Multiple platform build/check report for BioC 3.13 - CHECK results for TAPseq on tokay2

Package: TAPseq

Version: 1.4.0

Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TAPseq.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings TAPseq_1.4.0.tar.gz

StartedAt: 2021-10-15 06:26:41 -0400 (Fri, 15 Oct 2021)

EndedAt: 2021-10-15 06:37:44 -0400 (Fri, 15 Oct 2021)

EllapsedTime: 663.3 seconds

RetCode: 0

Status: WARNINGS

CheckDir: TAPseq.Rcheck

Warnings: 2

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TAPseq.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings TAPseq_1.4.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/TAPseq.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.4.0'
* 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-3.13-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 ... WARNING
Missing link or links in documentation object 'truncateTxsPolyA.Rd':
  '[rtracklayer:export]{import}'

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 55.36   1.22   56.61
TAPseqInput        8.34   0.55    8.89
truncateTxsPolyA   7.88   0.05    7.93
pickPrimers        5.05   0.06    5.11
inferPolyASites    2.16   0.14   22.43
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
selectTargetGenes 47.73   0.68   48.57
truncateTxsPolyA   6.61   0.04    6.65
TAPseqInput        6.30   0.09    6.39
pickPrimers        5.30   0.06    5.37
inferPolyASites    2.45   0.08   19.47
* 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: 2 WARNINGs, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/TAPseq.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/TAPseq_1.4.0.tar.gz && rm -rf TAPseq.buildbin-libdir && mkdir TAPseq.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TAPseq.buildbin-libdir TAPseq_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL TAPseq_1.4.0.zip && rm TAPseq_1.4.0.tar.gz TAPseq_1.4.0.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_1.4.0.zip
* DONE (TAPseq)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'TAPseq' successfully unpacked and MD5 sums checked


R version 4.1.1 (2021-08-10) -- "Kick Things"
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(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 
  53.87    2.57   56.42


R version 4.1.1 (2021-08-10) -- "Kick Things"
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(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 
  58.35    1.46   59.82

name	user	system	elapsed
TAPseqInput	8.34	0.55	8.89
TsIO-class	0.10	0.02	0.11
TsIOList-class	0.24	0.06	0.37
accessors	0.59	0.11	0.71
checkPrimers	2.39	0.11	2.50
createIORecord	2.33	0.03	2.36
designPrimers	0.09	0.00	0.10
estimateOffTargets	0	0	0
exportPrimers	3.63	0.14	3.76
getTxsSeq	0.87	0.22	1.10
inferPolyASites	2.16	0.14	22.43
parsePrimer3Output	0	0	0
pickPrimers	5.05	0.06	5.11
selectTargetGenes	55.36	1.22	56.61
truncateTxsPolyA	7.88	0.05	7.93

name	user	system	elapsed
TAPseqInput	6.30	0.09	6.39
TsIO-class	0.04	0.03	0.08
TsIOList-class	0.18	0.03	0.21
accessors	0.29	0.05	0.34
checkPrimers	2.22	0.01	2.23
createIORecord	2.39	0.02	2.41
designPrimers	0.10	0.00	0.09
estimateOffTargets	0	0	0
exportPrimers	4.14	0.08	4.22
getTxsSeq	0.78	0.04	0.83
inferPolyASites	2.45	0.08	19.47
parsePrimer3Output	0	0	0
pickPrimers	5.30	0.06	5.37
selectTargetGenes	47.73	0.68	48.57
truncateTxsPolyA	6.61	0.04	6.65

CHECK results for TAPseq on tokay2

Summary

Command output

Installation output

Tests output

Example timings