Back to Mac ARM64 build report for BioC 3.17
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2023-10-20 09:38:12 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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

Package 1927/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SIMLR 1.26.1  (landing page)
Luca De Sano
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/SIMLR
git_branch: RELEASE_3_17
git_last_commit: 940a7aa
git_last_commit_date: 2023-05-01 20:07:50 -0400 (Mon, 01 May 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for SIMLR on kjohnson2


To the developers/maintainers of the SIMLR package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: SIMLR
Version: 1.26.1
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_1.26.1.tar.gz
StartedAt: 2023-10-19 01:30:18 -0400 (Thu, 19 Oct 2023)
EndedAt: 2023-10-19 01:38:47 -0400 (Thu, 19 Oct 2023)
EllapsedTime: 509.3 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_1.26.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/SIMLR.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SIMLR/DESCRIPTION’ ... OK
* this is package ‘SIMLR’ version ‘1.26.1’
* 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
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                    user system elapsed
SIMLR_Feature_Ranking             57.827  1.627 104.566
SIMLR                             18.038  0.789  38.935
SIMLR_Estimate_Number_of_Clusters  2.386  0.156   9.769
* 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-3.17-bioc-mac-arm64/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/4.3-arm64/Resources/library’
* installing *source* package ‘SIMLR’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c Rtsne.cpp -o Rtsne.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c package_init.c -o package_init.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c projsplx_R.c -o projsplx_R.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c sptree.cpp -o sptree.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c tsne.cpp -o tsne.o
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: could not create compact unwind for ___emutls_get_address: registers 23 and 24 not saved contiguously in frame
installing to /Library/Frameworks/R.framework/Versions/4.3-arm64/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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:  0.08812746 
Epoch: Iteration # 200  error is:  0.0610051 
Epoch: Iteration # 300  error is:  0.06053452 
Epoch: Iteration # 400  error is:  0.0601809 
Epoch: Iteration # 500  error is:  0.05990576 
Epoch: Iteration # 600  error is:  0.05968556 
Epoch: Iteration # 700  error is:  0.05950308 
Epoch: Iteration # 800  error is:  0.05934516 
Epoch: Iteration # 900  error is:  0.05921187 
Epoch: Iteration # 1000  error is:  0.05909402 
Performing Kmeans.
Performing t-SNE.
Epoch: Iteration # 100  error is:  11.49566 
Epoch: Iteration # 200  error is:  0.9850059 
Epoch: Iteration # 300  error is:  0.6186328 
Epoch: Iteration # 400  error is:  0.4911176 
Epoch: Iteration # 500  error is:  0.3669238 
Epoch: Iteration # 600  error is:  0.329277 
Epoch: Iteration # 700  error is:  0.293753 
Epoch: Iteration # 800  error is:  0.2851944 
Epoch: Iteration # 900  error is:  0.2736433 
Epoch: Iteration # 1000  error is:  0.185667 
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:  0.08216232 
Epoch: Iteration # 200  error is:  0.07563201 
Epoch: Iteration # 300  error is:  0.06893776 
Epoch: Iteration # 400  error is:  0.06755836 
Epoch: Iteration # 500  error is:  0.0673405 
Epoch: Iteration # 600  error is:  0.06716571 
Epoch: Iteration # 700  error is:  0.06702459 
Epoch: Iteration # 800  error is:  0.06690541 
Epoch: Iteration # 900  error is:  0.06680621 
Epoch: Iteration # 1000  error is:  0.0667205 
Performing Kmeans.
Performing t-SNE.
Epoch: Iteration # 100  error is:  11.69876 
Epoch: Iteration # 200  error is:  0.9928375 
Epoch: Iteration # 300  error is:  0.7613085 
Epoch: Iteration # 400  error is:  0.6077821 
Epoch: Iteration # 500  error is:  0.450706 
Epoch: Iteration # 600  error is:  0.4413018 
Epoch: Iteration # 700  error is:  0.436055 
Epoch: Iteration # 800  error is:  0.7656463 
Epoch: Iteration # 900  error is:  0.5678758 
Epoch: Iteration # 1000  error is:  0.5802756 
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:  0.1302889 
Epoch: Iteration # 200  error is:  0.08471752 
Epoch: Iteration # 300  error is:  0.05825463 
Epoch: Iteration # 400  error is:  0.05817764 
Epoch: Iteration # 500  error is:  0.05813089 
Epoch: Iteration # 600  error is:  0.05808742 
Epoch: Iteration # 700  error is:  0.05804713 
Epoch: Iteration # 800  error is:  0.05800894 
Epoch: Iteration # 900  error is:  0.05797385 
Epoch: Iteration # 1000  error is:  0.05794067 
Performing Kmeans.
Performing t-SNE.
Epoch: Iteration # 100  error is:  11.13476 
Epoch: Iteration # 200  error is:  0.7171618 
Epoch: Iteration # 300  error is:  0.5494215 
Epoch: Iteration # 400  error is:  0.5471795 
Epoch: Iteration # 500  error is:  0.4257836 
Epoch: Iteration # 600  error is:  0.3958304 
Epoch: Iteration # 700  error is:  0.4413581 
Epoch: Iteration # 800  error is:  0.3157737 
Epoch: Iteration # 900  error is:  0.30365 
Epoch: Iteration # 1000  error is:  0.2929148 
1 
2 
3 
4 
5 
6 
7 
8 
9 
10 
11 
12 
13 
14 
15 
16 
17 
18 
19 
20 
21 
22 
23 
24 
25 
26 
27 
28 
29 
30 
31 
32 
33 
34 
35 
36 
37 
38 
39 
40 
41 
42 
43 
44 
45 
46 
47 
48 
49 
50 
51 
52 
53 
54 
55 
56 
57 
58 
59 
60 
61 
62 
63 
64 
65 
66 
67 
68 
69 
70 
71 
72 
73 
74 
75 
76 
77 
78 
79 
80 
81 
82 
83 
84 
85 
86 
87 
88 
89 
90 
91 
92 
93 
94 
95 
96 
97 
98 
99 
100 
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 4 ]

[ FAIL 0 | WARN 3 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
116.275   3.967 227.631 

Example timings

SIMLR.Rcheck/SIMLR-Ex.timings

nameusersystemelapsed
SIMLR18.038 0.78938.935
SIMLR_Estimate_Number_of_Clusters2.3860.1569.769
SIMLR_Feature_Ranking 57.827 1.627104.566
SIMLR_Large_Scale0.0400.0040.064