: warning: variable 'minDelta' set but not used [-Wunused-but-set-variable]
double minDelta = FLTMAX;
^
em_meta.cpp: In member function 'int em_meta::final(int*, double*, int*)':
em_meta.cpp:1118:10: warning: variable 'maxLike' set but not used [-Wunused-but-set-variable]
double maxLike = 0;
^
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/i386/include -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c em_mvn.cpp -o em_mvn.o
em_mvn.cpp: In member function 'int em_gaussian::build(const int*, double*, int*)':
em_mvn.cpp:595:18: warning: unused variable 'status' [-Wunused-variable]
int i, k, p, q, status = 0;
^
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/i386/include -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c em_mvt.cpp -o em_mvt.o
em_mvt.cpp: In member function 'int em_mvt::t_step()':
em_mvt.cpp:522:9: warning: variable 'minNk' set but not used [-Wunused-but-set-variable]
double minNk = T_sum;
^
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/i386/include -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c hc_meta.cpp -o hc_meta.o
hc_meta.cpp: In member function 'int mvn_dendro::mahalanobis_w(int*, int*, double*)':
hc_meta.cpp:814:16: warning: variable 'S_i' set but not used [-Wunused-but-set-variable]
const double *S_i, *S_j;
^
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/i386/include -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c hc_mvn.cpp -o hc_mvn.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/i386/include -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c immunoClust.c -o immunoClust.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/i386/include -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c meta_gpa.cpp -o meta_gpa.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/i386/include -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c meta_norm.cpp -o meta_norm.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/i386/include -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c meta_scale.cpp -o meta_scale.o
meta_scale.cpp: In member function 'void meta_scale::quantile()':
meta_scale.cpp:846:10: warning: variable 'w' set but not used [-Wunused-but-set-variable]
double *w, *m, *s;
^
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/i386/include -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c normalize.cpp -o normalize.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/i386/include -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c sub_mvn.cpp -o sub_mvn.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/i386/include -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c util.cpp -o util.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/i386/include -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c vs_htrans.cpp -o vs_htrans.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o immunoClust.dll tmp.def R_meta.o R_model.o dist_mvn.o em_meta.o em_mvn.o em_mvt.o hc_meta.o hc_mvn.o immunoClust.o meta_gpa.o meta_norm.o meta_scale.o normalize.o sub_mvn.o util.o vs_htrans.o -L/i386/lib -lgsl -lgslcblas -lm -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/immunoClust.buildbin-libdir/immunoClust/libs/i386
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'immunoClust'
finding HTML links ... done
cell.ClustData html
cell.EM html
cell.FitModel html
cell.ME html
cell.SubClustering html
cell.hclust html
cell.process html
cell.removed html
dat.exp html
dat.fcs html
dat.meta html
immunoClust-package html
immunoClust.object html
meta.ME html
meta.SubClustering html
meta.clustering html
meta.export html
meta.exprs html
meta.hclust html
meta.normalize html
meta.plot html
meta.process html
meta.regnorm html
plot.immunoClust html
splom.immunoClust html
trans.ApplyToData html
trans.FitToData html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'immunoClust' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c R_meta.cpp -o R_meta.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c R_model.cpp -o R_model.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c dist_mvn.cpp -o dist_mvn.o
dist_mvn.cpp: In member function 'int dist_mvn::hellinger(double*)':
dist_mvn.cpp:56:14: warning: variable 'det_k' set but not used [-Wunused-but-set-variable]
double det, det_k, det_l, logD;
^
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c em_meta.cpp -o em_meta.o
em_meta.cpp: In member function 'double em_meta::bt_step()':
em_meta.cpp:438:10: warning: variable 'sndLike' set but not used [-Wunused-but-set-variable]
double sndLike = 0.0;
^
em_meta.cpp: In member function 'int em_meta::wt_step()':
em_meta.cpp:539:9: warning: variable 'minNk' set but not used [-Wunused-but-set-variable]
double minNk = T_sum;
^
em_meta.cpp:541:9: warning: variable 'minDelta' set but not used [-Wunused-but-set-variable]
double minDelta = FLTMAX;
^
em_meta.cpp: In member function 'int em_meta::st_step()':
em_meta.cpp:609:9: warning: variable 'minNk' set but not used [-Wunused-but-set-variable]
double minNk = T_sum;
^
em_meta.cpp:611:9: warning: variable 'minDelta' set but not used [-Wunused-but-set-variable]
double minDelta = FLTMAX;
^
em_meta.cpp: In member function 'int em_meta::final(int*, double*, int*)':
em_meta.cpp:1118:10: warning: variable 'maxLike' set but not used [-Wunused-but-set-variable]
double maxLike = 0;
^
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c em_mvn.cpp -o em_mvn.o
em_mvn.cpp: In member function 'int em_gaussian::build(const int*, double*, int*)':
em_mvn.cpp:595:18: warning: unused variable 'status' [-Wunused-variable]
int i, k, p, q, status = 0;
^
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c em_mvt.cpp -o em_mvt.o
em_mvt.cpp: In member function 'int em_mvt::t_step()':
em_mvt.cpp:522:9: warning: variable 'minNk' set but not used [-Wunused-but-set-variable]
double minNk = T_sum;
^
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c hc_meta.cpp -o hc_meta.o
hc_meta.cpp: In member function 'int mvn_dendro::mahalanobis_w(int*, int*, double*)':
hc_meta.cpp:814:16: warning: variable 'S_i' set but not used [-Wunused-but-set-variable]
const double *S_i, *S_j;
^
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c hc_mvn.cpp -o hc_mvn.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c immunoClust.c -o immunoClust.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c meta_gpa.cpp -o meta_gpa.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c meta_norm.cpp -o meta_norm.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c meta_scale.cpp -o meta_scale.o
meta_scale.cpp: In member function 'void meta_scale::quantile()':
meta_scale.cpp:846:10: warning: variable 'w' set but not used [-Wunused-but-set-variable]
double *w, *m, *s;
^
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c normalize.cpp -o normalize.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c sub_mvn.cpp -o sub_mvn.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c util.cpp -o util.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c vs_htrans.cpp -o vs_htrans.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o immunoClust.dll tmp.def R_meta.o R_model.o dist_mvn.o em_meta.o em_mvn.o em_mvt.o hc_meta.o hc_mvn.o immunoClust.o meta_gpa.o meta_norm.o meta_scale.o normalize.o sub_mvn.o util.o vs_htrans.o -L/x64/lib -lgsl -lgslcblas -lm -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/immunoClust.buildbin-libdir/immunoClust/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'immunoClust' as immunoClust_1.12.0.zip
* DONE (immunoClust)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'immunoClust' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
immunoClust.Rcheck/examples_i386/immunoClust-Ex.timings
|
immunoClust.Rcheck/examples_x64/immunoClust-Ex.timings
|