Till Soerensen
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/immunoClust |
| Branch: RELEASE_3_9 |
| Last Commit: 297d6f2 |
| Last Changed Date: 2019-05-02 11:53:53 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:06:17 -0400 (Wed, 16 Oct 2019).
| Package 807/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| immunoClust 1.16.0 Till Soerensen
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: immunoClust |
| Version: 1.16.0 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:immunoClust.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings immunoClust_1.16.0.tar.gz |
| StartedAt: 2019-10-16 02:29:39 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 02:34:34 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 294.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: immunoClust.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:immunoClust.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings immunoClust_1.16.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/immunoClust.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘immunoClust/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘immunoClust’ version ‘1.16.0’
* 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 for sufficient/correct file permissions ... 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
* 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
dat.fcs 103.385 0.079 103.497
cell.process 96.405 0.032 96.448
cell.SubClustering 17.837 0.000 17.837
* 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
‘/home/biocbuild/bbs-3.9-bioc/meat/immunoClust.Rcheck/00check.log’
for details.
immunoClust.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL immunoClust
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘immunoClust’ ...
** using staged installation
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for GSL... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c R_meta.cpp -o R_meta.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c R_model.cpp -o R_model.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -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;
^~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c em_meta.cpp -o em_meta.o
em_meta.cpp: In member function ‘double em_meta::bt_step()’:
em_meta.cpp:704:10: 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:1047:9: warning: variable ‘minNk’ set but not used [-Wunused-but-set-variable]
double minNk = T_sum;
^~~~~
em_meta.cpp:1049:9: 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:1117:9: warning: variable ‘minNk’ set but not used [-Wunused-but-set-variable]
double minNk = T_sum;
^~~~~
em_meta.cpp:1119:9: warning: variable ‘minDelta’ set but not used [-Wunused-but-set-variable]
double minDelta = FLTMAX;
^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -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:721:13: warning: variable ‘maxClust’ set but not used [-Wunused-but-set-variable]
int maxClust = -1;
^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c em_mvt.cpp -o em_mvt.o
em_mvt.cpp: In member function ‘int em_mvt::t_step()’:
em_mvt.cpp:521:9: warning: variable ‘minNk’ set but not used [-Wunused-but-set-variable]
double minNk = T_sum;
^~~~~
em_mvt.cpp: In member function ‘int em_mvt::build(const int*, double*, int*)’:
em_mvt.cpp:771:13: warning: variable ‘maxClust’ set but not used [-Wunused-but-set-variable]
int maxClust = -1;
^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c em_mvt2.cpp -o em_mvt2.o
em_mvt2.cpp: In member function ‘int em_mvt2::t_step()’:
em_mvt2.cpp:508:9: warning: variable ‘minNk’ set but not used [-Wunused-but-set-variable]
double minNk = T_sum;
^~~~~
em_mvt2.cpp: In member function ‘int em_mvt2::build(const int*, double*, int*)’:
em_mvt2.cpp:805:13: warning: variable ‘maxClust’ set but not used [-Wunused-but-set-variable]
int maxClust = -1;
^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -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;
^~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c hc_mvn.cpp -o hc_mvn.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c immunoClust.c -o immunoClust.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c meta_norm.cpp -o meta_norm.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -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;
^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c normalize.cpp -o normalize.o
normalize.cpp: In member function ‘int normalize::linear_X(int, int)’:
normalize.cpp:156:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
if( L < COEFF )
^~
normalize.cpp:159:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
int k, j, p;
^~~
normalize.cpp: In member function ‘int normalize::scale_X(int, int)’:
normalize.cpp:271:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
if( L < COEFF )
^~
normalize.cpp:274:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
int k, j, p;
^~~
normalize.cpp: In member function ‘int normalize::linear_Y(int, int)’:
normalize.cpp:377:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
if( L < COEFF )
^~
normalize.cpp:380:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
int k, j, p;
^~~
normalize.cpp: In member function ‘int normalize::scale_Y(int, int)’:
normalize.cpp:459:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
if( L < COEFF )
^~
normalize.cpp:462:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
int k, j, p;
^~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c sub_mvn.cpp -o sub_mvn.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c util.cpp -o util.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c vs_htrans.cpp -o vs_htrans.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o immunoClust.so R_meta.o R_model.o dist_mvn.o em_meta.o em_mvn.o em_mvt.o em_mvt2.o hc_meta.o hc_mvn.o immunoClust.o meta_norm.o meta_scale.o normalize.o sub_mvn.o util.o vs_htrans.o -lgsl -lgslcblas -lm -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-immunoClust/00new/immunoClust/libs
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (immunoClust)
immunoClust.Rcheck/immunoClust-Ex.timings
| name | user | system | elapsed | |
| cell.ClustData | 1.437 | 0.020 | 1.479 | |
| cell.EM | 1.158 | 0.016 | 1.173 | |
| cell.FitModel | 0.926 | 0.000 | 0.927 | |
| cell.ME | 0.643 | 0.000 | 0.644 | |
| cell.SubClustering | 17.837 | 0.000 | 17.837 | |
| cell.hclust | 0.007 | 0.000 | 0.007 | |
| cell.process | 96.405 | 0.032 | 96.448 | |
| cell.removed | 0.009 | 0.004 | 0.013 | |
| dat.exp | 1.446 | 0.000 | 1.454 | |
| dat.fcs | 103.385 | 0.079 | 103.497 | |
| dat.meta | 0.004 | 0.000 | 0.003 | |
| immunoClust.object | 0.000 | 0.004 | 0.005 | |
| meta.ME | 0.015 | 0.000 | 0.016 | |
| meta.SubClustering | 0.095 | 0.000 | 0.095 | |
| meta.clustering | 0.977 | 0.000 | 0.977 | |
| meta.export | 0.922 | 0.000 | 0.922 | |
| meta.exprs | 0.008 | 0.000 | 0.008 | |
| meta.hclust | 0.003 | 0.000 | 0.003 | |
| meta.normalize | 0.002 | 0.000 | 0.002 | |
| meta.plot | 2.185 | 0.040 | 2.224 | |
| meta.process | 0.903 | 0.004 | 0.907 | |
| meta.regnorm | 0.004 | 0.000 | 0.005 | |
| plot.immunoClust | 0.716 | 0.000 | 0.716 | |
| splom.immunoClust | 0.758 | 0.004 | 0.761 | |
| trans.ApplyToData | 0.048 | 0.000 | 0.048 | |
| trans.FitToData | 0.230 | 0.000 | 0.244 | |