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R CMD BUILD
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* checking for file BulkSignalR/DESCRIPTION ... OK
* preparing BulkSignalR:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a data/datalist file should be added
* building BulkSignalR_0.99.8.tar.gz
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BiocCheckGitClone('BulkSignalR')
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sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3554/016b50b72d624d8ce75d4729080b05b94d177406/BulkSignalR
BiocVersion: 3.21
Package: BulkSignalR
PackageVersion: 0.99.8
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3554/016b50b72d624d8ce75d4729080b05b94d177406/BulkSignalR.BiocCheck
BiocCheckVersion: 1.43.2
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3554/016b50b72d624d8ce75d4729080b05b94d177406/BulkSignalR
installDir: NULL
isTarBall: FALSE
platform: unix
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
BiocCheck v1.43.2 results
0 ERRORS | 0 WARNINGS | i 0 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
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R CMD CHECK
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* using log directory /home/pkgbuild/packagebuilder/workers/jobs/3554/016b50b72d624d8ce75d4729080b05b94d177406/BulkSignalR.Rcheck
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* using option --no-vignettes
* checking for file BulkSignalR/DESCRIPTION ... OK
* checking extension type ... Package
* this is package BulkSignalR version 0.99.8
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
INFO
Imports includes 28 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* 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 BulkSignalR can be installed ... OK
* 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 ... [13s/14s] OK
* checking whether the package can be loaded with stated dependencies ... [12s/13s] OK
* checking whether the package can be unloaded cleanly ... [12s/12s] OK
* checking whether the namespace can be loaded with stated dependencies ... [12s/13s] OK
* checking whether the namespace can be unloaded cleanly ... [13s/14s] OK
* checking loading without being on the library search path ... [13s/14s] OK
* checking whether startup messages can be suppressed ... [13s/14s] OK
* checking use of S3 registration ... 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 ... [49s/51s] NOTE
Found the following calls to attach():
File BulkSignalR/R/zzz.R:
attach(myEnv, name = nameEnv)
See section Good practice in ?attach.
* checking Rd files ... [1s/1s] OK
* 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 contents of data directory ... OK
* checking data for non-ASCII characters ... [14s/14s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in vignettes ... OK
* checking examples ... [125s/137s] ERROR
Running examples in BulkSignalR-Ex.R failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: resetToInitialOrganism
> ### Title: Reset gene names to initial organism providen in first instance
> ### Aliases: resetToInitialOrganism
> ### resetToInitialOrganism,BSRInference-method
>
> ### ** Examples
>
> data(bodyMap.mouse)
> set.seed(123)
> idx <- sample(nrow(bodyMap.mouse), 5000)
>
> bodyMap.mouse <- bodyMap.mouse[idx,1:3]
>
> ortholog.dict <- findOrthoGenes(
+ from_organism = "mmusculus",
+ from_values = rownames(bodyMap.mouse)
+ )
Dictionary Size: 3062 genes
-> 137 : Ligands
-> 142 : Receptors
>
> matrix.expression.human <- convertToHuman(
+ counts = bodyMap.mouse,
+ dictionary = ortholog.dict
+ )
>
> bsrdm <- prepareDataset(
+ counts = matrix.expression.human,
+ species = "mmusculus",
+ conversion.dict = ortholog.dict,
+ min.LR.found = 30
+ )
>
> bsrdm <- learnParameters(bsrdm,
+ quick = TRUE
+ )
Warning messages:
1: In ks.test.default(d, y) :
p-value will be approximate in the presence of ties
2: In ks.test.default(d, y) :
p-value will be approximate in the presence of ties
3: In ks.test.default(d, df$y) :
p-value will be approximate in the presence of ties
4: In ks.test.default(d, y) :
p-value will be approximate in the presence of ties
> subset <- c("REACTOME_BASIGIN_INTERACTIONS",
+ "REACTOME_SYNDECAN_INTERACTIONS",
+ "REACTOME_ECM_PROTEOGLYCANS",
+ "REACTOME_CELL_JUNCTION_ORGANIZATION")
>
> BulkSignalR_Reactome <- BulkSignalR_Reactome[
+ BulkSignalR_Reactome$`Reactome name` %in% subset,]
>
> bsrinf <- initialInference(bsrdm,reference="REACTOME")
Error in `[.data.frame`(conf.pairs, , c("L", "R", "corr", "pwid", "pwname", :
undefined columns selected
Calls: initialInference ... .checkReceptorSignaling -> .downstreamSignaling -> [ -> [.data.frame
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
learnParameters 10.985 0.037 11.024
generateSpatialPlots 9.537 0.775 10.694
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [14s/14s]
[14s/15s] OK
* 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 ... [6s/6s] OK
* DONE
Status: 1 ERROR, 1 NOTE
See
/home/pkgbuild/packagebuilder/workers/jobs/3554/016b50b72d624d8ce75d4729080b05b94d177406/BulkSignalR.Rcheck/00check.log
for details.
WARNING: R CMD check exceeded 10 min requirement
===============================
BiocCheck('BulkSignalR_0.99.8.tar.gz')
===============================
Installing BulkSignalR
Package installed successfully
BulkSignalR session metadata
sourceDir: /tmp/Rtmp2vFnq3/file10e4ec21c3fdb7/BulkSignalR
BiocVersion: 3.21
Package: BulkSignalR
PackageVersion: 0.99.8
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3554/016b50b72d624d8ce75d4729080b05b94d177406/BulkSignalR.BiocCheck
BiocCheckVersion: 1.43.2
sourceDir: /tmp/Rtmp2vFnq3/file10e4ec21c3fdb7/BulkSignalR
installDir: /tmp/Rtmp2vFnq3/file10e4ec48214722
isTarBall: TRUE
platform: unix
Running BiocCheck on BulkSignalR
* 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...
* 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 proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (19%).
* Checking for pinned package versions in DESCRIPTION...
* 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 BulkSignalR...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 53
functions greater than 50 lines.
The longest 5 functions are:
.downstreamRegulatedSignaling() (R/regulatedInference.R): 207 lines
...
getLRIntracellNetwork() (R/networks.R): 173 lines
* Checking man page documentation...
Local "database" is up to date.
Local "resources" are up to date.
* 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...
i Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
i Maintainer is registered at support site.
i Package is in the Support Site Watched Tags.
BiocCheck v1.43.2 results
0 ERRORS | 0 WARNINGS | i 1 NOTES
i See the BulkSignalR.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.