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

Version: 1.0.0

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scanMiRApp.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings scanMiRApp_1.0.0.tar.gz

StartedAt: 2022-04-13 02:17:20 -0400 (Wed, 13 Apr 2022)

EndedAt: 2022-04-13 02:23:40 -0400 (Wed, 13 Apr 2022)

EllapsedTime: 380.9 seconds

RetCode: 0

Status: OK

CheckDir: scanMiRApp.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:scanMiRApp.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings scanMiRApp_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/scanMiRApp.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 'scanMiRApp/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'scanMiRApp' version '1.0.0'
* 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 'scanMiRApp' 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 ... NOTE
.fakeAnno: no visible binding for global variable 'SampleTranscript'
.fakeAnno: no visible binding for global variable 'SampleKdModel'
plotSitesOnUTR: no visible binding for global variable 'logKd'
plotSitesOnUTR: no visible binding for global variable 'note'
Undefined global functions or variables:
  SampleKdModel SampleTranscript logKd note
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* 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 NOTE
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/scanMiRApp.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/scanMiRApp_1.0.0.tar.gz && rm -rf scanMiRApp.buildbin-libdir && mkdir scanMiRApp.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=scanMiRApp.buildbin-libdir scanMiRApp_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL scanMiRApp_1.0.0.zip && rm scanMiRApp_1.0.0.tar.gz scanMiRApp_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
 89 32838   89 29491    0     0   111k      0 --:--:-- --:--:-- --:--:--  111k
100 32838  100 32838    0     0   123k      0 --:--:-- --:--:-- --:--:--  123k

install for i386

* installing *source* package 'scanMiRApp' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'scanMiRApp'
    finding HTML links ... done
    IndexedFst-class                        html  
    ScanMiRAnno-methods                     html  
    ScanMiRAnno                             html  
    enrichedMirTxPairs                      html  
    finding level-2 HTML links ... done

    getTranscriptSequence                   html  
    plotSitesOnUTR                          html  
    runFullScan                             html  
    save-load-IndexedFst                    html  
    scanMiRApp                              html  
    scanMiRserver                           html  
    scanMiRui                               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 'scanMiRApp' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'scanMiRApp' as scanMiRApp_1.0.0.zip
* DONE (scanMiRApp)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'scanMiRApp' 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(scanMiRApp)
> 
> test_check("scanMiRApp")
Loading annotation
Extracting transcripts
Scanning with 1 thread(s)
Loading annotation
Extracting transcripts
Scanning with 1 thread(s)
Prepare miRNA model
Get Transcript Sequence
Scan
Prepare miRNA model
Get Transcript Sequence
Scan
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 13 ]

== Skipped tests ===============================================================
* On CRAN (1)
* empty test (1)

[ FAIL 0 | WARN 0 | SKIP 2 | PASS 13 ]
> 
> proc.time()
   user  system elapsed 
  18.90    1.96   21.18


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(scanMiRApp)
> 
> test_check("scanMiRApp")
Loading annotation
Extracting transcripts
Error in (function (x)  : attempt to apply non-function
Scanning with 1 thread(s)
Loading annotation
Extracting transcripts
Scanning with 1 thread(s)
Prepare miRNA model
Get Transcript Sequence
Scan
Prepare miRNA model
Get Transcript Sequence
Scan
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 13 ]

== Skipped tests ===============================================================
* On CRAN (1)
* empty test (1)

[ FAIL 0 | WARN 0 | SKIP 2 | PASS 13 ]
Warning message:
call dbDisconnect() when finished working with a connection 
> 
> proc.time()
   user  system elapsed 
  20.26    0.57   20.90

name	user	system	elapsed
IndexedFst-class	0.04	0.00	0.05
ScanMiRAnno	0.99	0.20	1.19
enrichedMirTxPairs	1.37	0.00	1.37
getTranscriptSequence	1.47	0.20	1.67
plotSitesOnUTR	1.88	0.02	1.89
runFullScan	0.98	0.00	0.99
save-load-IndexedFst	0.02	0.00	0.01
scanMiRApp	0	0	0
scanMiRserver	0.46	0.00	0.47
scanMiRui	0.22	0.03	0.25

name	user	system	elapsed
IndexedFst-class	0.05	0.00	0.05
ScanMiRAnno	0.94	0.07	1.00
enrichedMirTxPairs	0.7	0.0	0.7
getTranscriptSequence	1.88	0.00	1.87
plotSitesOnUTR	3.03	0.01	3.05
runFullScan	1.23	0.00	1.23
save-load-IndexedFst	0.02	0.00	0.02
scanMiRApp	0	0	0
scanMiRserver	0.76	0.00	0.77
scanMiRui	0.28	0.02	0.29

CHECK results for scanMiRApp on tokay2

Summary

Command output

Installation output

Tests output

Example timings