===============================
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_0.99.6.tar.gz’
===============================
BiocCheckGitClone('CustomGenome')
===============================
─ BiocCheckVersion: 1.39.5
─ BiocVersion: 3.19
─ Package: CustomGenome
─ PackageVersion: 0.99.6
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3224/1d973511bf3aa102b4e5d390c63a4b2bf0b18ffa/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/3224/1d973511bf3aa102b4e5d390c63a4b2bf0b18ffa/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 ‘0.99.6’
* 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 ... [9s/9s] OK
* checking loading without being on the library search path ... [9s/9s] 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 ... [30s/30s] 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 files in ‘vignettes’ ... OK
* checking examples ... [13s/14s] ERROR
Running examples in ‘CustomGenome-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: check_sum_matches
> ### Title: Compute Unix checksums for downloaded genome files
> ### Aliases: check_sum_matches
>
> ### ** Examples
>
> get_genome_files(fasta_type = "dna_rm.nonchromosomal",
+ gtf_type = "abinitio.gtf", output_folder = tempdir())
Downloading: Mus_musculus.GRCm39.105.abinitio.gtf.gz
http://ftp.ensembl.org/pub/release-105/gtf/mus_musculus/Mus_musculus.GRCm39.105.abinitio.gtf.gz
/tmp/RtmpYo9tjx/Mus_musculus.GRCm39.105.abinitio.gtf.gz
--2023-12-27 17:33:35-- http://ftp.ensembl.org/pub/release-105/gtf/mus_musculus/Mus_musculus.GRCm39.105.abinitio.gtf.gz
Resolving ftp.ensembl.org (ftp.ensembl.org)... 193.62.193.169
Connecting to ftp.ensembl.org (ftp.ensembl.org)|193.62.193.169|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 110 [application/x-gzip]
Saving to: ‘/tmp/RtmpYo9tjx/Mus_musculus.GRCm39.105.abinitio.gtf.gz’
0K 100% 24.6M=0s
2023-12-27 17:33:36 (24.6 MB/s) - ‘/tmp/RtmpYo9tjx/Mus_musculus.GRCm39.105.abinitio.gtf.gz’ saved [110/110]
Downloading: /tmp/RtmpYo9tjx/Mus_musculus.GRCm39.105.abinitio.gtf.gz.sum
trying URL 'http://ftp.ensembl.org/pub/release-105/gtf/mus_musculus/CHECKSUMS'
Content type 'unknown' length 161 bytes
==================================================
downloaded 161 bytes
Writing:/tmp/RtmpYo9tjx/Mus_musculus.GRCm39.105.abinitio.gtf.gz.sum
Error in res_split[[3]] : subscript out of bounds
Calls: get_genome_files -> check_sum_matches -> parse_check_sum
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [56s/56s]
[56s/56s] OK
* 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 ... [3s/3s] OK
* DONE
Status: 1 ERROR
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3224/1d973511bf3aa102b4e5d390c63a4b2bf0b18ffa/CustomGenome.Rcheck/00check.log’
for details.
===============================
BiocCheck('CustomGenome_0.99.6.tar.gz')
===============================
─ BiocCheckVersion: 1.39.5
─ BiocVersion: 3.19
─ Package: CustomGenome
─ PackageVersion: 0.99.6
─ sourceDir: /tmp/RtmpgYbdbe/file3340fb29910561/CustomGenome
─ installDir: /tmp/RtmpgYbdbe/file3340fb5686b6de
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3224/1d973511bf3aa102b4e5d390c63a4b2bf0b18ffa/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...
* NOTE: Consider adding runnable examples to man pages that
document exported objects.
* 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; 32 lines (2%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 59 lines
(3%) 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 | 4 NOTES
See the CustomGenome.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.