| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-06-13 12:07:42 -0400 (Tue, 13 Jun 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.0 RC (2023-04-13 r84269) -- "Already Tomorrow" | 4628 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.0 RC (2023-04-13 r84269 ucrt) -- "Already Tomorrow" | 4379 |
| 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 | ||||
| Package 929/2229 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| HiContacts 1.2.0 (landing page) Jacques Serizay
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK |  | ||||||||
|
To the developers/maintainers of the HiContacts package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/HiContacts.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: HiContacts |
| Version: 1.2.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:HiContacts.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings HiContacts_1.2.0.tar.gz |
| StartedAt: 2023-06-12 21:54:02 -0400 (Mon, 12 Jun 2023) |
| EndedAt: 2023-06-12 21:59:34 -0400 (Mon, 12 Jun 2023) |
| EllapsedTime: 332.8 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: HiContacts.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:HiContacts.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings HiContacts_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/HiContacts.Rcheck’
* using R version 4.3.0 RC (2023-04-13 r84269)
* using platform: x86_64-pc-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 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘HiContacts/DESCRIPTION’ ... OK
* this is package ‘HiContacts’ version ‘1.2.0’
* 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 ‘HiContacts’ 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 loading without being on the library search path ... 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘HiContacts-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: distanceLaw
> ### Title: Compute the law of distance-dependent contact frequency, a.k.a.
> ### P(s)
> ### Aliases: distanceLaw Ps distanceLaw,HiCExperiment,missing-method
> ### distanceLaw,PairsFile,missing-method
> ### distanceLaw,PairsFile,GRanges-method localDistanceLaw
> ### distanceLaw,HiCExperiment,GRanges-method
>
> ### ** Examples
>
> contacts_yeast <- contacts_yeast()
see ?HiContactsData and browseVignettes('HiContactsData') for documentation
loading from cache
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'con' in selecting a method for function 'import': Provided file is not a .cool/.mcool file.
Aborting now.
Calls: contacts_yeast ... import -> FileForFormat -> <Anonymous> -> .check_cool_file
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
3. │ ├─BiocIO::import(fpath, "II", resolution = 16000, format = "cool")
4. │ └─BiocIO::import(fpath, "II", resolution = 16000, format = "cool")
5. │ ├─BiocIO::import(FileForFormat(con, format), ...)
6. │ └─BiocIO::FileForFormat(con, format)
7. │ └─get(constructorName, ns)(path)
8. │ └─HiCExperiment:::.check_cool_file(path)
9. │ └─base::stop("Provided file is not a .cool/.mcool file.\n Aborting now.")
10. ├─base::.handleSimpleError(...)
11. │ └─base (local) h(simpleError(msg, call))
12. └─base::.handleSimpleError(...)
13. └─base (local) h(simpleError(msg, call))
[ FAIL 11 | WARN 0 | SKIP 0 | PASS 1 ]
Error: Test failures
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘HiContacts.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘HiContacts.Rmd’ using rmarkdown
Quitting from lines 87-93 [unnamed-chunk-5] (HiContacts.Rmd)
Error: processing vignette 'HiContacts.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'plotMatrix': error in evaluating the argument 'con' in selecting a method for function 'import': Provided file is not a .cool/.mcool file.
Aborting now.
--- failed re-building ‘HiContacts.Rmd’
SUMMARY: processing the following file failed:
‘HiContacts.Rmd’
Error: Vignette re-building failed.
Execution halted
* checking PDF version of manual ... OK
* DONE
Status: 3 ERRORs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/HiContacts.Rcheck/00check.log’
for details.
HiContacts.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL HiContacts ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’ * installing *source* package ‘HiContacts’ ... ** using staged installation ** R ** 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 (HiContacts)
HiContacts.Rcheck/tests/testthat.Rout.fail
R version 4.3.0 RC (2023-04-13 r84269) -- "Already Tomorrow"
Copyright (C) 2023 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.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(HiContacts)
Loading required package: HiCExperiment
Consider using the `HiContacts` package to perform advanced genomic operations
on `HiCExperiment` objects.
Read "Orchestrating Hi-C analysis with Bioconductor" online book to learn more:
https://js2264.github.io/OHCA/
>
> test_check("HiContacts")
[ FAIL 11 | WARN 0 | SKIP 0 | PASS 1 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-arithmetics.R:2:5'): arithmetics works ─────────────────────────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'refocus': error in evaluating the argument 'x' in selecting a method for function 'zoom': error in evaluating the argument 'con' in selecting a method for function 'import': Provided file is not a .cool/.mcool file.
Aborting now.
Backtrace:
▆
1. ├─HiCExperiment::refocus(...) at test-arithmetics.R:2:4
2. ├─HiCExperiment::zoom(HiCExperiment::contacts_yeast(), 4000)
3. ├─HiCExperiment::contacts_yeast()
4. │ ├─BiocIO::import(fpath, "II", resolution = 16000, format = "cool")
5. │ └─BiocIO::import(fpath, "II", resolution = 16000, format = "cool")
6. │ ├─BiocIO::import(FileForFormat(con, format), ...)
7. │ └─BiocIO::FileForFormat(con, format)
8. │ └─get(constructorName, ns)(path)
9. │ └─HiCExperiment:::.check_cool_file(path)
10. │ └─base::stop("Provided file is not a .cool/.mcool file.\n Aborting now.")
11. ├─base::.handleSimpleError(...)
12. │ └─base (local) h(simpleError(msg, call))
13. ├─base::.handleSimpleError(...)
14. │ └─base (local) h(simpleError(msg, call))
15. └─base::.handleSimpleError(...)
16. └─base (local) h(simpleError(msg, call))
── Error ('test-comps-insulation-scalogram.R:5:5'): compartments works ─────────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'con' in selecting a method for function 'import': Provided file is not a .cool/.mcool file.
Aborting now.
Backtrace:
▆
1. ├─HiCExperiment::contacts_yeast(full = TRUE) at test-comps-insulation-scalogram.R:5:4
2. │ ├─BiocIO::import(fpath, resolution = 16000, format = "cool")
3. │ └─BiocIO::import(fpath, resolution = 16000, format = "cool")
4. │ ├─BiocIO::import(FileForFormat(con, format), ...)
5. │ └─BiocIO::FileForFormat(con, format)
6. │ └─get(constructorName, ns)(path)
7. │ └─HiCExperiment:::.check_cool_file(path)
8. │ └─base::stop("Provided file is not a .cool/.mcool file.\n Aborting now.")
9. └─base::.handleSimpleError(...)
10. └─base (local) h(simpleError(msg, call))
── Error ('test-comps-insulation-scalogram.R:30:5'): insulation works ──────────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'zoom': error in evaluating the argument 'x' in selecting a method for function 'refocus': error in evaluating the argument 'con' in selecting a method for function 'import': Provided file is not a .cool/.mcool file.
Aborting now.
Backtrace:
▆
1. ├─HiCExperiment::zoom(...) at test-comps-insulation-scalogram.R:30:4
2. ├─HiCExperiment::refocus(HiCExperiment::contacts_yeast(), "II:1-300000")
3. ├─HiCExperiment::contacts_yeast()
4. │ ├─BiocIO::import(fpath, "II", resolution = 16000, format = "cool")
5. │ └─BiocIO::import(fpath, "II", resolution = 16000, format = "cool")
6. │ ├─BiocIO::import(FileForFormat(con, format), ...)
7. │ └─BiocIO::FileForFormat(con, format)
8. │ └─get(constructorName, ns)(path)
9. │ └─HiCExperiment:::.check_cool_file(path)
10. │ └─base::stop("Provided file is not a .cool/.mcool file.\n Aborting now.")
11. ├─base::.handleSimpleError(...)
12. │ └─base (local) h(simpleError(msg, call))
13. ├─base::.handleSimpleError(...)
14. │ └─base (local) h(simpleError(msg, call))
15. └─base::.handleSimpleError(...)
16. └─base (local) h(simpleError(msg, call))
── Error ('test-comps-insulation-scalogram.R:52:5'): scalogram works ───────────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'con' in selecting a method for function 'import': Provided file is not a .cool/.mcool file.
Aborting now.
Backtrace:
▆
1. ├─HiCExperiment::contacts_yeast() at test-comps-insulation-scalogram.R:52:4
2. │ ├─BiocIO::import(fpath, "II", resolution = 16000, format = "cool")
3. │ └─BiocIO::import(fpath, "II", resolution = 16000, format = "cool")
4. │ ├─BiocIO::import(FileForFormat(con, format), ...)
5. │ └─BiocIO::FileForFormat(con, format)
6. │ └─get(constructorName, ns)(path)
7. │ └─HiCExperiment:::.check_cool_file(path)
8. │ └─base::stop("Provided file is not a .cool/.mcool file.\n Aborting now.")
9. └─base::.handleSimpleError(...)
10. └─base (local) h(simpleError(msg, call))
── Error ('test-data.R:2:5'): Data works ───────────────────────────────────────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'con' in selecting a method for function 'import': Provided file is not a .cool/.mcool file.
Aborting now.
Backtrace:
▆
1. ├─testthat::expect_s4_class(contacts_yeast(), "HiCExperiment") at test-data.R:2:4
2. │ └─testthat::quasi_label(enquo(object), arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─HiCExperiment::contacts_yeast()
5. │ ├─BiocIO::import(fpath, "II", resolution = 16000, format = "cool")
6. │ └─BiocIO::import(fpath, "II", resolution = 16000, format = "cool")
7. │ ├─BiocIO::import(FileForFormat(con, format), ...)
8. │ └─BiocIO::FileForFormat(con, format)
9. │ └─get(constructorName, ns)(path)
10. │ └─HiCExperiment:::.check_cool_file(path)
11. │ └─base::stop("Provided file is not a .cool/.mcool file.\n Aborting now.")
12. └─base::.handleSimpleError(...)
13. └─base (local) h(simpleError(msg, call))
── Error ('test-plotMatrix.R:2:5'): plotMatrix works ───────────────────────────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'con' in selecting a method for function 'import': Provided file is not a .cool/.mcool file.
Aborting now.
Backtrace:
▆
1. ├─HiCExperiment::contacts_yeast() at test-plotMatrix.R:2:4
2. │ ├─BiocIO::import(fpath, "II", resolution = 16000, format = "cool")
3. │ └─BiocIO::import(fpath, "II", resolution = 16000, format = "cool")
4. │ ├─BiocIO::import(FileForFormat(con, format), ...)
5. │ └─BiocIO::FileForFormat(con, format)
6. │ └─get(constructorName, ns)(path)
7. │ └─HiCExperiment:::.check_cool_file(path)
8. │ └─base::stop("Provided file is not a .cool/.mcool file.\n Aborting now.")
9. └─base::.handleSimpleError(...)
10. └─base (local) h(simpleError(msg, call))
── Error ('test-v4C-cistrans-Ps-utils.R:2:5'): Contacts works ──────────────────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'con' in selecting a method for function 'import': Provided file is not a .cool/.mcool file.
Aborting now.
Backtrace:
▆
1. ├─HiCExperiment::contacts_yeast() at test-v4C-cistrans-Ps-utils.R:2:4
2. │ ├─BiocIO::import(fpath, "II", resolution = 16000, format = "cool")
3. │ └─BiocIO::import(fpath, "II", resolution = 16000, format = "cool")
4. │ ├─BiocIO::import(FileForFormat(con, format), ...)
5. │ └─BiocIO::FileForFormat(con, format)
6. │ └─get(constructorName, ns)(path)
7. │ └─HiCExperiment:::.check_cool_file(path)
8. │ └─base::stop("Provided file is not a .cool/.mcool file.\n Aborting now.")
9. └─base::.handleSimpleError(...)
10. └─base (local) h(simpleError(msg, call))
── Error ('test-v4C-cistrans-Ps-utils.R:11:5'): v4C works ──────────────────────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'refocus': error in evaluating the argument 'con' in selecting a method for function 'import': Provided file is not a .cool/.mcool file.
Aborting now.
Backtrace:
▆
1. ├─HiCExperiment::refocus(HiCExperiment::contacts_yeast(), "II") at test-v4C-cistrans-Ps-utils.R:11:4
2. ├─HiCExperiment::contacts_yeast()
3. │ ├─BiocIO::import(fpath, "II", resolution = 16000, format = "cool")
4. │ └─BiocIO::import(fpath, "II", resolution = 16000, format = "cool")
5. │ ├─BiocIO::import(FileForFormat(con, format), ...)
6. │ └─BiocIO::FileForFormat(con, format)
7. │ └─get(constructorName, ns)(path)
8. │ └─HiCExperiment:::.check_cool_file(path)
9. │ └─base::stop("Provided file is not a .cool/.mcool file.\n Aborting now.")
10. ├─base::.handleSimpleError(...)
11. │ └─base (local) h(simpleError(msg, call))
12. └─base::.handleSimpleError(...)
13. └─base (local) h(simpleError(msg, call))
── Error ('test-v4C-cistrans-Ps-utils.R:24:5'): cistrans works ─────────────────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'con' in selecting a method for function 'import': Provided file is not a .cool/.mcool file.
Aborting now.
Backtrace:
▆
1. ├─HiCExperiment::contacts_yeast() at test-v4C-cistrans-Ps-utils.R:24:4
2. │ ├─BiocIO::import(fpath, "II", resolution = 16000, format = "cool")
3. │ └─BiocIO::import(fpath, "II", resolution = 16000, format = "cool")
4. │ ├─BiocIO::import(FileForFormat(con, format), ...)
5. │ └─BiocIO::FileForFormat(con, format)
6. │ └─get(constructorName, ns)(path)
7. │ └─HiCExperiment:::.check_cool_file(path)
8. │ └─base::stop("Provided file is not a .cool/.mcool file.\n Aborting now.")
9. └─base::.handleSimpleError(...)
10. └─base (local) h(simpleError(msg, call))
── Error ('test-v4C-cistrans-Ps-utils.R:31:5'): Ps works ───────────────────────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'con' in selecting a method for function 'import': Provided file is not a .cool/.mcool file.
Aborting now.
Backtrace:
▆
1. ├─HiCExperiment::contacts_yeast() at test-v4C-cistrans-Ps-utils.R:31:4
2. │ ├─BiocIO::import(fpath, "II", resolution = 16000, format = "cool")
3. │ └─BiocIO::import(fpath, "II", resolution = 16000, format = "cool")
4. │ ├─BiocIO::import(FileForFormat(con, format), ...)
5. │ └─BiocIO::FileForFormat(con, format)
6. │ └─get(constructorName, ns)(path)
7. │ └─HiCExperiment:::.check_cool_file(path)
8. │ └─base::stop("Provided file is not a .cool/.mcool file.\n Aborting now.")
9. └─base::.handleSimpleError(...)
10. └─base (local) h(simpleError(msg, call))
── Error ('test-v4C-cistrans-Ps-utils.R:55:5'): checks and utils work ──────────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'refocus': error in evaluating the argument 'con' in selecting a method for function 'import': Provided file is not a .cool/.mcool file.
Aborting now.
Backtrace:
▆
1. ├─HiCExperiment::refocus(HiCExperiment::contacts_yeast(), "II:1-30000") at test-v4C-cistrans-Ps-utils.R:55:4
2. ├─HiCExperiment::contacts_yeast()
3. │ ├─BiocIO::import(fpath, "II", resolution = 16000, format = "cool")
4. │ └─BiocIO::import(fpath, "II", resolution = 16000, format = "cool")
5. │ ├─BiocIO::import(FileForFormat(con, format), ...)
6. │ └─BiocIO::FileForFormat(con, format)
7. │ └─get(constructorName, ns)(path)
8. │ └─HiCExperiment:::.check_cool_file(path)
9. │ └─base::stop("Provided file is not a .cool/.mcool file.\n Aborting now.")
10. ├─base::.handleSimpleError(...)
11. │ └─base (local) h(simpleError(msg, call))
12. └─base::.handleSimpleError(...)
13. └─base (local) h(simpleError(msg, call))
[ FAIL 11 | WARN 0 | SKIP 0 | PASS 1 ]
Error: Test failures
Execution halted
HiContacts.Rcheck/HiContacts-Ex.timings
| name | user | system | elapsed | |
| Contacts | 4.255 | 0.761 | 5.455 | |