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

Version: 1.6.0

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TAPseq.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings TAPseq_1.6.0.tar.gz

StartedAt: 2022-04-13 03:53:06 -0400 (Wed, 13 Apr 2022)

EndedAt: 2022-04-13 04:04:06 -0400 (Wed, 13 Apr 2022)

EllapsedTime: 659.3 seconds

RetCode: 0

Status: WARNINGS

CheckDir: TAPseq.Rcheck

Warnings: 1

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TAPseq.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings TAPseq_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/TAPseq.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 'TAPseq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TAPseq' 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 'TAPseq' can be installed ... WARNING
Found the following significant warnings:
  Warning: Following software required by TAPseq is not installed or not in PATH:
See 'C:/Users/biocbuild/bbs-3.14-bioc/meat/TAPseq.Rcheck/00install.out' for details.
* 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 ... NOTE
Warning: Following software required by TAPseq is not installed or not in PATH:

	primer3_core
	makeblastdb
	blastn

Please install these tools before trying to use this package!

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
** 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 ... NOTE
Warning: Following software required by TAPseq is not installed or not in PATH:

	primer3_core
	makeblastdb
	blastn

Please install these tools before trying to use this package!

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
** 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 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
selectTargetGenes 52.13   1.38   53.53
TAPseqInput        7.46   0.48    7.94
exportPrimers      6.10   0.04    6.14
truncateTxsPolyA   6.03   0.04    6.08
inferPolyASites    2.88   0.11   22.08
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
selectTargetGenes 50.71   1.36   53.13
TAPseqInput        7.08   0.13    7.21
truncateTxsPolyA   6.46   0.09    6.54
pickPrimers        5.65   0.06    5.78
inferPolyASites    2.59   0.08   21.86
* 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: 1 WARNING, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/TAPseq.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/TAPseq_1.6.0.tar.gz && rm -rf TAPseq.buildbin-libdir && mkdir TAPseq.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TAPseq.buildbin-libdir TAPseq_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL TAPseq_1.6.0.zip && rm TAPseq_1.6.0.tar.gz TAPseq_1.6.0.zip
###
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install for i386

* installing *source* package 'TAPseq' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'TAPseq'
    finding HTML links ... done
    TAPseq                                  html  
    TAPseqInput                             html  
    TsIO-class                              html  
    TsIOList-class                          html  
    accessors                               html  
    bone_marrow_genex                       html  
    checkPrimers                            html  
    check_tool_installation                 html  
    chr11_genes                             html  
    chr11_polyA_sites                       html  
    chr11_primers                           html  
    chr11_truncated_txs                     html  
    chr11_truncated_txs_seq                 html  
    createIORecord                          html  
    designPrimers                           html  
    estimateOffTargets                      html  
    exportPrimers                           html  
    getTxsSeq                               html  
    get_gt_sequences                        html  
    inferPolyASites                         html  
    parsePrimer3Output                      html  
    pickPrimers                             html  
    selectTargetGenes                       html  
    truncateTxsPolyA                        html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Following software required by TAPseq is not installed or not in PATH:

	primer3_core
	makeblastdb
	blastn

Please install these tools before trying to use this package!
** testing if installed package can be loaded from final location
Warning: Following software required by TAPseq is not installed or not in PATH:

	primer3_core
	makeblastdb
	blastn

Please install these tools before trying to use this package!
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'TAPseq' ...
** testing if installed package can be loaded
Warning: Following software required by TAPseq is not installed or not in PATH:

	primer3_core
	makeblastdb
	blastn

Please install these tools before trying to use this package!
* MD5 sums
packaged installation of 'TAPseq' as TAPseq_1.6.0.zip
* DONE (TAPseq)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'TAPseq' 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(TAPseq)

TAPseq is using the following tools:
primer3_core: NA
makeblastdb: NA
blastn: NA

Warning message:
Following software required by TAPseq is not installed or not in PATH:

	primer3_core
	makeblastdb
	blastn

Please install these tools before trying to use this package! 
> 
> test_check("TAPseq")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 209 ]
> 
> proc.time()
   user  system elapsed 
  51.43    2.81   54.23


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(TAPseq)

TAPseq is using the following tools:
primer3_core: NA
makeblastdb: NA
blastn: NA

Warning message:
Following software required by TAPseq is not installed or not in PATH:

	primer3_core
	makeblastdb
	blastn

Please install these tools before trying to use this package! 
> 
> test_check("TAPseq")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 209 ]
> 
> proc.time()
   user  system elapsed 
  55.76    1.46   57.21

name	user	system	elapsed
TAPseqInput	7.46	0.48	7.94
TsIO-class	0.08	0.02	0.09
TsIOList-class	0.31	0.06	0.44
accessors	0.53	0.05	0.58
checkPrimers	2.96	0.07	3.03
createIORecord	4.03	0.04	4.06
designPrimers	0.15	0.00	0.16
estimateOffTargets	0	0	0
exportPrimers	6.10	0.04	6.14
getTxsSeq	1.43	0.19	1.63
inferPolyASites	2.88	0.11	22.08
parsePrimer3Output	0	0	0
pickPrimers	4.90	0.06	4.97
selectTargetGenes	52.13	1.38	53.53
truncateTxsPolyA	6.03	0.04	6.08

name	user	system	elapsed
TAPseqInput	7.08	0.13	7.21
TsIO-class	0.06	0.02	0.08
TsIOList-class	0.19	0.04	0.23
accessors	0.36	0.05	0.41
checkPrimers	2.25	0.08	2.32
createIORecord	2.56	0.01	2.58
designPrimers	0.08	0.02	0.10
estimateOffTargets	0	0	0
exportPrimers	3.87	0.01	3.89
getTxsSeq	0.93	0.05	0.97
inferPolyASites	2.59	0.08	21.86
parsePrimer3Output	0	0	0
pickPrimers	5.65	0.06	5.78
selectTargetGenes	50.71	1.36	53.13
truncateTxsPolyA	6.46	0.09	6.54

CHECK results for TAPseq on tokay2

Summary

Command output

Installation output

Tests output

Example timings