Back to Multiple platform build/check report for BioC 3.16:   simplified   long
ABCDEFGHIJKLM[N]OPQRSTUVWXYZ

This page was generated on 2023-04-12 11:05:43 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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 palomino4


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? 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 1326/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NanoTube 1.4.0  (landing page)
Caleb Class
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/NanoTube
git_branch: RELEASE_3_16
git_last_commit: 7d37b55
git_last_commit_date: 2022-11-01 11:25:13 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: NanoTube
Version: 1.4.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:NanoTube.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings NanoTube_1.4.0.tar.gz
StartedAt: 2023-04-11 03:53:31 -0400 (Tue, 11 Apr 2023)
EndedAt: 2023-04-11 03:56:40 -0400 (Tue, 11 Apr 2023)
EllapsedTime: 189.1 seconds
RetCode: 1
Status:   ERROR  
CheckDir: NanoTube.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:NanoTube.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings NanoTube_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/NanoTube.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'NanoTube/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'NanoTube' 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 '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
* 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
untar_dirs: no visible global function definition for 'untar'
Undefined global functions or variables:
  untar
Consider adding
  importFrom("utils", "untar")
to your NAMESPACE file.
* 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 ...Warning in file(con, "r") :
  cannot open file 'NanoTube-Ex.Rout': Permission denied
Error in file(con, "r") : cannot open the connection
Execution halted

Installation output

NanoTube.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL NanoTube
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
* installing *source* package 'NanoTube' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (NanoTube)

Tests output


Example timings

NanoTube.Rcheck/NanoTube-Ex.timings

nameusersystemelapsed
deVolcano0.160.060.22
fgseaPostprocessing 1.07 0.0316.05
fgseaPostprocessingXLSX 0.80 0.0314.21
fgseaToLEdge 0.72 0.0215.39
gm_mean000
groupFGSEA 0.64 0.0513.78
groupedGSEAtoStackedReport 0.69 0.0313.37
limmaToFGSEA 1.39 0.0423.05
makeDiffExprFile0.040.000.05
makeNanoStringSetFromEset0.380.050.75
nanostringPCA0.700.162.31
negativeQC0.230.010.25
normalize_housekeeping0.240.020.25
normalize_pos_controls0.120.000.12
nsdiffToFGSEA000
positiveQC2.630.002.63
processNanostringData0.390.040.45
read_merge_rcc0.120.000.12
read_rcc000
read_sampleData0.080.030.11
remove_background0.210.000.22
runLimmaAnalysis0.160.020.17