===============================
R CMD BUILD
===============================
* checking for file ‘BSgenomeForge/DESCRIPTION’ ... OK
* preparing ‘BSgenomeForge’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘UsingBSgenomeForge.Rmd’ using rmarkdown
Quitting from lines 76-79 (UsingBSgenomeForge.Rmd)
Error: processing vignette 'UsingBSgenomeForge.Rmd' failed with diagnostics:
cannot open URL 'https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/009/729/545/GCA_009729545.1_ASM972954v1/GCA_009729545.1_ASM972954v1_assembly_report.txt'
--- failed re-building ‘UsingBSgenomeForge.Rmd’
SUMMARY: processing the following file failed:
‘UsingBSgenomeForge.Rmd’
Error: Vignette re-building failed.
Execution halted
===============================
R CMD BUILD
===============================
* checking for file ‘BSgenomeForge/DESCRIPTION’ ... OK
* preparing ‘BSgenomeForge’:
* 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
WARNING: directory ‘BSgenomeForge/inst/pkgtemplates/NCBI_BSgenome_datapkg/inst/extdata’ is empty
WARNING: directory ‘BSgenomeForge/inst/pkgtemplates/UCSC_BSgenome_datapkg/inst/extdata’ is empty
* building ‘BSgenomeForge_0.99.2.tar.gz’
===============================
BiocCheckGitClone('BSgenomeForge')
===============================
─ BiocCheckVersion: 1.35.15
─ BiocVersion: 3.17
─ Package: BSgenomeForge
─ PackageVersion: 0.99.2
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2943/bbe059e940e8e09ff6efb8159df2f32636483a79/BSgenomeForge
─ 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/2943/bbe059e940e8e09ff6efb8159df2f32636483a79/BSgenomeForge.Rcheck’
* using R Under development (unstable) (2023-03-16 r83996)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BSgenomeForge/DESCRIPTION’ ... OK
* this is package ‘BSgenomeForge’ version ‘0.99.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'BiocGenerics', 'S4Vectors', 'IRanges', 'GenomeInfoDb', 'Biostrings',
'BSgenome'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘BSgenomeForge’ 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 ... [8s/8s] 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 ... [26s/26s] 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 ... [14s/20s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [11s/18s]
[12s/18s] 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 ... [2s/2s] OK
* DONE
Status: 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2943/bbe059e940e8e09ff6efb8159df2f32636483a79/BSgenomeForge.Rcheck/00check.log’
for details.
===============================
BiocCheck('BSgenomeForge_0.99.2.tar.gz')
===============================
─ BiocCheckVersion: 1.35.15
─ BiocVersion: 3.17
─ Package: BSgenomeForge
─ PackageVersion: 0.99.2
─ sourceDir: /tmp/RtmpmkU50G/file1af3931d40d01/BSgenomeForge
─ installDir: /tmp/RtmpmkU50G/file1af3932e7bfee
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2943/bbe059e940e8e09ff6efb8159df2f32636483a79/BSgenomeForge.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...
* NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R'
with 'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* 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.
6 code chunks / 12 total = 50% percent unevaluated
3 non-exec code chunks (e.g., '``` r')
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of BSgenomeForge...
* 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 2 functions greater than 50 lines.
* 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; 3 lines (0%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 230 lines
(17%) 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 BSgenomeForge.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.