Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-06-11 15:41 -0400 (Tue, 11 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
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 96/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ASAFE 1.31.0 (landing page) Qian Zhang
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
To the developers/maintainers of the ASAFE package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ASAFE.git to reflect on this report. See Troubleshooting Build Report for more information. - 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. |
Package: ASAFE |
Version: 1.31.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ASAFE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ASAFE_1.31.0.tar.gz |
StartedAt: 2024-06-09 23:49:59 -0400 (Sun, 09 Jun 2024) |
EndedAt: 2024-06-09 23:50:53 -0400 (Sun, 09 Jun 2024) |
EllapsedTime: 54.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ASAFE.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ASAFE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ASAFE_1.31.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ASAFE.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * using platform: x86_64-apple-darwin20 * 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 12.7.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ASAFE/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ASAFE’ version ‘1.31.0’ * 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 ‘ASAFE’ 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 code 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 LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: OK
ASAFE.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ASAFE ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘ASAFE’ ... ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ASAFE)
ASAFE.Rcheck/tests/testthat.Rout
R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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. > # The line you need to have R CMD check work, > # and avoid some weird error I got from R CMD check. > > Sys.setenv("R_TESTS" = "") > > # The following commands model off of > # https://github.com/hadley/testthat > > library(testthat) > library(ASAFE) > > test_check("ASAFE") [1] "alleles_1 and ancestries_1 have been defined so that\n n is an 18-long vector of 1's,\n algorithm_1snp(alleles_1, ancestries_1) =\n em(n = replicate(n = 18, expr = 1), epsilon = 10^-8, iteration_cap = 1000).\n algorithm_1snp(alleles_1, ancestries_1) = " [1] 0.5 0.5 0.5 [1] "alleles are: " rs1 rs2 [1,] 0 0 [2,] 0 0 [3,] 0 0 [4,] 0 0 [5,] 0 0 [6,] 0 0 [7,] 0 0 [8,] 0 0 [9,] 0 0 [10,] 0 0 [11,] 0 0 [12,] 0 0 [13,] 0 0 [14,] 1 1 [15,] 0 0 [16,] 1 1 [17,] 0 0 [18,] 1 1 [19,] 0 0 [20,] 1 1 [21,] 0 0 [22,] 1 1 [23,] 0 0 [24,] 1 1 [25,] 1 1 [26,] 1 1 [27,] 1 1 [28,] 1 1 [29,] 1 1 [30,] 1 1 [31,] 1 1 [32,] 1 1 [33,] 1 1 [34,] 1 1 [35,] 1 1 [36,] 1 1 [1] "ancestries are: " [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] ancestries_1 0 0 0 1 0 2 1 1 1 2 2 2 ancestries_1 0 0 0 1 0 2 1 1 1 2 2 2 [,13] [,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] ancestries_1 0 0 0 1 0 2 1 1 1 2 2 ancestries_1 0 0 0 1 0 2 1 1 1 2 2 [,24] [,25] [,26] [,27] [,28] [,29] [,30] [,31] [,32] [,33] [,34] ancestries_1 2 0 0 0 1 0 2 1 1 1 2 ancestries_1 2 0 0 0 1 0 2 1 1 1 2 [,35] [,36] ancestries_1 2 2 ancestries_1 2 2 [1] "algorithm_1snp_wrapper(i = 1,\n alleles = alleles,\n ancestries = ancestries)" [1] "rs1" "0.5" "0.5" "0.5" [1] "algorithm_1snp_wrapper(i = 2,\n alleles = alleles,\n ancestries = ancestries)" [1] "rs2" "0.5" "0.5" "0.5" [1] "change_ancestry(anc = 0, error_rate = 1) should be 1 or 2" [1] 2 [1] "change_ancestry(anc = 1, error_rate = 1) should be 0 or 2" [1] 2 [1] "change_ancestry(anc = 2, error_rate = 1) should be 0 or 1" [1] 0 [1] "draw_allele_given_anc(anc = 0, freqs = c(1, 0, 0)) should return 1" [1] "draw_allele_given_anc(anc = 0, freqs = c(0, 0, 0)) should return 0" [1] "draw_allele_given_anc(anc = 1, freqs = c(0, 1, 0)) should return 1" [1] "draw_allele_given_anc(anc = 1, freqs = c(0, 0, 0)) should return 0" [1] "draw_allele_given_anc(anc = 2, freqs = c(0, 0, 1)) should return 1" [1] "draw_allele_given_anc(anc = 2, freqs = c(0, 0, 0)) should return 0" [1] "draw_allele_given_anc(anc = 3, freqs = c(0, 0, 0)) should return error" [1] "em(n = replicate(n = 18, expr = 1),\n epsilon = 10^-8, iteration_cap = 1000) = " [1] 0.5 0.5 0.5 [1] "The following should run: " [1] "n_ind = 3" [1] "n_markers = 2" [1] "ancestries_matrix = " [,1] [,2] [1,] 0 0 [2,] 0 0 [3,] 1 1 [4,] 1 1 [5,] 2 2 [6,] 2 2 [1] "get_errors_1_scenario(p0 = 1, p1 = 1, p2 = 1,\n ancestries_matrix_true = ancestries_matrix,\n ancestries_matrix_estimated = ancestries_matrix)" [,1] [,2] [1,] -3e-08 -3e-08 [2,] -3e-08 -3e-08 [3,] -3e-08 -3e-08 [1] "The following should run: " [1] "n_ind = 3" [1] "n_markers = 2" [1] "ancestries_matrix = " [,1] [,2] [1,] 0 0 [2,] 0 0 [3,] 1 1 [4,] 1 1 [5,] 2 2 [6,] 2 2 [1] "get_errors_1_scenario(p0 = 1, p1 = 1, p2 = 1,\n ancestries_matrix_true = ancestries_matrix,\n ancestries_matrix_estimated = ancestries_matrix)" [,1] [,2] [1,] -3e-08 -3e-08 [2,] -3e-08 -3e-08 [3,] -3e-08 -3e-08 [1] "get_errors_summary_stats_1_scenario(p0 = 1, p1 = 1, p2 = 1,\n ancestries_matrix_true = ancestries_matrix,\n ancestries_matrix_estimated = ancestries_matrix)\n takes mean error over snp columns, and errors across snps should be identical,\n so mean errors should be the same as a column from the output of\n the get_errors_1_scenario() call" mean_errors sd_errors [1,] -3e-08 0 [2,] -3e-08 0 [3,] -3e-08 0 [1] "Constructing an example where I know what to expect\n from this function." [1] "Say estimates are: " rsid Freq1_Anc0 Freq1_Anc1 Freq1_Anc2 [1,] 1 0.15 0.15 0.15 [2,] 2 0.36 0.36 0.36 [3,] 3 0.57 0.57 0.57 [4,] 4 0.78 0.78 0.78 [5,] 5 0.99 0.99 0.99 [1] "Say truth is: " rsid Freq1_Anc0 Freq1_Anc1 Freq1_Anc2 [1,] 1 0.1 0.1 0.1 [2,] 2 0.3 0.3 0.3 [3,] 3 0.5 0.5 0.5 [4,] 4 0.7 0.7 0.7 [5,] 5 0.9 0.9 0.9 [1] "Constructing an example where I know what to expect\n from this function." [1] "Say estimates are: " rsid Freq1_Anc0 Freq1_Anc1 Freq1_Anc2 [1,] 1 0.1 0.1 0.1 [2,] 2 0.1 0.1 0.1 [3,] 3 0.1 0.1 0.1 [4,] 4 0.9 0.9 0.9 [5,] 5 0.9 0.9 0.9 [6,] 6 0.9 0.9 0.9 [1] "Say truth is: " rsid Freq1_Anc0 Freq1_Anc1 Freq1_Anc2 [1,] 1 0.2 0.2 0.2 [2,] 2 0.2 0.2 0.2 [3,] 3 0.5 0.5 0.5 [4,] 4 0.5 0.5 0.5 [5,] 5 0.8 0.8 0.8 [6,] 6 0.8 0.8 0.8 [1] "n_ind = 3" [1] "n_markers = 2" [1] "anc_spec_freqs = " [,1] [,2] [,3] [1,] 1.0 1.0 1.0 [2,] 0.0 0.0 0.0 [3,] 0.5 0.5 0.5 [1] "ancestries_matrix = " [,1] [,2] [1,] 0 0 [2,] 0 0 [3,] 1 1 [4,] 1 1 [5,] 2 2 [6,] 2 2 [1] "get_results_error(error_rate = 0,\n anc_spec_freqs, ancestries_matrix_true) = " p0 p1 p2 Mean SD Abs_Error_Afr_Freq 1.0 1.0 1.0 -3e-08 0 Abs_Error_Eur_Freq 1.0 1.0 1.0 -3e-08 0 Abs_Error_NA_Freq 1.0 1.0 1.0 -3e-08 0 Abs_Error_Afr_Freq 0.0 0.0 0.0 3e-08 0 Abs_Error_Eur_Freq 0.0 0.0 0.0 3e-08 0 Abs_Error_NA_Freq 0.0 0.0 0.0 3e-08 0 Abs_Error_Afr_Freq 0.5 0.5 0.5 -3e-08 0 Abs_Error_Eur_Freq 0.5 0.5 0.5 0e+00 0 Abs_Error_NA_Freq 0.5 0.5 0.5 -3e-08 0 [1] "get_results_error(error_rate = 1,\n anc_spec_freqs, ancestries_matrix_true) = " p0 p1 p2 Mean SD Abs_Error_Afr_Freq 1.0 1.0 1.0 -6.000000e-08 0.000000e+00 Abs_Error_Eur_Freq 1.0 1.0 1.0 -1.750000e-08 3.535534e-09 Abs_Error_NA_Freq 1.0 1.0 1.0 -4.500000e-08 2.121320e-08 Abs_Error_Afr_Freq 0.0 0.0 0.0 6.000000e-08 0.000000e+00 Abs_Error_Eur_Freq 0.0 0.0 0.0 1.750000e-08 3.535534e-09 Abs_Error_NA_Freq 0.0 0.0 0.0 4.500000e-08 2.121320e-08 Abs_Error_Afr_Freq 0.5 0.5 0.5 2.500000e-01 3.535533e-01 Abs_Error_Eur_Freq 0.5 0.5 0.5 -2.083333e-01 6.481812e-01 Abs_Error_NA_Freq 0.5 0.5 0.5 -1.718066e-09 7.071068e-01 [1] "anc_spec_freqs = " [,1] [,2] [,3] [1,] 1.0 1.0 1.0 [2,] 0.0 0.0 0.0 [3,] 0.5 0.5 0.5 [1] "ancestries_matrix = " [,1] [,2] [1,] 0 0 [2,] 0 0 [3,] 1 1 [4,] 1 1 [5,] 2 2 [6,] 2 2 [1] "get_scenario_errors(row = 1, anc_spec_freqs = anc_spec_freqs,\n ancestries_matrix_true = ancestries_matrix,\n ancestries_matrix_estimated = ancestries_matrix)" p0 p1 p2 mean_errors sd_errors [1,] 1 1 1 -3e-08 0 [2,] 1 1 1 -3e-08 0 [3,] 1 1 1 -3e-08 0 [1] "get_scenario_errors(row = 2, anc_spec_freqs = anc_spec_freqs,\n ancestries_matrix_true = ancestries_matrix,\n ancestries_matrix_estimated = ancestries_matrix)" p0 p1 p2 mean_errors sd_errors [1,] 0 0 0 3e-08 0 [2,] 0 0 0 3e-08 0 [3,] 0 0 0 3e-08 0 [1] "get_scenario_errors(row = 3, anc_spec_freqs = anc_spec_freqs,\n ancestries_matrix_true = ancestries_matrix,\n ancestries_matrix_estimated = ancestries_matrix)" p0 p1 p2 mean_errors sd_errors [1,] 0.5 0.5 0.5 1.5e-08 2.12132e-08 [2,] 0.5 0.5 0.5 -1.5e-08 2.12132e-08 [3,] 0.5 0.5 0.5 1.5e-08 2.12132e-08 [1] "get_true_freqs_1snp(alleles_1 = c(0, 0, 1, 0, 1, 1),\n ancestries_1 = c(0, 1, 0, 2, 1, 2))\n should return [0.5, 0.5, 0.5]" [1] "sample_ancestry(0) = Should be something other than 0" [1] 2 [1] "sample_ancestry(1) = Should be something other than 1" [1] 0 [1] "sample_ancestry(2) = Should be something other than 2" [1] 1 [ FAIL 0 | WARN 0 | SKIP 5 | PASS 63 ] ══ Skipped tests (5) ═══════════════════════════════════════════════════════════ • empty test (5): 'test_algorithm_1snp_wrapper.R:1:1', 'test_get_errors_1_scenario.R:1:1', 'test_get_results_error.R:1:1', 'test_get_scenario_errors.R:1:1', 'test_sample_ancestry.R:1:1' [ FAIL 0 | WARN 0 | SKIP 5 | PASS 63 ] > > # Note that in the directory tests/testthat, > # there's 1 test file per function. I like that format, > # because I don't have to scroll through a long file. > # Hadley does the same thing here: > # https://github.com/hadley/testthat/tree/master/tests/testthat. > > proc.time() user system elapsed 2.167 0.301 2.689
ASAFE.Rcheck/ASAFE-Ex.timings
name | user | system | elapsed | |
algorithm_1snp | 0.152 | 0.016 | 0.171 | |
algorithm_1snp_wrapper | 0.446 | 0.005 | 0.457 | |