Back to Multiple platform build/check report for BioC 3.17
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This page was generated on 2023-01-28 11:08:35 -0500 (Sat, 28 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4465
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-01-10 r83596 ucrt) -- "Unsuffered Consequences" 4246
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4269
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 merida1


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? 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 483/2162HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
deconvR 1.5.0  (landing page)
İrem B. Gündüz
Snapshot Date: 2023-01-27 14:00:19 -0500 (Fri, 27 Jan 2023)
git_url: https://git.bioconductor.org/packages/deconvR
git_branch: master
git_last_commit: 0b15c5d
git_last_commit_date: 2022-11-15 04:12:58 -0500 (Tue, 15 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: deconvR
Version: 1.5.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:deconvR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings deconvR_1.5.0.tar.gz
StartedAt: 2023-01-28 00:22:55 -0500 (Sat, 28 Jan 2023)
EndedAt: 2023-01-28 00:55:21 -0500 (Sat, 28 Jan 2023)
EllapsedTime: 1946.2 seconds
RetCode: 0
Status:   OK  
CheckDir: deconvR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:deconvR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings deconvR_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/deconvR.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* R was compiled by
    Apple clang version 12.0.0 (clang-1200.0.32.29)
    GNU Fortran (GCC) 8.2.0
* running under: macOS Mojave 10.14.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘deconvR/DESCRIPTION’ ... OK
* this is package ‘deconvR’ version ‘1.5.0’
* 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 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
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
BSmeth2Probe 4.069  0.116   5.377
* 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:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL deconvR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3/Resources/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) (2023-01-10 r83596) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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: 
else 
that 
this 
CELL TYPES IN EXTENDED ATLAS: 
else 
that 
this 
CELL TYPES IN EXTENDED ATLAS: 
else_v2 
else 
this_v2 
that 
that_v2 
Monocytes_EPIC 
this 
CELL TYPES IN EXTENDED ATLAS: 
example_cell_type 
Monocytes_EPIC 
B.cells_EPIC 
CD4T.cells_EPIC 
NK.cells_EPIC 
CD8T.cells_EPIC 
Neutrophils_EPIC 
Erythrocyte_progenitors 
Adipocytes 
Cortical_neurons 
Hepatocytes 
Lung_cells 
Pancreatic_beta_cells 
Pancreatic_acinar_cells 
Pancreatic_duct_cells 
Vascular_endothelial_cells 
Colon_epithelial_cells 
Left_atrium 
Bladder 
Breast 
Head_and_neck_larynx 
Kidney 
Prostate 
Thyroid 
Upper_GI 
Uterus_cervix 
Unique used IDs: 0
example_cell_type

Unique used IDs: 200
Monocytes_EPIC

Unique used IDs: 400
B.cells_EPIC

Unique used IDs: 600
CD4T.cells_EPIC

Unique used IDs: 800
NK.cells_EPIC

Unique used IDs: 1000
CD8T.cells_EPIC

Unique used IDs: 1200
Neutrophils_EPIC

Unique used IDs: 1400
Erythrocyte_progenitors

Unique used IDs: 1600
Adipocytes

Unique used IDs: 1800
Cortical_neurons

Unique used IDs: 2000
Hepatocytes

Unique used IDs: 2200
Lung_cells

Unique used IDs: 2400
Pancreatic_beta_cells

Unique used IDs: 2600
Pancreatic_acinar_cells

Unique used IDs: 2800
Pancreatic_duct_cells

Unique used IDs: 3000
Vascular_endothelial_cells

Unique used IDs: 3200
Colon_epithelial_cells

Unique used IDs: 3400
Left_atrium

Unique used IDs: 3600
Bladder

Unique used IDs: 3800
Breast

Unique used IDs: 4000
Head_and_neck_larynx

Unique used IDs: 4200
Kidney

Unique used IDs: 4400
Prostate

Unique used IDs: 4600
Thyroid

Unique used IDs: 4800
Upper_GI

Unique used IDs: 5000
Uterus_cervix

[ FAIL 0 | WARN 189 | SKIP 0 | PASS 151 ]

[ FAIL 0 | WARN 189 | SKIP 0 | PASS 151 ]
> 
> proc.time()
    user   system  elapsed 
 973.200    6.912 1381.389 

Example timings

deconvR.Rcheck/deconvR-Ex.timings

nameusersystemelapsed
BSmeth2Probe4.0690.1165.377
deconvolute2.7520.1013.646
findSignatures0.7900.0301.066
simulateCellMix0.4520.0140.603