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This page was generated on 2024-05-07 11:32:34 -0400 (Tue, 07 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4461 |
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 825/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GenomAutomorphism 1.6.0 (landing page) Robersy Sanchez
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | ERROR | OK | ||||||||
To the developers/maintainers of the GenomAutomorphism 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. |
Package: GenomAutomorphism |
Version: 1.6.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GenomAutomorphism.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GenomAutomorphism_1.6.0.tar.gz |
StartedAt: 2024-05-06 21:44:57 -0400 (Mon, 06 May 2024) |
EndedAt: 2024-05-06 21:47:17 -0400 (Mon, 06 May 2024) |
EllapsedTime: 140.5 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: GenomAutomorphism.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GenomAutomorphism.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GenomAutomorphism_1.6.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/GenomAutomorphism.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: aarch64-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 Ventura 13.6.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GenomAutomorphism/DESCRIPTION’ ... OK * this is package ‘GenomAutomorphism’ 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 ‘GenomAutomorphism’ 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 ... WARNING Undocumented S4 methods: generic '[' and siglist 'AutomorphismList,ANY' generic '[' and siglist 'ListCodonMatrix,ANY' generic '[' and siglist 'MatrixSeq,ANY' generic '[[' and siglist 'AutomorphismList' generic '[[' and siglist 'ListCodonMatrix' generic 'names<-' and siglist 'AutomorphismList' generic 'names<-' and siglist 'MatrixSeq' All user-level objects in a package (including S4 classes and methods) should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed automorphisms 2.399 0.058 21.053 autZ64 0.842 0.021 7.025 autZ125 0.764 0.019 5.794 aut3D 0.720 0.060 7.229 autZ5 0.574 0.020 6.916 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘spelling.R’ Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: > library(GenomAutomorphism) > > test_check("GenomAutomorphism") [ FAIL 1 | WARN 0 | SKIP 0 | PASS 32 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-aa_mutmat.R:7:6'): multiplication works ────────────────────── mat && aa is not TRUE `actual`: FALSE `expected`: TRUE [ FAIL 1 | WARN 0 | SKIP 0 | PASS 32 ] Error: Test failures Execution halted * 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: 1 ERROR, 1 WARNING See ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/GenomAutomorphism.Rcheck/00check.log’ for details.
GenomAutomorphism.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GenomAutomorphism ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘GenomAutomorphism’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (GenomAutomorphism)
GenomAutomorphism.Rcheck/tests/spelling.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-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. > if (requireNamespace("spelling", quietly = TRUE)) { + spelling::spell_check_test( + vignettes = TRUE, error = FALSE, + skip_on_cran = TRUE + ) + } NULL > > proc.time() user system elapsed 0.075 0.018 0.090
GenomAutomorphism.Rcheck/tests/testthat.Rout.fail
R version 4.4.0 (2024-04-24) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-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. > library(testthat) > library(GenomAutomorphism) > > test_check("GenomAutomorphism") [ FAIL 1 | WARN 0 | SKIP 0 | PASS 32 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-aa_mutmat.R:7:6'): multiplication works ────────────────────── mat && aa is not TRUE `actual`: FALSE `expected`: TRUE [ FAIL 1 | WARN 0 | SKIP 0 | PASS 32 ] Error: Test failures Execution halted
GenomAutomorphism.Rcheck/GenomAutomorphism-Ex.timings
name | user | system | elapsed | |
AutomorphismByCoef | 0.150 | 0.003 | 0.153 | |
AutomorphismList | 0.897 | 0.011 | 0.909 | |
CodonMatrix | 0.056 | 0.001 | 0.056 | |
CodonSeq | 0.123 | 0.009 | 0.131 | |
GRangesMatrixSeq | 0.073 | 0.005 | 0.077 | |
ListCodonMatrix | 0.070 | 0.001 | 0.071 | |
MatrixSeq | 0.039 | 0.001 | 0.039 | |
aa_phychem_index | 0.037 | 0.003 | 0.039 | |
aaindex1 | 0.013 | 0.001 | 0.013 | |
aaindex2 | 0.006 | 0.000 | 0.006 | |
aaindex3 | 0.004 | 0.001 | 0.004 | |
aln | 0.020 | 0.001 | 0.021 | |
aminoacid_dist | 1.203 | 0.539 | 3.647 | |
as.AutomorphismList | 0.186 | 0.016 | 0.202 | |
aut3D | 0.720 | 0.060 | 7.229 | |
autZ125 | 0.764 | 0.019 | 5.794 | |
autZ5 | 0.574 | 0.020 | 6.916 | |
autZ64 | 0.842 | 0.021 | 7.025 | |
autby_coef | 0.097 | 0.002 | 0.100 | |
autm | 0.023 | 0.002 | 0.024 | |
autm_3d | 0.034 | 0.002 | 0.036 | |
autm_z125 | 0.027 | 0.001 | 0.029 | |
automorphismByRanges | 0.042 | 0.003 | 0.044 | |
automorphism_bycoef | 0.038 | 0.003 | 0.041 | |
automorphisms | 2.399 | 0.058 | 21.053 | |
base2codon | 0.021 | 0.002 | 0.024 | |
base2int | 0.002 | 0.000 | 0.003 | |
base_methods | 0.117 | 0.008 | 0.126 | |
brca1_aln | 0.018 | 0.001 | 0.019 | |
brca1_aln2 | 0.024 | 0.004 | 0.028 | |
brca1_autm | 0.140 | 0.002 | 0.141 | |
cdm_z64 | 0.069 | 0.133 | 0.208 | |
codon_coord | 0.376 | 0.002 | 0.379 | |
codon_dist | 0.094 | 0.002 | 0.096 | |
codon_dist_matrix | 0.013 | 0.005 | 2.347 | |
codon_matrix | 0.167 | 0.006 | 0.175 | |
conserved_regions | 0.133 | 0.004 | 0.136 | |
covid_aln | 0.024 | 0.001 | 0.025 | |
covid_autm | 0.029 | 0.001 | 0.031 | |
cyc_aln | 0.030 | 0.002 | 0.031 | |
cyc_autm | 0.049 | 0.001 | 0.051 | |
dna_phyche | 0.001 | 0.000 | 0.003 | |
dna_phychem | 0.000 | 0.000 | 0.001 | |
extract-methods | 0.171 | 0.003 | 0.173 | |
getAutomorphisms | 0.062 | 0.002 | 0.065 | |
get_coord | 0.230 | 0.002 | 0.232 | |
get_mutscore | 0.064 | 0.002 | 0.067 | |
matrices | 0.206 | 0.006 | 0.212 | |
mod | 0.000 | 0.001 | 0.000 | |
modeq | 0.001 | 0.000 | 0.000 | |
modlineq | 0.000 | 0.000 | 0.001 | |
mut_type | 0.001 | 0.000 | 0.001 | |
peptide_phychem_index | 0.044 | 0.003 | 0.046 | |
reexports | 0.042 | 0.002 | 0.043 | |
seqranges | 0.211 | 0.001 | 0.213 | |
slapply | 0.001 | 0.000 | 0.001 | |
sortByChromAndStart | 0.017 | 0.000 | 0.017 | |
str2chr | 0 | 0 | 0 | |
str2dig | 0.001 | 0.000 | 0.000 | |
translation | 0.324 | 0.003 | 0.327 | |