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This page was generated on 2022-01-24 13:06:19 -0500 (Mon, 24 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
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

CHECK results for ggmsa on tokay2


To the developers/maintainers of the ggmsa package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ggmsa.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 777/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ggmsa 1.0.0  (landing page)
Lang Zhou
Snapshot Date: 2022-01-23 01:55:04 -0500 (Sun, 23 Jan 2022)
git_url: https://git.bioconductor.org/packages/ggmsa
git_branch: RELEASE_3_14
git_last_commit: 17e4f08
git_last_commit_date: 2021-10-26 13:12:41 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ggmsa
Version: 1.0.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ggmsa.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ggmsa_1.0.0.tar.gz
StartedAt: 2022-01-23 20:07:01 -0500 (Sun, 23 Jan 2022)
EndedAt: 2022-01-23 20:10:10 -0500 (Sun, 23 Jan 2022)
EllapsedTime: 188.7 seconds
RetCode: 0
Status:   OK  
CheckDir: ggmsa.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ggmsa.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ggmsa_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/ggmsa.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ggmsa/DESCRIPTION' ... OK
* this is package 'ggmsa' version '1.0.0'
* 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 'ggmsa' 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 R/sysdata.rda ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
ggSeqBundle 6.25   0.44     6.7
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
ggSeqBundle 6.31   0.69       7
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

ggmsa.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/ggmsa_1.0.0.tar.gz && rm -rf ggmsa.buildbin-libdir && mkdir ggmsa.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ggmsa.buildbin-libdir ggmsa_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL ggmsa_1.0.0.zip && rm ggmsa_1.0.0.tar.gz ggmsa_1.0.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 81 1593k   81 1294k    0     0  2702k      0 --:--:-- --:--:-- --:--:-- 2702k
100 1593k  100 1593k    0     0  3077k      0 --:--:-- --:--:-- --:--:-- 3075k

install for i386

* installing *source* package 'ggmsa' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Note: wrong number of arguments to 'seq_len' 
** help
*** installing help indices
  converting help for package 'ggmsa'
    finding HTML links ... done
    GVariation                              html  
    Gram-negative_AKL.fasta                 html  
    Gram-positive_AKL.fasta                 html  
    LeaderRepeat_All.fa                     html  
    Rfam                                    html  
    TP53_genes.xlsx                         html  
    available_colors                        html  
    available_fonts                         html  
    available_msa                           html  
    facet_msa                               html  
    geom_GC                                 html  
    geom_helix                              html  
    geom_msa                                html  
    geom_msaBar                             html  
    geom_seed                               html  
    geom_seqlogo                            html  
    ggSeqBundle                             html  
    gghelix                                 html  
    ggmsa                                   html  
    plot-methods                            html  
    readSSfile                              html  
    sample.fasta                            html  
    seedSample.fa                           html  
    seqdiff                                 html  
    seqlogo                                 html  
    sequence-link-tree.fasta                html  
    show-methods                            html  
    simplot                                 html  
    tidy_msa                                html  
    tp53.fa                                 html  
*** 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

install for x64

* installing *source* package 'ggmsa' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ggmsa' as ggmsa_1.0.0.zip
* DONE (ggmsa)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'ggmsa' successfully unpacked and MD5 sums checked

Tests output

ggmsa.Rcheck/tests_i386/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

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(ggmsa)
ggmsa v1.0.0  Document: http://yulab-smu.top/ggmsa/

If you use ggmsa in published research, please cite: DOI: 10.18129/B9.bioc.ggmsa 
> 
> test_check("ggmsa")
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: XVector
Loading required package: GenomeInfoDb

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Loading required package: ape

Attaching package: 'ape'

The following object is masked from 'package:Biostrings':

    complement

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 16 ]
> 
> proc.time()
   user  system elapsed 
   6.65    0.45    7.15 

ggmsa.Rcheck/tests_x64/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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(ggmsa)
ggmsa v1.0.0  Document: http://yulab-smu.top/ggmsa/

If you use ggmsa in published research, please cite: DOI: 10.18129/B9.bioc.ggmsa 
> 
> test_check("ggmsa")
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: XVector
Loading required package: GenomeInfoDb

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Loading required package: ape

Attaching package: 'ape'

The following object is masked from 'package:Biostrings':

    complement

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 16 ]
> 
> proc.time()
   user  system elapsed 
   6.45    0.29    6.92 

Example timings

ggmsa.Rcheck/examples_i386/ggmsa-Ex.timings

nameusersystemelapsed
available_colors000
available_fonts0.010.000.01
available_msa000
facet_msa0.680.000.67
geom_GC0.280.000.28
geom_helix0.860.050.95
geom_msa0.200.000.21
geom_msaBar0.770.000.76
geom_seed2.840.012.86
geom_seqlogo0.750.000.75
ggSeqBundle6.250.446.70
gghelix0.910.010.93
ggmsa1.960.072.03
plot-methods0.430.000.42
readSSfile0.030.000.03
seqdiff0.010.000.02
seqlogo0.440.000.43
show-methods0.020.000.02
simplot0.480.040.56
tidy_msa0.050.000.05

ggmsa.Rcheck/examples_x64/ggmsa-Ex.timings

nameusersystemelapsed
available_colors000
available_fonts000
available_msa000
facet_msa0.600.030.63
geom_GC0.20.00.2
geom_helix0.580.000.58
geom_msa0.150.020.17
geom_msaBar0.710.000.70
geom_seed2.710.032.75
geom_seqlogo0.680.000.68
ggSeqBundle6.310.697.00
gghelix1.280.011.29
ggmsa1.530.001.53
plot-methods0.740.020.75
readSSfile0.010.000.02
seqdiff0.020.000.01
seqlogo0.400.010.43
show-methods0.000.020.01
simplot0.30.00.3
tidy_msa0.030.000.03