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R CMD BUILD
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* checking for file ‘TSSr/DESCRIPTION’ ... OK
* preparing ‘TSSr’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed 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 ‘TSSr_0.99.19.tar.gz’
===============================
BiocCheckGitClone('TSSr')
===============================
── Running Git clone checks on TSSr ────────────────────────────────────────────
* Checking valid files...
* Checking for inst/doc folders...
* Checking DESCRIPTION readability...
* Checking for valid use of maintainer fields...
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2222/TSSr_20260804073429/TSSr.Rcheck’
* using R version 4.6.1 (2026-06-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-08-04 11:37:32 UTC
* using option ‘--no-vignettes’
* checking for file ‘TSSr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TSSr’ version ‘0.99.19’
* 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 ‘TSSr’ 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 ... [12s/12s] OK
* checking whether the package can be loaded with stated dependencies ... [11s/11s] OK
* checking whether the package can be unloaded cleanly ... [12s/12s] OK
* checking whether the namespace can be loaded with stated dependencies ... [12s/12s] OK
* checking whether the namespace can be unloaded cleanly ... [12s/12s] OK
* checking loading without being on the library search path ... [12s/12s] 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 ... [40s/40s] 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [11s/11s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [97s/97s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
consensusCluster 17.846 0.214 18.032
clusterTSS 17.729 0.127 17.756
exportClustersToBed 10.793 0.050 10.844
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [210s/209s]
[210s/210s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
actual$treat[668, ] 2.035203e+00 113548 1
actual$treat$tags != expected$treat$tags but don't know how to show the difference
`actual$treat$q_0.9[134:140]`: 68947 69178 69367 70133 70360 70603 70688
`expected$treat$q_0.9[134:140]`: 68947 69178 69367 70136 70360 70603 70688
actual$treat$interquantile_width[134:140] vs expected$treat$interquantile_width[134:140]
28.0
12.0
1.0
- 123.0
+ 126.0
39.0
172.0
1.0
[ FAIL 1 | WARN 75 | SKIP 0 | PASS 991 ]
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 ... [3s/3s] OK
* DONE
Status: 1 ERROR
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2222/TSSr_20260804073429/TSSr.Rcheck/00check.log’
for details.
===============================
BiocCheck('TSSr_0.99.19.tar.gz')
===============================
── Installing TSSr ─────────────────────────────────────────────────────────────
✔ Package installed successfully
── TSSr session metadata ───────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpomlmBR/file2a2f963060f772/TSSr
→ BiocVersion: 3.23
→ Package: TSSr
→ PackageVersion: 0.99.19
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2222/TSSr_20260804073429/TSSr.BiocCheck
→ BiocCheckVersion: 1.49.30
→ sourceDir: /tmp/RtmpomlmBR/file2a2f963060f772/TSSr
→ installDir: /tmp/RtmpomlmBR/file2a2f965e533df/lib
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on TSSr ───────────────────────────────────────────────────
* 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...
i NOTE: Consider adding these automatically suggested biocViews:
MultipleSequenceAlignment
i Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking if 'Package:' field matches directory / tarball...
* Checking for Version: field...
* Checking DESCRIPTION readability...
* Checking validity of DESCRIPTION fields...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for whitespace in DESCRIPTION field names...
* Checking for proper Description: field...
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (47%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
* Checking NAMESPACE...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of TSSr...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 17
functions greater than 50 lines.
The longest 5 functions are:
• .assign2gene() (R/AnnotationFunctions.R): 118 lines
• ...
• .getTSS_from_bam() (R/ImportFunctions.R): 97 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...
i NOTE: Consider shorter lines; 342 lines (8%) are > 80 characters long.
First few lines:
• R/Aclasses.R#L3 #' TSSr is designed to analyze transcrip ...
• ...
• vignettes/vignette.Rmd#L57 For technical questions, bug reports and ...
i NOTE: Consider multiples of 4 spaces for line indents; 71 lines (2%) are not.
First few lines:
• R/Aclasses.R#L219 inputFiles = character( ...
• ...
• R/ShiftingMethods.R#L38 pval ...
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 'tssr' is already in your 'Watched Tags' on the Support Site.
── BiocCheck v1.49.30 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 4 NOTES
i See the TSSr.BiocCheck folder and run
`browseVignettes(package = 'BiocCheck')`
for details.