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R CMD BUILD
===============================
* checking for file ‘drugfindR/DESCRIPTION’ ... OK
* preparing ‘drugfindR’:
* 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
Omitted ‘LazyData’ from DESCRIPTION
* building ‘drugfindR_0.99.654.tar.gz’
===============================
BiocCheckGitClone('drugfindR')
===============================
─ BiocCheckVersion: 1.41.2
─ BiocVersion: 3.20
─ Package: drugfindR
─ PackageVersion: 0.99.654
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3151/5248ea9cb787e12febd79b046bdac1f8c103167d/drugfindR
─ 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...
* NOTE: (Optional) CITATION file not found. Only include a CITATION
file if there is a preprint or publication for this Bioconductor
package. Note that Bioconductor packages are not required to have
a CITATION file but it is useful both for users and for tracking
Bioconductor project-wide metrics. When including a CITATION
file, add the publication using the 'doi' argument of
'bibentry()'.
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 1 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3151/5248ea9cb787e12febd79b046bdac1f8c103167d/drugfindR.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* 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 ‘drugfindR/DESCRIPTION’ ... OK
* this is package ‘drugfindR’ version ‘0.99.654’
* 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 ‘drugfindR’ 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 ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/1s] 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 ... [5s/5s] OK
* checking Rd files ... [0s/0s] 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [2s/2s] ERROR
Running examples in ‘drugfindR-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: consensusConcordants
> ### Title: Generate a Consensus list of Targets *[Experimental]*
> ### Aliases: consensusConcordants
>
> ### ** Examples
>
> # Get the L1000 signature for LINCSKD_28
> kdSignature <- getSignature("LINCSKD_28")
>
> # Get concordant gene knockdown signatures
> concordantSignatures <- getConcordants(kdSignature, ilincsLibrary = "KD")
Error in getConcordants(kdSignature, ilincsLibrary = "KD") :
signature must be a data frame or data frame like object
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [10s/21s]
[10s/22s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(drugfindR)
>
> test_check("drugfindR")
Starting 2 test processes
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 79 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-get_signature.R:32:5'): correct content for the knockdown signature ──
`validSignature` (`actual`) not equal to exampleSignature() (`expected`).
`actual` is an S4 object of class <DFrame>
`expected` is an S3 object of class <tbl_df/tbl/data.frame>, a list
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 79 ]
Error: Test failures
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/2s] OK
* DONE
Status: 2 ERRORs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3151/5248ea9cb787e12febd79b046bdac1f8c103167d/drugfindR.Rcheck/00check.log’
for details.
===============================
BiocCheck('drugfindR_0.99.654.tar.gz')
===============================
─ BiocCheckVersion: 1.41.2
─ BiocVersion: 3.20
─ Package: drugfindR
─ PackageVersion: 0.99.654
─ sourceDir: /tmp/RtmpJwutz8/file2530b12a9bc009/drugfindR
─ installDir: /tmp/RtmpJwutz8/file2530b17d0f6a8d
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3151/5248ea9cb787e12febd79b046bdac1f8c103167d/drugfindR.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...
* 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 (9%).
* 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 drugfindR...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 4 functions greater than 50 lines.
* Checking man page documentation...
* NOTE: Consider adding runnable examples to man pages that
document exported objects.
* NOTE: Usage of dontrun{} / donttest{} tags found in man page
examples. 11% of man pages use at least one of these tags.
* 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 | 3 NOTES
See the drugfindR.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.