Multiple platform build/check report for BioC 3.14 - CHECK results for ggmsa on tokay2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4137
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: 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: 2022-04-12 20:32:14 -0400 (Tue, 12 Apr 2022)

EndedAt: 2022-04-12 20:35:35 -0400 (Tue, 12 Apr 2022)

EllapsedTime: 201.6 seconds

RetCode: 0

Status: OK

CheckDir: ggmsa.Rcheck

Warnings: 0

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###
### 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
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/ggmsa.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 6.41   0.59    7.03
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
ggSeqBundle 6.34   0.48    6.83
* 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

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

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 20 1593k   20  321k    0     0   714k      0  0:00:02 --:--:--  0:00:02  714k
100 1593k  100 1593k    0     0  1213k      0  0:00:01  0:00:01 --:--:-- 1214k

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


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 
   5.90    0.28    6.17


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 
   6.50    0.45    7.45

name	user	system	elapsed
available_colors	0	0	0
available_fonts	0.01	0.00	0.02
available_msa	0	0	0
facet_msa	0.86	0.03	0.96
geom_GC	0.25	0.03	0.29
geom_helix	0.71	0.04	0.79
geom_msa	0.18	0.00	0.19
geom_msaBar	0.68	0.00	0.67
geom_seed	2.45	0.03	2.49
geom_seqlogo	0.72	0.00	0.72
ggSeqBundle	6.41	0.59	7.03
gghelix	0.78	0.05	0.83
ggmsa	1.53	0.03	1.56
plot-methods	0.38	0.00	0.38
readSSfile	0.03	0.00	0.03
seqdiff	0.01	0.00	0.01
seqlogo	0.43	0.00	0.43
show-methods	0	0	0
simplot	0.50	0.00	1.59
tidy_msa	0.03	0.00	0.03

name	user	system	elapsed
available_colors	0	0	0
available_fonts	0.00	0.02	0.02
available_msa	0	0	0
facet_msa	0.62	0.00	0.62
geom_GC	0.22	0.00	0.22
geom_helix	0.53	0.02	0.55
geom_msa	0.16	0.00	0.16
geom_msaBar	0.56	0.00	0.56
geom_seed	2.58	0.00	2.58
geom_seqlogo	0.67	0.00	0.67
ggSeqBundle	6.34	0.48	6.83
gghelix	0.93	0.02	0.93
ggmsa	1.51	0.00	1.52
plot-methods	0.41	0.00	0.41
readSSfile	0.03	0.00	0.03
seqdiff	0.01	0.00	0.01
seqlogo	0.46	0.00	0.46
show-methods	0.01	0.00	0.01
simplot	0.28	0.00	0.28
tidy_msa	0.04	0.00	0.03

CHECK results for ggmsa on tokay2

Summary

Command output

Installation output

Tests output

Example timings