Till Soerensen
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/immunoClust |
| Branch: RELEASE_3_11 |
| Last Commit: a98e9b4 |
| Last Changed Date: 2020-08-12 05:39:36 -0400 (Wed, 12 Aug 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:54:58 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE immunoClust PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 870/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| immunoClust 1.20.1 Till Soerensen
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |
| Package: immunoClust |
| Version: 1.20.1 |
| Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:immunoClust.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings immunoClust_1.20.1.tar.gz |
| StartedAt: 2020-10-17 02:20:34 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 02:24:45 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 250.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: immunoClust.Rcheck |
| Warnings: 1 |
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### Running command:
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### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:immunoClust.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings immunoClust_1.20.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/immunoClust.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.20.1’
* 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 ... OK
* 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 use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... WARNING
Found the following significant warnings:
Warning: '.local' is deprecated.
Warning: '.local' is deprecated.
Warning: '.local' is deprecated.
Warning: '.local' is deprecated.
Warning: '.local' is deprecated.
Warning: '.local' is deprecated.
Warning: '.local' is deprecated.
Warning: '.local' is deprecated.
Warning: '.local' is deprecated.
Warning: '.local' is deprecated.
Warning: '.local' is deprecated.
Warning: '.local' is deprecated.
Warning: '.local' is deprecated.
Warning: '.local' is deprecated.
Warning: '.local' is deprecated.
Warning: '.local' is deprecated.
Warning: '.local' is deprecated.
Warning: '.local' is deprecated.
Warning: '.local' is deprecated.
Warning: '.local' is deprecated.
Warning: '.local' is deprecated.
Warning: '.local' is deprecated.
Warning: '.local' is deprecated.
Warning: '.local' is deprecated.
Warning: '.local' is deprecated.
Warning: '.local' is deprecated.
Warning: '.local' is deprecated.
Warning: '.local' is deprecated.
Warning: '.local' is deprecated.
Warning: '.local' is deprecated.
Warning: '.local' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
dat.fcs 82.687 0.016 82.706
cell.process 78.448 0.012 78.477
cell.SubClustering 13.819 0.019 13.838
* 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: 1 WARNING, 1 NOTE
See
‘/home/biocbuild/bbs-3.11-bioc/meat/immunoClust.Rcheck/00check.log’
for details.
immunoClust.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL immunoClust
###
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* installing to library ‘/home/biocbuild/bbs-3.11-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-3.11-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-3.11-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-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c dist_mvn.cpp -o dist_mvn.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-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::et_step()’:
em_meta.cpp:412:16: warning: variable ‘sndLike’ set but not used [-Wunused-but-set-variable]
double sndLike = 0.0;
^~~~~~~
em_meta.cpp: In member function ‘double em_meta::fixedN_et_step()’:
em_meta.cpp:697:16: warning: variable ‘maxLike’ set but not used [-Wunused-but-set-variable]
double maxLike = 0.0;
^~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c em_meta_bc.cpp -o em_meta_bc.o
em_meta_bc.cpp: In member function ‘double em_meta::bc_et_step()’:
em_meta_bc.cpp:237:16: warning: variable ‘maxLike’ set but not used [-Wunused-but-set-variable]
double maxLike = 0.0;
^~~~~~~
em_meta_bc.cpp: In member function ‘double em_meta::bc_fixedN_et_step()’:
em_meta_bc.cpp:523:16: warning: variable ‘maxLike’ set but not used [-Wunused-but-set-variable]
double maxLike = 0.0;
^~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c em_meta_kl.cpp -o em_meta_kl.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c em_mvn.cpp -o em_mvn.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c em_mvt.cpp -o em_mvt.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c em_mvt2.cpp -o em_mvt2.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c hc_meta.cpp -o hc_meta.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-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-3.11-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-3.11-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-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c meta_scale.cpp -o meta_scale.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-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::scale_X(int, int)’:
normalize.cpp:272:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
if( L < COEFF )
^~
normalize.cpp:275:2: 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:458:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
if( L < COEFF )
^~
normalize.cpp:461:2: 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-3.11-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-3.11-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-3.11-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-3.11-bioc/R/lib -L/usr/local/lib -o immunoClust.so R_meta.o R_model.o dist_mvn.o em_meta.o em_meta_bc.o em_meta_kl.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-3.11-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.11-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 | 1.497 | 0.006 | 1.524 | |
| cell.EM | 1.276 | 0.008 | 1.283 | |
| cell.FitModel | 1.348 | 0.020 | 1.367 | |
| cell.ME | 0.907 | 0.016 | 0.927 | |
| cell.SubClustering | 13.819 | 0.019 | 13.838 | |
| cell.hclust | 0.009 | 0.000 | 0.009 | |
| cell.process | 78.448 | 0.012 | 78.477 | |
| cell.removed | 0.009 | 0.000 | 0.009 | |
| dat.exp | 0.978 | 0.000 | 0.990 | |
| dat.fcs | 82.687 | 0.016 | 82.706 | |
| dat.meta | 0.008 | 0.000 | 0.008 | |
| immunoClust.methods | 0.003 | 0.000 | 0.004 | |
| immunoClust.object | 0.005 | 0.000 | 0.005 | |
| immunoMeta.methods | 0.003 | 0.000 | 0.003 | |
| immunoMeta.object | 0.011 | 0.000 | 0.012 | |
| meta.ME | 0.008 | 0.004 | 0.012 | |
| meta.SubClustering | 0.099 | 0.003 | 0.103 | |
| meta.clustering | 1.041 | 0.000 | 1.041 | |
| meta.export | 1.45 | 0.00 | 1.45 | |
| meta.exprs | 0.011 | 0.003 | 0.015 | |
| meta.hclust | 0.002 | 0.004 | 0.006 | |
| meta.normalize | 0.004 | 0.000 | 0.004 | |
| meta.process | 1.290 | 0.000 | 1.289 | |
| meta.regnorm | 0.009 | 0.000 | 0.009 | |
| plot.immunoClust | 0.676 | 0.016 | 0.692 | |
| plot.immunoMeta | 1.915 | 0.008 | 1.923 | |
| splom.immunoClust | 1.562 | 0.012 | 1.574 | |
| trans.ApplyToData | 0.08 | 0.00 | 0.08 | |
| trans.FitToData | 0.331 | 0.000 | 0.343 | |