===============================
R CMD BUILD
===============================
* checking for file ‘CustomGenome/DESCRIPTION’ ... OK
* preparing ‘CustomGenome’:
* 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
* building ‘CustomGenome_0.99.4.tar.gz’
===============================
BiocCheckGitClone('CustomGenome')
===============================
─ BiocCheckVersion: 1.39.5
─ BiocVersion: 3.19
─ Package: CustomGenome
─ PackageVersion: 0.99.4
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3224/4ad4318a3cef1df2d87ea278507046de3e0a0851/CustomGenome
─ 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...
─ 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/3224/4ad4318a3cef1df2d87ea278507046de3e0a0851/CustomGenome.Rcheck’
* using R Under development (unstable) (2023-11-11 r85510)
* 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 22.04.3 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CustomGenome/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CustomGenome’ version ‘0.99.4’
* 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 serialization versions ... OK
* checking whether package ‘CustomGenome’ 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [9s/9s] OK
* checking whether the package can be loaded with stated dependencies ... [9s/9s] OK
* checking whether the package can be unloaded cleanly ... [9s/9s] OK
* checking whether the namespace can be loaded with stated dependencies ... [9s/9s] OK
* checking whether the namespace can be unloaded cleanly ... [10s/10s] OK
* checking loading without being on the library search path ... [10s/10s] 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 ... [34s/34s] OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘add_seqs_to_gtf_and_fasta’ ‘generate_count_matrix’
‘get_genome_files’ ‘perform_alignment’ ‘prime_fastq_files’
‘retrieve_index’ ‘summarize_alignment’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... NONE
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [58s/60s]
[59s/60s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
\\============================================================================//
Counting : finished
Stats written to: /tmp/RtmpQCInjk-stats/count.exon.gene_id.stats.tsv
Counts written to: /tmp/RtmpQCInjk-counts/exon.gene_id.matrix.tsv
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 28 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-custom_genome.r:56:3'): get_genome_files ───────────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `res_split[[3]]`: subscript out of bounds
Backtrace:
▆
1. ├─testthat::capture_messages(...) at test-custom_genome.r:56:3
2. │ └─base::withCallingHandlers(...)
3. └─CustomGenome::get_genome_files(...)
4. └─CustomGenome:::check_sum_matches(urls$gtf, outfile$gtf)
5. └─CustomGenome (local) parse_check_sum(system(paste0("sum ", outfile), intern = TRUE))
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 28 ]
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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... [2s/2s] OK
* DONE
Status: 1 ERROR, 1 WARNING
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3224/4ad4318a3cef1df2d87ea278507046de3e0a0851/CustomGenome.Rcheck/00check.log’
for details.
===============================
BiocCheck('CustomGenome_0.99.4.tar.gz')
===============================
─ BiocCheckVersion: 1.39.5
─ BiocVersion: 3.19
─ Package: CustomGenome
─ PackageVersion: 0.99.4
─ sourceDir: /tmp/RtmprGHX7q/file2a5757679b0d9e/CustomGenome
─ installDir: /tmp/RtmprGHX7q/file2a575773eae8f5
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3224/4ad4318a3cef1df2d87ea278507046de3e0a0851/CustomGenome.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 recommeded fields in DESCRIPTION...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* WARNING: Evaluate more vignette chunks.
10 out of 13 code chunks = 76% unevaluated
10 non-exec code chunk(s) (e.g., '```r')
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of CustomGenome...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1
times)
* 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...
* NOTE: Consider shorter lines; 24 lines (2%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 59 lines
(5%) are not.
See https://contributions.bioconductor.org/r-code.html
See styler package: https://cran.r-project.org/package=styler as
described in the BiocCheck vignette.
* 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 name is in support site watched tags.
─ BiocCheck results ──
0 ERRORS | 1 WARNINGS | 3 NOTES
See the CustomGenome.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.