| Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-03-28 11:36:30 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
| 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 817/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GenomAutomorphism 1.5.0 (landing page) Robersy Sanchez
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the GenomAutomorphism package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GenomAutomorphism.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: GenomAutomorphism |
| Version: 1.5.0 |
| Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:GenomAutomorphism.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings GenomAutomorphism_1.5.0.tar.gz |
| StartedAt: 2024-03-27 22:48:32 -0400 (Wed, 27 Mar 2024) |
| EndedAt: 2024-03-27 22:52:45 -0400 (Wed, 27 Mar 2024) |
| EllapsedTime: 252.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GenomAutomorphism.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:GenomAutomorphism.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings GenomAutomorphism_1.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/GenomAutomorphism.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘GenomAutomorphism/DESCRIPTION’ ... OK
* this is package ‘GenomAutomorphism’ version ‘1.5.0’
* 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 loading without being on the library search path ... 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 ... NOTE
checkRd: (-1) mut_type.Rd:20: Lost braces; missing escapes or markup?
20 | number of hydrogen bonds (on DNA/RNA double helix): strong S={C,G} (three
| ^
checkRd: (-1) mut_type.Rd:21: Lost braces; missing escapes or markup?
21 | hydrogen bonds) and weak W={A,U} (two hydrogen bonds). According to the
| ^
checkRd: (-1) mut_type.Rd:22: Lost braces; missing escapes or markup?
22 | chemical type: purines R={A, G} and pyrimidines Y={C,U}. 3). According to
| ^
checkRd: (-1) mut_type.Rd:22: Lost braces; missing escapes or markup?
22 | chemical type: purines R={A, G} and pyrimidines Y={C,U}. 3). According to
| ^
checkRd: (-1) mut_type.Rd:23: Lost braces; missing escapes or markup?
23 | the presence of amino or keto groups on the base rings: amino M={C,A} and
| ^
checkRd: (-1) mut_type.Rd:24: Lost braces; missing escapes or markup?
24 | keto K={G,U}. So, each mutational event can be classified as according to
| ^
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘mod’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
aminoacid_dist 4.898 0.979 5.264
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘spelling.R’
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.19-bioc/meat/GenomAutomorphism.Rcheck/00check.log’
for details.
GenomAutomorphism.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL GenomAutomorphism ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘GenomAutomorphism’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘mod’ in package ‘GenomAutomorphism’ ** 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 Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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
0.176 0.016 0.181
GenomAutomorphism.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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 0 | WARN 7 | SKIP 0 | PASS 31 ]
[ FAIL 0 | WARN 7 | SKIP 0 | PASS 31 ]
>
> proc.time()
user system elapsed
19.405 2.048 21.291
GenomAutomorphism.Rcheck/GenomAutomorphism-Ex.timings
| name | user | system | elapsed | |
| AutomorphismByCoef | 0.444 | 0.004 | 0.449 | |
| AutomorphismList | 2.439 | 0.132 | 2.571 | |
| CodonSeq | 0.350 | 0.004 | 0.354 | |
| aa_mutmat | 0.016 | 0.008 | 0.023 | |
| aaindex2 | 0.008 | 0.000 | 0.008 | |
| aaindex3 | 0.002 | 0.003 | 0.006 | |
| aminoacid_dist | 4.898 | 0.979 | 5.264 | |
| as.AutomorphismList | 0.618 | 0.107 | 0.571 | |
| aut3D | 1.298 | 0.291 | 1.394 | |
| autZ125 | 2.422 | 0.807 | 2.350 | |
| autZ5 | 0.793 | 0.219 | 0.831 | |
| autZ64 | 1.515 | 0.324 | 1.664 | |
| autm | 0.054 | 0.012 | 0.065 | |
| automorphismByRanges | 0.118 | 0.008 | 0.127 | |
| automorphism_bycoef | 0.097 | 0.012 | 0.110 | |
| automorphisms | 4.007 | 0.875 | 4.377 | |
| base2codon | 0.052 | 0.004 | 0.057 | |
| base2int | 0.002 | 0.000 | 0.002 | |
| base_coord | 0.147 | 0.020 | 0.167 | |
| cdm_z64 | 0.021 | 0.003 | 0.024 | |
| codon_coord | 0.879 | 0.116 | 0.994 | |
| codon_dist | 0.269 | 0.008 | 0.276 | |
| codon_dist_matrix | 0.052 | 0.028 | 2.017 | |
| conserved_regions | 2.210 | 0.246 | 0.482 | |
| extract-methods | 0.469 | 0.040 | 0.508 | |
| getAutomorphisms | 0.172 | 0.036 | 0.207 | |
| get_coord | 0.575 | 0.056 | 0.631 | |
| get_mutscore | 0.105 | 0.004 | 0.109 | |
| matrices | 0.469 | 0.012 | 0.481 | |
| mod | 0.002 | 0.000 | 0.002 | |
| modeq | 0.000 | 0.001 | 0.001 | |
| modlineq | 0.001 | 0.002 | 0.004 | |
| mut_type | 0.002 | 0.000 | 0.002 | |
| reexports | 0.096 | 0.000 | 0.096 | |
| seqranges | 0.515 | 0.000 | 0.516 | |
| slapply | 0.003 | 0.000 | 0.003 | |
| sortByChromAndStart | 0.056 | 0.000 | 0.056 | |
| str2chr | 0.000 | 0.001 | 0.001 | |
| str2dig | 0.000 | 0.000 | 0.001 | |
| translation | 0.897 | 0.045 | 0.942 | |