Back to Multiple platform build/check report for BioC 3.15
ABC[D]EFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2022-01-22 11:05:41 -0500 (Sat, 22 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4163
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4058
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4000
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4117
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 deconvR on nebbiolo1


To the developers/maintainers of the deconvR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/deconvR.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 469/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
deconvR 1.1.1  (landing page)
İrem B. Gündüz
Snapshot Date: 2022-01-21 13:55:18 -0500 (Fri, 21 Jan 2022)
git_url: https://git.bioconductor.org/packages/deconvR
git_branch: master
git_last_commit: 7cf3911
git_last_commit_date: 2021-10-28 04:16:08 -0500 (Thu, 28 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    NA    NA  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'S4Vectors' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: deconvR
Version: 1.1.1
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:deconvR.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings deconvR_1.1.1.tar.gz
StartedAt: 2022-01-21 18:53:04 -0500 (Fri, 21 Jan 2022)
EndedAt: 2022-01-21 18:59:30 -0500 (Fri, 21 Jan 2022)
EllapsedTime: 386.3 seconds
RetCode: 0
Status:   OK  
CheckDir: deconvR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:deconvR.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings deconvR_1.1.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/deconvR.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘deconvR/DESCRIPTION’ ... OK
* this is package ‘deconvR’ version ‘1.1.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘deconvR’ 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 ... 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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

deconvR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL deconvR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘deconvR’ ...
** 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 (deconvR)

Tests output

deconvR.Rcheck/tests/testthat.Rout


R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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(deconvR)
Loading required package: data.table
> 
> test_check("deconvR")
Received list of locations.
Reading file.
Reading file.
uniting...
BSmeth2Probe couldn't find any match between the probe IDs and
        WGBS data you have provided. Please make sure that you're using an
        appropriate probe ID locations with your WGBS data.
Received list of locations.
Reading file.
Reading file.
Received list of locations.
Reading file.
Reading file.
uniting...
BSmeth2Probe couldn't find any match between the probe IDs and
        WGBS data you have provided. Please make sure that you're using an
        appropriate probe ID locations with your WGBS data.
Received list of locations.
Reading file.
Reading file.
uniting...
BSmeth2Probe couldn't find any match between the probe IDs and
        WGBS data you have provided. Please make sure that you're using an
        appropriate probe ID locations with your WGBS data.
DECONVOLUTION WITH NNLS
SUMMARY OF PARTIAL R-SQUARED VALUES FOR NNLS: 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
      1       1       1       1       1       1 
DECONVOLUTION WITH NNLS
SUMMARY OF PARTIAL R-SQUARED VALUES FOR NNLS: 
DECONVOLUTION WITH NNLS
DECONVOLUTION WITH NNLS
SUMMARY OF PARTIAL R-SQUARED VALUES FOR NNLS: 
SUMMARY OF PARTIAL R-SQUARED VALUES FOR NNLS : 
DECONVOLUTION WITH NNLS
SUMMARY OF PARTIAL R-SQUARED VALUES FOR NNLS: 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
      1       1       1       1       1       1 
[1] "double"
DECONVOLUTION WITH NNLS
DECONVOLUTION WITH NNLS
SUMMARY OF PARTIAL R-SQUARED VALUES FOR NNLS: 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
      1       1       1       1       1       1 
DECONVOLUTION WITH NNLS
DECONVOLUTION WITH NNLS
DECONVOLUTION WITH NNLS
DECONVOLUTION WITH SVR
SUMMARY OF PARTIAL R-SQUARED VALUES FOR SVR: 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
      1       1       1       1       1       1 
DECONVOLUTION WITH SVR
SUMMARY OF PARTIAL R-SQUARED VALUES FOR SVR: 
DECONVOLUTION WITH SVR
DECONVOLUTION WITH SVR
SUMMARY OF PARTIAL R-SQUARED VALUES FOR SVR: 
SUMMARY OF PARTIAL R-SQUARED VALUES FOR SVR : 
DECONVOLUTION WITH SVR
SUMMARY OF PARTIAL R-SQUARED VALUES FOR SVR: 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
      1       1       1       1       1       1 
[1] "double"
DECONVOLUTION WITH SVR
DECONVOLUTION WITH SVR
SUMMARY OF PARTIAL R-SQUARED VALUES FOR SVR: 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
      1       1       1       1       1       1 
DECONVOLUTION WITH SVR
DECONVOLUTION WITH SVR
DECONVOLUTION WITH QP
SUMMARY OF PARTIAL R-SQUARED VALUES FOR QP: 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
      1       1       1       1       1       1 
DECONVOLUTION WITH QP
SUMMARY OF PARTIAL R-SQUARED VALUES FOR QP: 
DECONVOLUTION WITH QP
DECONVOLUTION WITH QP
SUMMARY OF PARTIAL R-SQUARED VALUES FOR QP: 
SUMMARY OF PARTIAL R-SQUARED VALUES FOR QP : 
DECONVOLUTION WITH QP
SUMMARY OF PARTIAL R-SQUARED VALUES FOR QP: 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
      1       1       1       1       1       1 
[1] "double"
DECONVOLUTION WITH QP
DECONVOLUTION WITH QP
SUMMARY OF PARTIAL R-SQUARED VALUES FOR QP: 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
      1       1       1       1       1       1 
DECONVOLUTION WITH QP
DECONVOLUTION WITH QP
DECONVOLUTION WITH RLM
SUMMARY OF PARTIAL R-SQUARED VALUES FOR RLM: 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
      1       1       1       1       1       1 
DECONVOLUTION WITH RLM
SUMMARY OF PARTIAL R-SQUARED VALUES FOR RLM: 
DECONVOLUTION WITH RLM

DECONVOLUTION WITH RLM
SUMMARY OF PARTIAL R-SQUARED VALUES FOR RLM: 
SUMMARY OF PARTIAL R-SQUARED VALUES FOR RLM : 
DECONVOLUTION WITH RLM
SUMMARY OF PARTIAL R-SQUARED VALUES FOR RLM: 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
      1       1       1       1       1       1 
[1] "double"
DECONVOLUTION WITH RLM
DECONVOLUTION WITH RLM
SUMMARY OF PARTIAL R-SQUARED VALUES FOR RLM: 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
      1       1       1       1       1       1 
DECONVOLUTION WITH RLM
DECONVOLUTION WITH RLM
CELL TYPES IN EXTENDED ATLAS: 
example_cell_type 
CELL TYPES IN EXTENDED ATLAS: 
that 
else 
this 
CELL TYPES IN EXTENDED ATLAS: 
that 
else 
this 
CELL TYPES IN EXTENDED ATLAS: 
else_v2 
this_v2 
else 
that_v2 
that 
this 
Monocytes_EPIC 
[ FAIL 0 | WARN 48 | SKIP 0 | PASS 146 ]

[ FAIL 0 | WARN 48 | SKIP 0 | PASS 146 ]
> 
> proc.time()
   user  system elapsed 
172.693   2.263 175.509 

Example timings

deconvR.Rcheck/deconvR-Ex.timings

nameusersystemelapsed
BSmeth2Probe2.3060.0962.402
deconvolute2.2800.3522.633
findSignatures0.2550.0040.240
simulateCellMix0.1990.0000.199