===============================
R CMD BUILD
===============================
* checking for file ‘igblastr/DESCRIPTION’ ... OK
* preparing ‘igblastr’:
* 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 ‘igblastr_0.99.2.tar.gz’
===============================
BiocCheckGitClone('igblastr')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3788/igblastr_20250501155058/igblastr
→ BiocVersion: 3.21
→ Package: igblastr
→ PackageVersion: 0.99.2
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3788/igblastr_20250501155058/igblastr.BiocCheck
→ BiocCheckVersion: 1.45.3
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3788/igblastr_20250501155058/igblastr
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
! WARNING: System files in '/inst' should not be Git tracked.
• inst/extdata/ncbi_igblast_data_files/optional_file/human_gl.aux
• ...
• inst/extdata/ncbi_igblast_data_files/optional_file/rhesus_monkey_gl.aux
* Checking individual file sizes...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
i 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 v1.45.3 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 1 WARNINGS | i 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3788/igblastr_20250501155058/igblastr.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘igblastr/DESCRIPTION’ ... OK
* this is package ‘igblastr’ version ‘0.99.2’
* 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 ‘igblastr’ 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 ... [3s/3s] OK
* checking whether the package can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the package can be unloaded cleanly ... [3s/3s] OK
* checking whether the namespace can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the namespace can be unloaded cleanly ... [3s/3s] OK
* checking loading without being on the library search path ... [3s/3s] OK
* checking whether startup messages can be suppressed ... [3s/3s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘jsonlite:::simplifyDataFrame’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [15s/15s] 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 ... [58s/34s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
igblastn 44.330 0.264 12.937
OAS-utils 0.798 0.048 5.315
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [7s/10s]
[7s/10s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
_AIRR.mouse.LEWES_EiJ.IGH+IGK+IGL.202501 169 11 22
_AIRR.mouse.MSM_MsJ.IGH+IGK+IGL.202501 172 9 22
_AIRR.mouse.NOD_ShiLtJ.IGH+IGK+IGL.202501 149 9 22
_AIRR.mouse.PWD_PhJ.IGH+IGK+IGL.202501 184 10 22
IMGT-202506-1.Homo_sapiens.IGH+IGK+IGL 700 47 34
IMGT-202506-1.Mus_musculus.IGH+IGK+IGL 862 61 27
[ FAIL 1 | WARN 0 | SKIP 1 | PASS 170 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test-precompiled-igblast-utils.R:1:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-igblastn.R:28:9'): igblastn() ──────────────────────────────────
Error in `.check_ncores(cores)`: 4 simultaneous processes spawned
Backtrace:
▆
1. └─parallel::mclapply(1:10, function(i) igblastn(query[i]), mc.cores = 4) at test-igblastn.R:28:9
2. └─parallel:::.check_ncores(cores)
[ FAIL 1 | WARN 0 | SKIP 1 | PASS 170 ]
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 ... [5s/4s] OK
* DONE
Status: 1 ERROR, 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3788/igblastr_20250501155058/igblastr.Rcheck/00check.log’
for details.
===============================
BiocCheck('igblastr_0.99.2.tar.gz')
===============================
── Installing igblastr ─────────────────────────────────────────────────────────
✔ Package installed successfully
── igblastr session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp4eYIaf/file4b6645caf4b26/igblastr
→ BiocVersion: 3.21
→ Package: igblastr
→ PackageVersion: 0.99.2
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3788/igblastr_20250501155058/igblastr.BiocCheck
→ BiocCheckVersion: 1.45.3
→ sourceDir: /tmp/Rtmp4eYIaf/file4b6645caf4b26/igblastr
→ installDir: /tmp/Rtmp4eYIaf/file4b66469212c80
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on igblastr ───────────────────────────────────────────────
* 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...
i NOTE: Update R version dependency from 4.4.0 to 4.5.0
* 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...
i NOTE: Consider adding these automatically suggested biocViews: Sequencing,
Alignment, SequenceMatching, DataImport
i Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (27%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
i NOTE: Vignette(s) found with missing chunk labels
Found in files:
• igblastr_overview.Rmd
✖ ERROR: Installation calls found in vignette(s)
Found in files:
• vignettes/igblastr_overview.Rmd (code line 17, column 5)
• vignettes/igblastr_overview.Rmd (code line 37, column 1)
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of igblastr...
* Checking coding practice...
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• db-utils.R (line 24, column 15)
• outfmt7-utils.R (line 320, column 64)
• outfmt7-utils.R (line 322, column 63)
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
• print() in R/db-utils.R (line 390, column 5)
• print() in R/utils.R (line 295, column 5)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
• R/auxiliary-data-utils.R (line 68, column 19)
• ...
• R/igblastn.R (line 353, column 19)
! WARNING: .Deprecated / .Defunct usage (found 2 times)
• .Deprecated() in R/long_to_wide_airr.R (line 12, column 5)
• .Deprecated() in R/long_to_wide_airr.R (line 69, column 5)
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 14 times)
• suppressWarnings() in R/file-utils.R (line 137, column 19)
• ...
• suppressWarnings() in R/utils.R (line 257, column 16)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 3
functions greater than 50 lines.
The longest 5 functions are:
• igblastn() (R/igblastn.R): 71 lines
• .copy_dir() (R/file-utils.R): 67 lines
• long_to_wide_airr() (R/long_to_wide_airr.R): 56 lines
* Checking man page documentation...
* Checking package NEWS...
i NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
i NOTE: Consider shorter lines; 2 lines (0%) are > 80 characters long.
First few lines:
• R/AIRR-utils.R#L11 ### https://wordpress.vdjbase.org/inde ...
• vignettes/igblastr_overview.Rmd#L251 query <- system.file(package="igblastr",
...
i NOTE: Consider 4 spaces instead of tabs; 2 lines (0%) contain tabs.
First few lines:
• R/cache-utils.R#L45 stop(wmsg("'which' must be one of ", ...
• R/igblast_info.R#L77 .IGBLAST_VERSION_cache[[cmdpath]] <- ra ...
i NOTE: Consider multiples of 4 spaces for line indents; 825 lines (11%) are
not.
First few lines:
• R/AIRR-utils.R#L85 release_version="published" ...
• ...
• vignettes/igblastr_overview.Rmd#L391 Open Germline Reference Database. ...
i See https://contributions.bioconductor.org/r-code.html
i 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...
i Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
i Maintainer is registered at support site.
i Package is in the Support Site Watched Tags.
── BiocCheck v1.45.3 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 1 WARNINGS | i 12 NOTES
i See the igblastr.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.