| Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-02-27 02:34:33 -0000 (Mon, 27 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4259 |
| 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 | ||||
|
To the developers/maintainers of the Dino package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Dino.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. |
| Package 532/2169 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Dino 1.5.0 (landing page) Jared Brown
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
| Package: Dino |
| Version: 1.5.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:Dino.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings Dino_1.5.0.tar.gz |
| StartedAt: 2023-02-24 10:14:37 -0000 (Fri, 24 Feb 2023) |
| EndedAt: 2023-02-24 10:22:50 -0000 (Fri, 24 Feb 2023) |
| EllapsedTime: 493.3 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: Dino.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:Dino.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings Dino_1.5.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/Dino.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘Dino/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Dino’ 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 ‘Dino’ 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
checkCounts: no visible global function definition for ‘as’
Undefined global functions or variables:
as
Consider adding
importFrom("methods", "as")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... ERROR
Running examples in ‘Dino-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Dino
> ### Title: Normalize scRNAseq data
> ### Aliases: Dino
>
> ### ** Examples
>
> # raw data
> data("pbmcSmall")
> str(pbmcSmall)
Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
..@ i : int [1:78331] 0 1 2 3 4 5 6 7 8 9 ...
..@ p : int [1:201] 0 410 834 1161 1661 2028 2419 2792 3093 3552 ...
..@ Dim : int [1:2] 1000 200
..@ Dimnames:List of 2
.. ..$ : chr [1:1000] "ENSG00000087086" "ENSG00000167996" "ENSG00000251562" "ENSG00000205542" ...
.. ..$ : chr [1:200] "CCAACCTGACGTAC-1" "ATCTGGGATTCCGC-1" "TACTTTCTTTTGGG-1" "CAGGCCGAACACGT-1" ...
..@ x : num [1:78331] 132 37 17 37 13 50 30 21 30 51 ...
..@ factors : list()
>
> # run Dino on raw expression matrix
> pbmcSmall_Norm <- Dino(pbmcSmall)
Computing sequencing depth
Calculating regression slope
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Normalizing counts by resampling
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|====================== | 32%Warning in parallel::mccollect(wait = FALSE, timeout = 1) :
1 parallel job did not deliver a result
Error in reducer$value.cache[[as.character(idx)]] <- values :
wrong args for environment subassignment
Calls: Dino ... .bploop_impl -> .collect_result -> .reducer_add -> .reducer_add
Execution halted
* 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 ...
‘Dino.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 1 NOTE
See
‘/home/biocbuild/bbs-3.17-bioc/meat/Dino.Rcheck/00check.log’
for details.
Dino.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL Dino ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘Dino’ ... ** 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 (Dino)
Dino.Rcheck/tests/testthat.Rout
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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(Dino)
>
> test_check("Dino")
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[ FAIL 0 | WARN 1 | SKIP 0 | PASS 9 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 9 ]
>
> proc.time()
user system elapsed
89.183 13.899 67.140
Dino.Rcheck/Dino-Ex.timings
| name | user | system | elapsed |