Multiple platform build/check report for BioC 3.14 - CHECK results for packFinder 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: packFinder

Version: 1.6.0

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:packFinder.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings packFinder_1.6.0.tar.gz

StartedAt: 2022-04-13 00:09:33 -0400 (Wed, 13 Apr 2022)

EndedAt: 2022-04-13 00:11:19 -0400 (Wed, 13 Apr 2022)

EllapsedTime: 106.1 seconds

RetCode: 0

Status: OK

CheckDir: packFinder.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:packFinder.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings packFinder_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/packFinder.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 'packFinder/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'packFinder' version '1.6.0'
* 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 'packFinder' 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 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
arabidopsisThalianaRefseq  4.8   0.31    5.14
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
arabidopsisThalianaRefseq 4.78   0.43    8.24
* 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

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/packFinder_1.6.0.tar.gz && rm -rf packFinder.buildbin-libdir && mkdir packFinder.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=packFinder.buildbin-libdir packFinder_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL packFinder_1.6.0.zip && rm packFinder_1.6.0.tar.gz packFinder_1.6.0.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
 62  874k   62  549k    0     0   640k      0  0:00:01 --:--:--  0:00:01  640k
100  874k  100  874k    0     0   625k      0  0:00:01  0:00:01 --:--:--  626k

install for i386

* installing *source* package 'packFinder' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'packFinder'
    finding HTML links ... done
    arabidopsisThalianaRefseq               html  
    blastAnalysis                           html  
    blastAnnotate                           html  
    collapseSeqs                            html  
    filterWildcards                         html  
    getPackSeqs                             html  
    getPacksFromCsv                         html  
    getPacksFromFasta                       html  
    getPacksFromGRanges                     html  
    getTsds                                 html  
    identifyPotentialPackElements           html  
    identifyTirMatches                      html  
    makeBlastDb                             html  
    packAlign                               html  
    packBlast                               html  
    packClust                               html  
    packFinder                              html  
    packMatches                             html  
    packSearch                              html  
    packsToCsv                              html  
    packsToFasta                            html  
    packsToGRanges                          html  
    readBlast                               html  
    readUc                                  html  
    tirClust                                html  
** 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 'packFinder' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'packFinder' as packFinder_1.6.0.zip
* DONE (packFinder)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'packFinder' 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(packFinder)
> 
> test_check("packFinder")
DNAStringSet object of length 1:
      width seq                                             names               
[1] 3800001 GGTGTTAAAAGGTTCTTGAGTG...TAGTCAGGTTTCTAACAGAAAA Chr3
[1] "File successfully written to tempTestOutput/packMatches.csv"
[1] "FASTA written to tempTestOutput/packMatches.fasta"
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 31 ]
> 
> proc.time()
   user  system elapsed 
   9.50    0.48   14.68


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(packFinder)
> 
> test_check("packFinder")
DNAStringSet object of length 1:
      width seq                                             names               
[1] 3800001 GGTGTTAAAAGGTTCTTGAGTG...TAGTCAGGTTTCTAACAGAAAA Chr3
[1] "File successfully written to tempTestOutput/packMatches.csv"
[1] "FASTA written to tempTestOutput/packMatches.fasta"
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 31 ]
> 
> proc.time()
   user  system elapsed 
   8.96    0.32   13.75

name	user	system	elapsed
arabidopsisThalianaRefseq	4.80	0.31	5.14
blastAnalysis	0	0	0
blastAnnotate	0.01	0.00	0.02
collapseSeqs	0.81	0.00	0.82
filterWildcards	0.16	0.02	0.18
getPackSeqs	1.41	0.02	1.43
getPacksFromCsv	0.01	0.00	0.02
getPacksFromFasta	0.14	0.00	0.14
getPacksFromGRanges	0.09	0.00	0.09
getTsds	0.17	0.01	0.19
identifyPotentialPackElements	0.72	0.02	0.73
identifyTirMatches	0.11	0.00	0.11
makeBlastDb	0	0	0
packAlign	0.10	0.01	0.11
packBlast	0	0	0
packClust	0.07	0.02	0.09
packMatches	0.96	0.00	0.96
packSearch	0.93	0.05	0.98
packsToCsv	0	0	0
packsToFasta	0.13	0.03	0.16
packsToGRanges	0.06	0.00	0.06
readBlast	0	0	0
readUc	0.02	0.00	0.02
tirClust	0.58	0.03	2.92

name	user	system	elapsed
arabidopsisThalianaRefseq	4.78	0.43	8.24
blastAnalysis	0	0	0
blastAnnotate	0.02	0.00	0.01
collapseSeqs	0.87	0.00	0.88
filterWildcards	0.09	0.00	0.09
getPackSeqs	1.14	0.00	1.14
getPacksFromCsv	0	0	0
getPacksFromFasta	0.07	0.02	0.08
getPacksFromGRanges	0.06	0.00	0.06
getTsds	0.09	0.00	0.10
identifyPotentialPackElements	0.46	0.00	0.45
identifyTirMatches	0.07	0.00	0.08
makeBlastDb	0	0	0
packAlign	0.07	0.00	0.06
packBlast	0	0	0
packClust	0.06	0.00	0.06
packMatches	0.91	0.02	0.93
packSearch	0.93	0.00	0.93
packsToCsv	0	0	0
packsToFasta	0.08	0.01	0.10
packsToGRanges	0.06	0.00	0.39
readBlast	0	0	0
readUc	0	0	0
tirClust	0.69	0.03	1.39

CHECK results for packFinder on tokay2

Summary

Command output

Installation output

Tests output

Example timings