===============================
R CMD BUILD
===============================
* checking for file ‘DeepTarget/DESCRIPTION’ ... OK
* preparing ‘DeepTarget’:
* 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 ‘DeepTarget_0.99.16.tar.gz’
===============================
BiocCheckGitClone('DeepTarget')
===============================
─ BiocCheckVersion: 1.39.26
─ BiocVersion: 3.19
─ Package: DeepTarget
─ PackageVersion: 0.99.16
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3066/4cb8f40f5826bd256739e289dfa79130d0f63e13/DeepTarget
─ 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/3066/4cb8f40f5826bd256739e289dfa79130d0f63e13/DeepTarget.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 ‘DeepTarget/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DeepTarget’ version ‘0.99.16’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://bioconductor.org/packages/3.19/bioc/src/contrib:
cannot open URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.19/data/annotation/src/contrib:
cannot open URL 'https://bioconductor.org/packages/3.19/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.19/data/experiment/src/contrib:
cannot open URL 'https://bioconductor.org/packages/3.19/data/experiment/src/contrib/PACKAGES'
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 ‘DeepTarget’ 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 ... [7s/7s] OK
* checking whether the package can be loaded with stated dependencies ... [6s/6s] OK
* checking whether the package can be unloaded cleanly ... [6s/6s] OK
* checking whether the namespace can be loaded with stated dependencies ... [6s/6s] OK
* checking whether the namespace can be unloaded cleanly ... [6s/6s] OK
* checking loading without being on the library search path ... [6s/6s] 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 ... [21s/21s] NOTE
Depmap2DeepTarget: no visible global function definition for ‘dmsets’
Depmap2DeepTarget: no visible global function definition for ‘dmfiles’
Depmap2DeepTarget: no visible binding for global variable ‘dataset_id’
Depmap2DeepTarget: no visible binding for global variable ‘name’
Undefined global functions or variables:
dataset_id dmfiles dmsets name
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [0s/0s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
TIMEOUT: R CMD check exceeded 15 mins
===============================
BiocCheck('DeepTarget_0.99.16.tar.gz')
===============================
─ BiocCheckVersion: 1.39.26
─ BiocVersion: 3.19
─ Package: DeepTarget
─ PackageVersion: 0.99.16
─ sourceDir: /tmp/RtmpJsnW6G/file3281b63fd3b84a/DeepTarget
─ installDir: /tmp/RtmpJsnW6G/file3281b6f3920ce
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3066/4cb8f40f5826bd256739e289dfa79130d0f63e13/DeepTarget.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* Checking for deprecated package usage...
Warning in file(con, "r") :
cannot open URL 'https://bioconductor.org/config.yaml': HTTP status was '502 Bad Gateway'
Warning in file(con, "r") :
cannot open URL 'https://bioconductor.org/config.yaml': HTTP status was '502 Bad Gateway'
adding rname 'https://bioconductor.org/checkResults/Bioconductor version cannot be validated; no internet connection?
See #troubleshooting section in vignette/bioc-LATEST/meat-index.dcf'
Warning: download failed
web resource path: ‘https://bioconductor.org/checkResults/Bioconductor version cannot be validated; no internet connection?
See #troubleshooting section in vignette/bioc-LATEST/meat-index.dcf’
local file path: ‘/home/pkgbuild/.cache/R/BiocCheck/3281b62e5d16e6_meat-index.dcf’
reason: URL using bad/illegal format or missing URL
Warning: bfcadd() failed; resource removed
rid: BFC5
fpath: ‘https://bioconductor.org/checkResults/Bioconductor version cannot be validated; no internet connection?
See #troubleshooting section in vignette/bioc-LATEST/meat-index.dcf’
reason: download failed
Warning in value[[3L]](cond) :
trying to add rname 'https://bioconductor.org/checkResults/Bioconductor version cannot be validated; no internet connection?
See #troubleshooting section in vignette/bioc-LATEST/meat-index.dcf' produced error:
bfcadd() failed; see warnings()
Error in bfcrpath(bfc, rnames = url, exact = TRUE, download = TRUE, rtype = "web") :
not all 'rnames' found or unique.
Calls: BiocCheck ... get_deprecated_status -> get_status_file_cache -> bfcrpath -> bfcrpath
Execution halted