Back to Multiple platform build/check report for BioC 3.16:   simplified   long
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This page was generated on 2023-04-12 11:06:26 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for SIMLR on lconway


To the developers/maintainers of the SIMLR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SIMLR.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1882/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SIMLR 1.24.3  (landing page)
Luca De Sano
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/SIMLR
git_branch: RELEASE_3_16
git_last_commit: 10cd5ee
git_last_commit_date: 2023-01-23 06:14:34 -0400 (Mon, 23 Jan 2023)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: SIMLR
Version: 1.24.3
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SIMLR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SIMLR_1.24.3.tar.gz
StartedAt: 2023-04-10 22:43:23 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 22:48:01 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 278.4 seconds
RetCode: 0
Status:   OK  
CheckDir: SIMLR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SIMLR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SIMLR_1.24.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/SIMLR.Rcheck’
* using R version 4.2.3 (2023-03-15)
* 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 ‘1.24.3’
* 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             57.920  1.253  59.288
SIMLR                             15.689  3.441  21.531
SIMLR_Estimate_Number_of_Clusters  2.133  0.260   5.137
* 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-3.16-bioc/meat/SIMLR.Rcheck/00check.log’
for details.



Installation output

SIMLR.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘SIMLR’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c Rtsne.cpp -o Rtsne.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/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/4.2/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++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c sptree.cpp -o sptree.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c tsne.cpp -o tsne.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -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
ld: warning: dylib (/usr/local/gfortran/lib/libquadmath.dylib) was built for newer macOS version (10.14) than being linked (10.13)
ld: warning: dylib (/usr/local/gfortran/lib/libgfortran.dylib) was built for newer macOS version (10.14) than being linked (10.13)
installing to /Library/Frameworks/R.framework/Versions/4.2/Resources/library/00LOCK-SIMLR/00new/SIMLR/libs
** R
** data
** 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 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 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:  11.11192 
Epoch: Iteration # 200  error is:  0.7317008 
Epoch: Iteration # 300  error is:  0.6640129 
Epoch: Iteration # 400  error is:  0.4542266 
Epoch: Iteration # 500  error is:  0.3244204 
Epoch: Iteration # 600  error is:  0.2912737 
Epoch: Iteration # 700  error is:  0.2639576 
Epoch: Iteration # 800  error is:  0.1449404 
Epoch: Iteration # 900  error is:  0.09348164 
Epoch: Iteration # 1000  error is:  0.08640509 
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:  16.26358 
Epoch: Iteration # 200  error is:  1.781918 
Epoch: Iteration # 300  error is:  1.183827 
Epoch: Iteration # 400  error is:  0.8207245 
Epoch: Iteration # 500  error is:  0.5271119 
Epoch: Iteration # 600  error is:  0.564886 
Epoch: Iteration # 700  error is:  0.6756433 
Epoch: Iteration # 800  error is:  0.5294341 
Epoch: Iteration # 900  error is:  0.6613938 
Epoch: Iteration # 1000  error is:  0.5218034 
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:  11.25394 
Epoch: Iteration # 200  error is:  0.9228333 
Epoch: Iteration # 300  error is:  0.4488531 
Epoch: Iteration # 400  error is:  0.6898382 
Epoch: Iteration # 500  error is:  0.4238117 
Epoch: Iteration # 600  error is:  0.3491274 
Epoch: Iteration # 700  error is:  0.3423546 
Epoch: Iteration # 800  error is:  0.3317496 
Epoch: Iteration # 900  error is:  0.3040265 
Epoch: Iteration # 1000  error is:  0.2930517 
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[ FAIL 0 | WARN 3 | SKIP 0 | PASS 4 ]

[ FAIL 0 | WARN 3 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
105.436  13.541 127.091 

Example timings

SIMLR.Rcheck/SIMLR-Ex.timings

nameusersystemelapsed
CIMLR0.0010.0010.001
CIMLR_Estimate_Number_of_Clusters0.0000.0010.001
SIMLR15.689 3.44121.531
SIMLR_Estimate_Number_of_Clusters2.1330.2605.137
SIMLR_Feature_Ranking57.920 1.25359.288
SIMLR_Large_Scale0.0340.0020.036