===============================
R CMD BUILD
===============================
* checking for file mulea/DESCRIPTION ... OK
* preparing mulea:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building mulea_0.99.10.tar.gz
===============================
BiocCheckGitClone('mulea')
===============================
BiocCheckVersion: 1.39.26
BiocVersion: 3.19
Package: mulea
PackageVersion: 0.99.10
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3328/mulea_20240321131247/mulea
platform: unix
isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
BiocCheck results
0 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory /home/pkgbuild/packagebuilder/workers/jobs/3328/mulea_20240321131247/mulea.Rcheck
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* using option --no-vignettes
* checking for file mulea/DESCRIPTION ... OK
* checking extension type ... Package
* this is package mulea version 0.99.10
* 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 mulea can be installed ... OK
* used C++ compiler: g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [2s/2s] OK
* checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the package can be unloaded cleanly ... [2s/2s] OK
* checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
* checking loading without being on the library search path ... [2s/2s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: devtools
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [8s/8s] OK
* checking Rd files ... [0s/0s] NOTE
checkRd: (-1) ora-class.Rd:37: Lost braces; missing escapes or markup?
37 | \item and all \code{method} options from \code{p.adjust} {stats} documentation.
| ^
* checking Rd metadata ... OK
* checking Rd line widths ... 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 line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in vignettes ... OK
* checking examples ... [5s/6s] ERROR
Running examples in mulea-Ex.R failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ora-class
> ### Title: An S4 class to represent a set based tests in mulea.
> ### Aliases: ora-class ora
>
> ### ** Examples
>
> library(mulea)
>
> # loading and filtering the example ontology from a GMT file
> tf_gmt <- read_gmt(file = system.file(
+ package="mulea", "extdata",
+ "Transcription_factor_RegulonDB_Escherichia_coli_GeneSymbol.gmt"))
> tf_gmt_filtered <- filter_ontology(gmt = tf_gmt, min_nr_of_elements = 3,
+ max_nr_of_elements = 400)
>
> # loading the example data
> sign_genes <- readLines(system.file(package = "mulea", "extdata",
+ "sign_genes.csv"))
> background_genes <- readLines(system.file(package="mulea", "extdata",
+ "background_genes.csv"))
>
> # creating the ORA model
> ora_model <- ora(gmt = tf_gmt_filtered,
+ # the test set variable
+ element_names = sign_genes,
+ # the background set variable
+ background_element_names = background_genes,
+ # the p-value adjustment method
+ p_value_adjustment_method = "eFDR",
+ # the number of permutations
+ number_of_permutations = 10000,
+ # the number of processor threads to use
+ nthreads = 2)
> # running the ORA
> ora_results <- run_test(ora_model)
Error in checkForRemoteErrors(lapply(cl, recvResult)) :
2 nodes produced errors; first error: Could not find a root 'DESCRIPTION' file that starts with '^Package' in
'/home/pkgbuild/packagebuilder/workers/jobs/3328/mulea_20240321131247/mulea.Rcheck'.
i Are you in your project directory and does your project have a 'DESCRIPTION'
file?
Calls: run_test ... clusterEvalQ -> clusterCall -> checkForRemoteErrors
Execution halted
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [3s/17s]
[4s/17s] ERROR
Running the tests in tests/testthat.R failed.
Last 20 lines of output:
8. mulea:::set.based.enrichment.test(...)
9. mulea:::do_the_simulation(...)
10. parallel::clusterEvalQ(cl, devtools::load_all())
11. parallel::clusterCall(cl, eval, substitute(expr), env = .GlobalEnv)
12. parallel:::checkForRemoteErrors(lapply(cl, recvResult))
Error ('testPermTest.R:20:3'): set.based.enrichment.test.
Error in `checkForRemoteErrors(lapply(cl, recvResult))`: 2 nodes produced errors; first error: Could not find a root 'DESCRIPTION' file that starts with '^Package' in
'/home/pkgbuild/packagebuilder/workers/jobs/3328/mulea_20240321131247/mulea.Rcheck/tests/testthat'.
i Are you in your project directory and does your project have a 'DESCRIPTION'
file?
Backtrace:
1. mulea:::set.based.enrichment.test(...) at testPermTest.R:20:3
2. mulea:::do_the_simulation(...)
3. parallel::clusterEvalQ(cl, devtools::load_all())
4. parallel::clusterCall(cl, eval, substitute(expr), env = .GlobalEnv)
5. parallel:::checkForRemoteErrors(lapply(cl, recvResult))
[ FAIL 11 | WARN 0 | SKIP 0 | PASS 27 ]
Error: Test failures
In addition: There were 22 warnings (use warnings() to see them)
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... [3s/3s] OK
* DONE
Status: 2 ERRORs, 3 NOTEs
See
/home/pkgbuild/packagebuilder/workers/jobs/3328/mulea_20240321131247/mulea.Rcheck/00check.log
for details.
===============================
BiocCheck('mulea_0.99.10.tar.gz')
===============================
BiocCheckVersion: 1.39.26
BiocVersion: 3.19
Package: mulea
PackageVersion: 0.99.10
sourceDir: /tmp/RtmpXjDihB/fileea601ac99742/mulea
installDir: /tmp/RtmpXjDihB/fileea60138c55323
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3328/mulea_20240321131247/mulea.BiocCheck
platform: unix
isTarBall: TRUE
* Installing package...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
* NOTE: Update R version dependency from 4.0.0 to 4.4.0.
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
Bioconductor dependencies found in Imports & Depends (5%).
* Checking for pinned package versions in DESCRIPTION...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of mulea...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* Checking man page documentation...
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
Maintainer is registered at support site.
Package is in the Support Site Watched Tags.
BiocCheck results
0 ERRORS | 0 WARNINGS | 1 NOTES
See the mulea.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.