===============================
R CMD BUILD
===============================
* checking for file iscream/DESCRIPTION ... OK
* preparing iscream:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* running cleanup
* installing the package to build vignettes
* creating vignettes ... OK
* cleaning src
* running cleanup
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building iscream_0.99.5.tar.gz
===============================
BiocCheckGitClone('iscream')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3877/2aac56205878ba39f14d6a39a2c9f45adce65a43/iscream
BiocVersion: 3.22
Package: iscream
PackageVersion: 0.99.5
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3877/2aac56205878ba39f14d6a39a2c9f45adce65a43/iscream.BiocCheck
BiocCheckVersion: 1.45.18
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3877/2aac56205878ba39f14d6a39a2c9f45adce65a43/iscream
installDir: NULL
isTarBall: FALSE
platform: unix
* Checking valid files...
* Checking individual file sizes...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking NAMESPACE...
* 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 v1.45.18 results
0 ERRORS | 0 WARNINGS | i 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory /home/pkgbuild/packagebuilder/workers/jobs/3877/2aac56205878ba39f14d6a39a2c9f45adce65a43/iscream.Rcheck
* using R version 4.5.1 (2025-06-13)
* 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 24.04.3 LTS
* using session charset: UTF-8
* using option --no-vignettes
* checking for file iscream/DESCRIPTION ... OK
* this is package iscream version 0.99.5
* 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 ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section Package
structure in the Writing R Extensions manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package iscream can be installed ... OK
* used C++ compiler: g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* checking C++ specification ... OK
* checking installed package size ... INFO
installed size is 20.2Mb
sub-directories of 1Mb or more:
libs 19.8Mb
* 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 ... [2s/2s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/1s] OK
* checking whether startup messages can be suppressed ... [1s/1s] 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 ... [12s/17s] OK
* checking Rd files ... [1s/1s] 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 line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... NOTE
Compilation used the following non-portable flag(s):
-Werror=format-security
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in vignettes ... OK
* checking examples ... [9s/9s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [14s/14s]
[14s/14s] OK
* 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: 3 NOTEs
See
/home/pkgbuild/packagebuilder/workers/jobs/3877/2aac56205878ba39f14d6a39a2c9f45adce65a43/iscream.Rcheck/00check.log
for details.
===============================
BiocCheck('iscream_0.99.5.tar.gz')
===============================
Installing iscream
Package installed successfully
iscream session metadata
sourceDir: /tmp/Rtmpetbq2L/filea8c5b2976c92a/iscream
BiocVersion: 3.22
Package: iscream
PackageVersion: 0.99.5
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3877/2aac56205878ba39f14d6a39a2c9f45adce65a43/iscream.BiocCheck
BiocCheckVersion: 1.45.18
sourceDir: /tmp/Rtmpetbq2L/filea8c5b2976c92a/iscream
installDir: /tmp/Rtmpetbq2L/filea8c5b6d036a1a
isTarBall: TRUE
platform: unix
Running BiocCheck on iscream
* 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 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...
! WARNING: No Bioconductor dependencies detected. Note that some infrastructure
packages may not have Bioconductor dependencies. For more information, reach
out to the Bioconductor community and/or consider a CRAN submission.
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
* Checking NAMESPACE...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
! WARNING: Evaluate more vignette chunks.
i 96 out of 124 code chunks = 77% unevaluated
i 93 non-exec code chunk(s) (e.g., '```r')
i NOTE: Vignette(s) found with missing chunk labels
Found in files:
data_structures.Rmd
htslib.rmd
iscream.Rmd
i NOTE: 'sessionInfo' not found in vignette(s)
Missing from file(s):
vignettes/htslib.rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of iscream...
* Checking coding practice...
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
tabix.R (line 205, column 44)
tabix.R (line 258, column 18)
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
suppressWarnings() in R/tabix.R (line 135, column 13)
* 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:
summarize_meth_regions() (R/summarize_meth_regions.R): 65 lines
summarize_regions() (R/summarize_regions.R): 60 lines
make_bsseq_mat() (R/make_bsseq_mat.R): 52 lines
* Checking man page documentation...
i NOTE: Usage of dontrun / donttest tags found in man page examples. 10% of man
pages use at least one of these tags.
Found in files:
make_bsseq_mat.Rd
set_threads.Rd
i NOTE: Use donttest instead of dontrun.
Found in files:
make_bsseq_mat.Rd
set_threads.Rd
* 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; 88 lines (3%) are > 80 characters long.
First few lines:
R/make_bsseq_mat.R#L5 #' `"iscream.threads"` option. The outpu ...
...
vignettes/TSS.Rmd#L275 ## BLAS/LAPACK: /nix/store/yf6dpab0gcjr9 ...
i NOTE: Consider multiples of 4 spaces for line indents; 486 lines (16%) are
not.
First few lines:
R/log.R#L21 n_threads <- get_threads()["use_thread ...
...
vignettes/TSS.Rmd#L253 labs(x = "Sample") ...
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 v1.45.18 results
0 ERRORS | 2 WARNINGS | i 9 NOTES
i See the iscream.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.