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This page was generated on 2022-01-24 13:06:39 -0500 (Mon, 24 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
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

CHECK results for NanoTube on tokay2


To the developers/maintainers of the NanoTube package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/NanoTube.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1269/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NanoTube 1.0.0  (landing page)
Caleb Class
Snapshot Date: 2022-01-23 01:55:04 -0500 (Sun, 23 Jan 2022)
git_url: https://git.bioconductor.org/packages/NanoTube
git_branch: RELEASE_3_14
git_last_commit: f066025
git_last_commit_date: 2021-10-26 13:10:49 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

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: 2022-01-23 23:15:09 -0500 (Sun, 23 Jan 2022)
EndedAt: 2022-01-23 23:21:26 -0500 (Sun, 23 Jan 2022)
EllapsedTime: 376.7 seconds
RetCode: 0
Status:   OK  
CheckDir: NanoTube.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/NanoTube.Rcheck'
* using R version 4.1.2 (2021-11-01)
* 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               1.34   0.03   29.42
fgseaPostprocessing        1.00   0.00   16.15
groupedGSEAtoStackedReport 0.75   0.01   14.86
fgseaPostprocessingXLSX    0.68   0.01   15.00
fgseaToLEdge               0.64   0.05   15.01
groupFGSEA                 0.60   0.08   14.63
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
limmaToFGSEA               1.54   0.03   29.61
fgseaPostprocessing        1.15   0.08   14.68
groupedGSEAtoStackedReport 0.86   0.01   15.36
fgseaToLEdge               0.78   0.06   15.31
groupFGSEA                 0.72   0.08   14.85
fgseaPostprocessingXLSX    0.71   0.03   14.98
* 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


Installation output

NanoTube.Rcheck/00install.out

##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


  % 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  1567k      0 --:--:-- --:--:-- --:--:-- 1571k

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

Tests output

NanoTube.Rcheck/tests_i386/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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(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 
   3.01    0.18    3.17 

NanoTube.Rcheck/tests_x64/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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(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 
   3.09    0.29    3.35 

Example timings

NanoTube.Rcheck/examples_i386/NanoTube-Ex.timings

nameusersystemelapsed
deVolcano0.170.020.18
fgseaPostprocessing 1.00 0.0016.15
fgseaPostprocessingXLSX 0.68 0.0115.00
fgseaToLEdge 0.64 0.0515.01
gm_mean000
groupFGSEA 0.60 0.0814.63
groupedGSEAtoStackedReport 0.75 0.0114.86
limmaToFGSEA 1.34 0.0329.42
makeDiffExprFile0.060.000.06
makeNanoStringSetFromEset0.680.102.30
nanostringPCA0.900.060.97
negativeQC0.240.020.25
normalize_housekeeping0.250.010.26
normalize_pos_controls0.110.000.11
nsdiffToFGSEA000
positiveQC2.310.052.36
processNanostringData0.390.000.39
read_merge_rcc0.090.000.10
read_rcc000
read_sampleData0.100.010.10
remove_background0.220.000.22
runLimmaAnalysis0.170.000.17

NanoTube.Rcheck/examples_x64/NanoTube-Ex.timings

nameusersystemelapsed
deVolcano0.20.00.2
fgseaPostprocessing 1.15 0.0814.68
fgseaPostprocessingXLSX 0.71 0.0314.98
fgseaToLEdge 0.78 0.0615.31
gm_mean000
groupFGSEA 0.72 0.0814.85
groupedGSEAtoStackedReport 0.86 0.0115.36
limmaToFGSEA 1.54 0.0329.61
makeDiffExprFile0.100.000.09
makeNanoStringSetFromEset0.560.040.59
nanostringPCA0.920.060.99
negativeQC0.300.030.33
normalize_housekeeping0.260.010.28
normalize_pos_controls0.110.020.12
nsdiffToFGSEA000
positiveQC3.040.003.03
processNanostringData0.620.000.63
read_merge_rcc0.170.020.19
read_rcc0.020.000.01
read_sampleData0.140.010.16
remove_background0.310.020.33
runLimmaAnalysis0.220.000.21