| Back to Mac ARM64 build report for BioC 3.20 |
|
This page was generated on 2024-05-20 11:32:12 -0400 (Mon, 20 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4381 |
| 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 796/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GenomAutomorphism 1.7.0 (landing page) Robersy Sanchez
| kjohnson1 | macOS 13.6.6 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: 1.7.0 |
| 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_1.7.0.tar.gz |
| StartedAt: 2024-05-19 14:11:36 -0400 (Sun, 19 May 2024) |
| EndedAt: 2024-05-19 14:18:52 -0400 (Sun, 19 May 2024) |
| EllapsedTime: 435.5 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: GenomAutomorphism.Rcheck |
| Warnings: NA |
##############################################################################
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###
### 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_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/GenomAutomorphism.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* 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 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomAutomorphism/DESCRIPTION’ ... OK
* this is package ‘GenomAutomorphism’ version ‘1.7.0’
* 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 7.073 0.169 65.527
aminoacid_dist 3.912 0.969 11.673
aut3D 2.459 0.178 23.410
autZ64 2.578 0.056 22.330
autZ125 2.295 0.051 18.033
autZ5 1.733 0.067 21.948
codon_dist_matrix 0.042 0.011 6.562
* 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-3.20-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 Patched (2024-04-24 r86482) -- "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
0.217 0.069 0.270
GenomAutomorphism.Rcheck/tests/testthat.Rout.fail
R version 4.4.0 Patched (2024-04-24 r86482) -- "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 | 0.484 | 0.010 | 0.495 | |
| AutomorphismList | 2.877 | 0.037 | 2.923 | |
| CodonMatrix | 0.203 | 0.003 | 0.209 | |
| CodonSeq | 0.468 | 0.016 | 0.486 | |
| GRangesMatrixSeq | 0.237 | 0.012 | 0.250 | |
| ListCodonMatrix | 0.246 | 0.006 | 0.253 | |
| MatrixSeq | 0.135 | 0.005 | 0.140 | |
| aa_phychem_index | 0.132 | 0.010 | 0.144 | |
| aaindex1 | 0.049 | 0.002 | 0.051 | |
| aaindex2 | 0.020 | 0.001 | 0.022 | |
| aaindex3 | 0.014 | 0.002 | 0.015 | |
| aln | 0.103 | 0.005 | 0.107 | |
| aminoacid_dist | 3.912 | 0.969 | 11.673 | |
| as.AutomorphismList | 0.608 | 0.068 | 0.685 | |
| aut3D | 2.459 | 0.178 | 23.410 | |
| autZ125 | 2.295 | 0.051 | 18.033 | |
| autZ5 | 1.733 | 0.067 | 21.948 | |
| autZ64 | 2.578 | 0.056 | 22.330 | |
| autby_coef | 0.330 | 0.007 | 0.346 | |
| autm | 0.094 | 0.007 | 0.103 | |
| autm_3d | 0.143 | 0.007 | 0.150 | |
| autm_z125 | 0.121 | 0.006 | 0.128 | |
| automorphismByRanges | 0.165 | 0.012 | 0.177 | |
| automorphism_bycoef | 0.146 | 0.010 | 0.155 | |
| automorphisms | 7.073 | 0.169 | 65.527 | |
| base2codon | 0.100 | 0.006 | 0.112 | |
| base2int | 0.007 | 0.001 | 0.008 | |
| base_methods | 0.480 | 0.030 | 0.511 | |
| brca1_aln | 0.065 | 0.004 | 0.069 | |
| brca1_aln2 | 0.080 | 0.006 | 0.086 | |
| brca1_autm | 0.470 | 0.007 | 0.478 | |
| cdm_z64 | 0.222 | 0.434 | 0.670 | |
| codon_coord | 1.178 | 0.015 | 1.194 | |
| codon_dist | 0.322 | 0.009 | 0.331 | |
| codon_dist_matrix | 0.042 | 0.011 | 6.562 | |
| codon_matrix | 0.422 | 0.020 | 0.448 | |
| conserved_regions | 0.434 | 0.008 | 0.444 | |
| covid_aln | 0.106 | 0.004 | 0.112 | |
| covid_autm | 0.117 | 0.005 | 0.122 | |
| cyc_aln | 0.121 | 0.004 | 0.127 | |
| cyc_autm | 0.272 | 0.007 | 0.292 | |
| dna_phyche | 0.007 | 0.002 | 0.009 | |
| dna_phychem | 0.002 | 0.001 | 0.003 | |
| extract-methods | 0.534 | 0.007 | 0.542 | |
| getAutomorphisms | 0.208 | 0.012 | 0.220 | |
| get_coord | 0.669 | 0.009 | 0.678 | |
| get_mutscore | 0.201 | 0.008 | 0.208 | |
| matrices | 0.667 | 0.010 | 0.677 | |
| mod | 0.002 | 0.001 | 0.003 | |
| modeq | 0.001 | 0.001 | 0.001 | |
| modlineq | 0.002 | 0.002 | 0.004 | |
| mut_type | 0.002 | 0.001 | 0.002 | |
| peptide_phychem_index | 0.155 | 0.009 | 0.163 | |
| reexports | 0.190 | 0.008 | 0.198 | |
| seqranges | 0.722 | 0.007 | 0.730 | |
| slapply | 0.002 | 0.000 | 0.003 | |
| sortByChromAndStart | 0.067 | 0.000 | 0.068 | |
| str2chr | 0.000 | 0.000 | 0.001 | |
| str2dig | 0.001 | 0.000 | 0.001 | |
| translation | 1.183 | 0.012 | 1.204 | |