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This page was generated on 2024-03-28 11:37:45 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4708
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4446
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4471
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R 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 817/2270HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomAutomorphism 1.5.0  (landing page)
Robersy Sanchez
Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/GenomAutomorphism
git_branch: devel
git_last_commit: cca057b
git_last_commit_date: 2023-10-24 11:43:17 -0400 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for GenomAutomorphism on palomino3


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.

raw results


Summary

Package: GenomAutomorphism
Version: 1.5.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GenomAutomorphism.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings GenomAutomorphism_1.5.0.tar.gz
StartedAt: 2024-03-28 02:21:53 -0400 (Thu, 28 Mar 2024)
EndedAt: 2024-03-28 02:28:56 -0400 (Thu, 28 Mar 2024)
EllapsedTime: 422.6 seconds
RetCode: 0
Status:   OK  
CheckDir: GenomAutomorphism.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GenomAutomorphism.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings GenomAutomorphism_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/GenomAutomorphism.Rcheck'
* using R Under development (unstable) (2024-03-16 r86144 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* 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 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 ... 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
automorphisms     4.90   0.47   35.14
aminoacid_dist    3.37   0.19   56.22
autZ64            2.03   0.33   11.20
aut3D             1.47   0.36   11.87
autZ125           1.42   0.38   11.89
autZ5             1.16   0.20   11.77
codon_dist_matrix 0.05   0.01    6.39
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'F:/biocbuild/bbs-3.19-bioc/meat/GenomAutomorphism.Rcheck/00check.log'
for details.


Installation output

GenomAutomorphism.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL GenomAutomorphism
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/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)

Tests output

GenomAutomorphism.Rcheck/tests/spelling.Rout


R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 
   0.20    0.03    0.28 

GenomAutomorphism.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 
  20.75    4.85   81.29 

Example timings

GenomAutomorphism.Rcheck/GenomAutomorphism-Ex.timings

nameusersystemelapsed
AutomorphismByCoef0.430.000.42
AutomorphismList2.170.312.48
CodonSeq0.640.611.25
aa_mutmat0.000.030.03
aaindex2000
aaindex30.020.000.02
aminoacid_dist 3.37 0.1956.22
as.AutomorphismList0.640.030.67
aut3D 1.47 0.3611.87
autZ125 1.42 0.3811.89
autZ5 1.16 0.2011.77
autZ64 2.03 0.3311.20
autm0.160.310.49
automorphismByRanges0.150.310.46
automorphism_bycoef0.200.270.47
automorphisms 4.90 0.4735.14
base2codon0.120.260.39
base2int0.020.000.02
base_coord0.260.250.52
cdm_z640.010.000.02
codon_coord1.020.271.28
codon_dist0.400.530.94
codon_dist_matrix0.050.016.39
conserved_regions0.520.751.27
extract-methods0.370.000.37
getAutomorphisms0.280.220.50
get_coord0.580.260.84
get_mutscore0.100.000.11
matrices0.580.270.84
mod000
modeq000
modlineq0.000.020.02
mut_type000
reexports0.280.540.82
seqranges0.590.310.91
slapply000
sortByChromAndStart0.070.000.06
str2chr000
str2dig000
translation1.000.611.63