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CHECK report for SIMLR on merida1

This page was generated on 2021-04-17 12:11:38 -0400 (Sat, 17 Apr 2021).

To the developers/maintainers of the SIMLR package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1718/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SIMLR 1.16.0  (landing page)
Luca De Sano
Snapshot Date: 2021-04-16 14:50:12 -0400 (Fri, 16 Apr 2021)
URL: https://git.bioconductor.org/packages/SIMLR
Branch: RELEASE_3_12
Last Commit: 596a86f
Last Changed Date: 2020-10-27 11:17:59 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: SIMLR
Version: 1.16.0
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_1.16.0.tar.gz
StartedAt: 2021-04-17 04:57:50 -0400 (Sat, 17 Apr 2021)
EndedAt: 2021-04-17 05:04:24 -0400 (Sat, 17 Apr 2021)
EllapsedTime: 393.8 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_1.16.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/SIMLR.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SIMLR/DESCRIPTION’ ... OK
* this is package ‘SIMLR’ version ‘1.16.0’
* 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 use of PKG_*FLAGS in Makefiles ... 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 (user + system) or elapsed time > 5s
                                    user system elapsed
SIMLR_Feature_Ranking             82.309  0.772  83.450
SIMLR                             29.964  2.282  36.589
SIMLR_Estimate_Number_of_Clusters  4.141  0.218   8.200
* 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-3.12-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/4.0/Resources/library’
* installing *source* package ‘SIMLR’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c Rtsne.cpp -o Rtsne.o
In file included from Rtsne.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
1 warning generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c package_init.c -o package_init.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c projsplx_R.c -o projsplx_R.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c tsne.cpp -o tsne.o
In file included from tsne.cpp:39:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -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 package_init.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-darwin18/8.2.0 -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/4.0/Resources/library/00LOCK-SIMLR/00new/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 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 (SIMLR)

Tests output

SIMLR.Rcheck/tests/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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:  11.20218 
Epoch: Iteration # 200  error is:  0.5555897 
Epoch: Iteration # 300  error is:  0.5292583 
Epoch: Iteration # 400  error is:  0.40384 
Epoch: Iteration # 500  error is:  0.5284363 
Epoch: Iteration # 600  error is:  0.337583 
Epoch: Iteration # 700  error is:  0.3563421 
Epoch: Iteration # 800  error is:  0.4613971 
Epoch: Iteration # 900  error is:  1.743407 
Epoch: Iteration # 1000  error is:  0.6812633 
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:  10.97827 
Epoch: Iteration # 200  error is:  1.011418 
Epoch: Iteration # 300  error is:  0.6168815 
Epoch: Iteration # 400  error is:  0.6263375 
Epoch: Iteration # 500  error is:  0.5338757 
Epoch: Iteration # 600  error is:  0.8573144 
Epoch: Iteration # 700  error is:  0.5210665 
Epoch: Iteration # 800  error is:  0.4299121 
Epoch: Iteration # 900  error is:  0.4358417 
Epoch: Iteration # 1000  error is:  0.440438 
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:  11.0081 
Epoch: Iteration # 200  error is:  0.7196632 
Epoch: Iteration # 300  error is:  0.5967358 
Epoch: Iteration # 400  error is:  0.5066606 
Epoch: Iteration # 500  error is:  0.4202105 
Epoch: Iteration # 600  error is:  0.5101123 
Epoch: Iteration # 700  error is:  0.3509927 
Epoch: Iteration # 800  error is:  0.3169094 
Epoch: Iteration # 900  error is:  0.3062862 
Epoch: Iteration # 1000  error is:  0.2942205 
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[ FAIL 0 | WARN 3 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
162.647   7.709 181.498 

Example timings

SIMLR.Rcheck/SIMLR-Ex.timings

nameusersystemelapsed
CIMLR0.0000.0000.001
CIMLR_Estimate_Number_of_Clusters0.0000.0010.001
SIMLR29.964 2.28236.589
SIMLR_Estimate_Number_of_Clusters4.1410.2188.200
SIMLR_Feature_Ranking82.309 0.77283.450
SIMLR_Large_Scale0.1020.0130.116