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

Version: 1.0.0

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:NanoTube.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings NanoTube_1.0.0.tar.gz

StartedAt: 2022-04-12 23:38:18 -0400 (Tue, 12 Apr 2022)

EndedAt: 2022-04-12 23:44:41 -0400 (Tue, 12 Apr 2022)

EllapsedTime: 383.4 seconds

RetCode: 0

Status: OK

CheckDir: NanoTube.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:NanoTube.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings NanoTube_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/NanoTube.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 'NanoTube/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'NanoTube' 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 'NanoTube' 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
limmaToFGSEA               1.28   0.07   32.33
fgseaPostprocessing        0.97   0.04   15.17
groupedGSEAtoStackedReport 0.80   0.00   15.38
fgseaPostprocessingXLSX    0.71   0.01   15.49
fgseaToLEdge               0.69   0.03   14.25
groupFGSEA                 0.68   0.03   16.04
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
limmaToFGSEA               1.50   0.05   32.06
fgseaPostprocessing        1.26   0.05   17.54
groupedGSEAtoStackedReport 0.88   0.04   17.42
fgseaToLEdge               0.81   0.00   16.69
groupFGSEA                 0.75   0.03   16.28
fgseaPostprocessingXLSX    0.75   0.02   15.25
* 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/NanoTube_1.0.0.tar.gz && rm -rf NanoTube.buildbin-libdir && mkdir NanoTube.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=NanoTube.buildbin-libdir NanoTube_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL NanoTube_1.0.0.zip && rm NanoTube_1.0.0.tar.gz NanoTube_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
100  466k  100  466k    0     0  1029k      0 --:--:-- --:--:-- --:--:-- 1032k

install for i386

* installing *source* package 'NanoTube' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'NanoTube'
    finding HTML links ... done
    ExamplePathways                         html  
    ExampleResults                          html  
    NanoTube                                html  
    deVolcano                               html  
    fgseaPostprocessing                     html  
    fgseaPostprocessingXLSX                 html  
    fgseaToLEdge                            html  
    gm_mean                                 html  
    groupFGSEA                              html  
    groupedGSEAtoStackedReport              html  
    limmaToFGSEA                            html  
    makeDiffExprFile                        html  
    makeFGSEAmasterTable                    html  
    makeNanoStringSetFromEset               html  
    nanostringPCA                           html  
    negativeQC                              html  
    normalize_housekeeping                  html  
    normalize_pos_controls                  html  
    nsdiffToFGSEA                           html  
    positiveQC                              html  
    processNanostringData                   html  
    read_cpdb_sourceDBs                     html  
    read_cpdb_tab                           html  
    read_merge_rcc                          html  
    read_rcc                                html  
    read_sampleData                         html  
    remove_background                       html  
    runLimmaAnalysis                        html  
    unzip_dirs                              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 'NanoTube' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'NanoTube' as NanoTube_1.0.0.zip
* DONE (NanoTube)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'NanoTube' 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(NanoTube)
Loading required package: Biobase
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

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: ggplot2
> 
> test_check("NanoTube")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
   3.59    0.12    3.70


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(NanoTube)
Loading required package: Biobase
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

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: ggplot2
> 
> test_check("NanoTube")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
   3.25    0.18    3.43

name	user	system	elapsed
deVolcano	0.16	0.04	0.20
fgseaPostprocessing	0.97	0.04	15.17
fgseaPostprocessingXLSX	0.71	0.01	15.49
fgseaToLEdge	0.69	0.03	14.25
gm_mean	0	0	0
groupFGSEA	0.68	0.03	16.04
groupedGSEAtoStackedReport	0.80	0.00	15.38
limmaToFGSEA	1.28	0.07	32.33
makeDiffExprFile	0.03	0.01	0.04
makeNanoStringSetFromEset	0.61	0.00	1.22
nanostringPCA	0.98	0.10	1.11
negativeQC	0.25	0.00	0.25
normalize_housekeeping	0.24	0.01	0.25
normalize_pos_controls	0.09	0.03	0.12
nsdiffToFGSEA	0	0	0
positiveQC	2.80	0.02	2.81
processNanostringData	0.59	0.01	0.61
read_merge_rcc	0.17	0.00	0.18
read_rcc	0.02	0.00	0.01
read_sampleData	0.14	0.00	0.14
remove_background	0.45	0.00	0.46
runLimmaAnalysis	0.35	0.05	0.39

name	user	system	elapsed
deVolcano	0.31	0.03	0.35
fgseaPostprocessing	1.26	0.05	17.54
fgseaPostprocessingXLSX	0.75	0.02	15.25
fgseaToLEdge	0.81	0.00	16.69
gm_mean	0	0	0
groupFGSEA	0.75	0.03	16.28
groupedGSEAtoStackedReport	0.88	0.04	17.42
limmaToFGSEA	1.50	0.05	32.06
makeDiffExprFile	0.03	0.02	0.05
makeNanoStringSetFromEset	0.58	0.01	0.59
nanostringPCA	0.87	0.02	0.89
negativeQC	0.36	0.00	0.36
normalize_housekeeping	0.38	0.01	0.39
normalize_pos_controls	0.12	0.00	0.13
nsdiffToFGSEA	0	0	0
positiveQC	2.61	0.00	2.61
processNanostringData	0.41	0.02	0.42
read_merge_rcc	0.09	0.02	0.11
read_rcc	0	0	0
read_sampleData	0.11	0.00	0.11
remove_background	0.25	0.00	0.25
runLimmaAnalysis	0.17	0.00	0.17

CHECK results for NanoTube on tokay2

Summary

Command output

Installation output

Tests output

Example timings