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CHECK report for SIMLR on merida2

This page was generated on 2018-10-17 08:57:11 -0400 (Wed, 17 Oct 2018).

Package 1377/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SIMLR 1.6.0
Daniele Ramazzotti
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/SIMLR
Branch: RELEASE_3_7
Last Commit: cc9b4e7
Last Changed Date: 2018-04-30 10:35:43 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: SIMLR
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SIMLR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SIMLR_1.6.0.tar.gz
StartedAt: 2018-10-17 00:06:44 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 00:15:06 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 501.8 seconds
RetCode: 0
Status:  OK 
CheckDir: SIMLR.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SIMLR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SIMLR_1.6.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/SIMLR.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SIMLR/DESCRIPTION’ ... OK
* this is package ‘SIMLR’ version ‘1.6.0’
* package encoding: UTF-8
* 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 ‘SIMLR’ 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 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                    user system elapsed
SIMLR_Feature_Ranking             79.408  0.789  80.866
SIMLR                             26.321  8.936  38.716
CIMLR                             25.315  0.509  33.969
CIMLR_Estimate_Number_of_Clusters  4.725  0.069  13.785
SIMLR_Estimate_Number_of_Clusters  3.264  0.908   6.859
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/SIMLR.Rcheck/00check.log’
for details.



Installation output

SIMLR.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL SIMLR
###
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##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘SIMLR’ ...
** libs
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c Rtsne.cpp -o Rtsne.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c projsplx_R.c -o projsplx_R.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c sptree.cpp -o sptree.o
In file included from sptree.cpp:39:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/RcppCommon.h:128:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/exceptions.h:109:53: warning: all paths through this function will call itself [-Winfinite-recursion]
    inline void warning(const std::string& message) {        // #nocov start
                                                    ^
1 warning generated.
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c tsne.cpp -o tsne.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o SIMLR.so RcppExports.o Rtsne.o projsplx_R.o sptree.o tsne.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/SIMLR/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (SIMLR)

Tests output

SIMLR.Rcheck/tests/testthat.Rout


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> Sys.setenv("R_TESTS" = "")
> 
> library(testthat)
> library(SIMLR)
> 
> test_check("SIMLR")
Computing the multiple Kernels.
Performing network diffiusion.
Iteration:  1 
Iteration:  2 
Iteration:  3 
Iteration:  4 
Iteration:  5 
Iteration:  6 
Iteration:  7 
Iteration:  8 
Iteration:  9 
Iteration:  10 
Iteration:  11 
Performing t-SNE.
Epoch: Iteration # 100  error is:  0.1140084 
Epoch: Iteration # 200  error is:  0.06181848 
Epoch: Iteration # 300  error is:  0.05932105 
Epoch: Iteration # 400  error is:  0.05923113 
Epoch: Iteration # 500  error is:  0.05914954 
Epoch: Iteration # 600  error is:  0.05907505 
Epoch: Iteration # 700  error is:  0.05900841 
Epoch: Iteration # 800  error is:  0.05894696 
Epoch: Iteration # 900  error is:  0.05889082 
Epoch: Iteration # 1000  error is:  0.0588387 
Performing Kmeans.
Performing t-SNE.
Epoch: Iteration # 100  error is:  11.42491 
Epoch: Iteration # 200  error is:  0.6193818 
Epoch: Iteration # 300  error is:  0.6806981 
Epoch: Iteration # 400  error is:  0.4335191 
Epoch: Iteration # 500  error is:  0.4304629 
Epoch: Iteration # 600  error is:  0.3758724 
Epoch: Iteration # 700  error is:  0.4344854 
Epoch: Iteration # 800  error is:  0.9234501 
Epoch: Iteration # 900  error is:  0.6881946 
Epoch: Iteration # 1000  error is:  0.4881821 
Computing the multiple Kernels.
Performing network diffiusion.
Iteration:  1 
Iteration:  2 
Iteration:  3 
Iteration:  4 
Iteration:  5 
Iteration:  6 
Iteration:  7 
Iteration:  8 
Iteration:  9 
Iteration:  10 
Iteration:  11 
Iteration:  12 
Iteration:  13 
Iteration:  14 
Iteration:  15 
Iteration:  16 
Iteration:  17 
Performing t-SNE.
Epoch: Iteration # 100  error is:  0.08442679 
Epoch: Iteration # 200  error is:  0.07563968 
Epoch: Iteration # 300  error is:  0.0686836 
Epoch: Iteration # 400  error is:  0.06687578 
Epoch: Iteration # 500  error is:  0.06663136 
Epoch: Iteration # 600  error is:  0.06645222 
Epoch: Iteration # 700  error is:  0.06630663 
Epoch: Iteration # 800  error is:  0.06618637 
Epoch: Iteration # 900  error is:  0.06608476 
Epoch: Iteration # 1000  error is:  0.0659978 
Performing Kmeans.
Performing t-SNE.
Epoch: Iteration # 100  error is:  10.51335 
Epoch: Iteration # 200  error is:  0.7638615 
Epoch: Iteration # 300  error is:  0.7096486 
Epoch: Iteration # 400  error is:  0.5608157 
Epoch: Iteration # 500  error is:  0.4867041 
Epoch: Iteration # 600  error is:  0.4818987 
Epoch: Iteration # 700  error is:  0.3927569 
Epoch: Iteration # 800  error is:  0.1924583 
Epoch: Iteration # 900  error is:  0.1454303 
Epoch: Iteration # 1000  error is:  0.1448273 
Computing the multiple Kernels.
Performing network diffiusion.
Iteration:  1 
Iteration:  2 
Iteration:  3 
Iteration:  4 
Iteration:  5 
Iteration:  6 
Iteration:  7 
Iteration:  8 
Iteration:  9 
Iteration:  10 
Iteration:  11 
Performing t-SNE.
Epoch: Iteration # 100  error is:  0.1302831 
Epoch: Iteration # 200  error is:  0.08219885 
Epoch: Iteration # 300  error is:  0.0587416 
Epoch: Iteration # 400  error is:  0.05864968 
Epoch: Iteration # 500  error is:  0.05856638 
Epoch: Iteration # 600  error is:  0.05849335 
Epoch: Iteration # 700  error is:  0.05842535 
Epoch: Iteration # 800  error is:  0.05836222 
Epoch: Iteration # 900  error is:  0.05830468 
Epoch: Iteration # 1000  error is:  0.05825144 
Performing Kmeans.
Performing t-SNE.
Epoch: Iteration # 100  error is:  10.84317 
Epoch: Iteration # 200  error is:  0.7847849 
Epoch: Iteration # 300  error is:  0.6502149 
Epoch: Iteration # 400  error is:  0.3334106 
Epoch: Iteration # 500  error is:  0.30851 
Epoch: Iteration # 600  error is:  0.2883943 
Epoch: Iteration # 700  error is:  0.2665119 
Epoch: Iteration # 800  error is:  0.1463635 
Epoch: Iteration # 900  error is:  0.1153952 
Epoch: Iteration # 1000  error is:  0.09685858 
Computing the multiple Kernels.
Performing network diffusion.
Iteration:  1 
Iteration:  2 
Iteration:  3 
Iteration:  4 
Iteration:  5 
Iteration:  6 
Iteration:  7 
Iteration:  8 
Iteration:  9 
Iteration:  10 
Iteration:  11 
Iteration:  12 
Iteration:  13 
Iteration:  14 
Iteration:  15 
Performing t-SNE.
Epoch: Iteration # 100  error is:  0.3839462 
Epoch: Iteration # 200  error is:  0.2236962 
Epoch: Iteration # 300  error is:  0.09802584 
Epoch: Iteration # 400  error is:  0.09667109 
Epoch: Iteration # 500  error is:  0.09599822 
Epoch: Iteration # 600  error is:  0.1047978 
Epoch: Iteration # 700  error is:  0.0968507 
Epoch: Iteration # 800  error is:  0.09639386 
Epoch: Iteration # 900  error is:  0.1018992 
Epoch: Iteration # 1000  error is:  0.09661557 
Performing Kmeans.
Performing t-SNE.
Epoch: Iteration # 100  error is:  21.8822 
Epoch: Iteration # 200  error is:  1.328059 
Epoch: Iteration # 300  error is:  0.9663129 
Epoch: Iteration # 400  error is:  0.7174836 
Epoch: Iteration # 500  error is:  0.7482522 
Epoch: Iteration # 600  error is:  0.5959278 
Epoch: Iteration # 700  error is:  1.67741 
Epoch: Iteration # 800  error is:  1.038892 
Epoch: Iteration # 900  error is:  3.869635 
Epoch: Iteration # 1000  error is:  1.397178 
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══ testthat results  ═══════════════════════════════════════════════════════════
OK: 8 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
208.811  33.069 263.707 

Example timings

SIMLR.Rcheck/SIMLR-Ex.timings

nameusersystemelapsed
CIMLR25.315 0.50933.969
CIMLR_Estimate_Number_of_Clusters 4.725 0.06913.785
SIMLR26.321 8.93638.716
SIMLR_Estimate_Number_of_Clusters3.2640.9086.859
SIMLR_Feature_Ranking79.408 0.78980.866
SIMLR_Large_Scale0.0440.0030.046