===============================
R CMD BUILD
===============================
* checking for file HiCParser/DESCRIPTION ... OK
* preparing HiCParser:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
WARNING: directory HiCParser/pkgdown is empty
* building HiCParser_0.99.3.tar.gz
===============================
BiocCheckGitClone('HiCParser')
===============================
sourceDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3498/7bc27ccdf740804daf0555cf74602cbc5266ffef/HiCParser
BiocVersion: 3.20
Package: HiCParser
PackageVersion: 0.99.3
BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3498/7bc27ccdf740804daf0555cf74602cbc5266ffef/HiCParser.BiocCheck
BiocCheckVersion: 1.43.1
sourceDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3498/7bc27ccdf740804daf0555cf74602cbc5266ffef/HiCParser
installDir: NULL
isTarBall: FALSE
platform: unix
* Checking valid files...
Warning in readLines(gitignore) :
incomplete final line found on '/media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3498/7bc27ccdf740804daf0555cf74602cbc5266ffef/HiCParser/.gitignore'
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
! WARNING: Unable to read CITATION file with 'utils::readCitationFile()'
BiocCheck v1.43.1 results
0 ERRORS | 1 WARNINGS | 0 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3498/7bc27ccdf740804daf0555cf74602cbc5266ffef/HiCParser.Rcheck
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* using option --no-vignettes
* checking for file HiCParser/DESCRIPTION ... OK
* checking extension type ... Package
* this is package HiCParser version 0.99.3
* 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 HiCParser can be installed ... OK
* used C++ compiler: g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* 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 ... [6s/6s] OK
* checking whether the package can be loaded with stated dependencies ... [6s/6s] OK
* checking whether the package can be unloaded cleanly ... [6s/6s] OK
* checking whether the namespace can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the namespace can be unloaded cleanly ... [6s/6s] OK
* checking loading without being on the library search path ... [6s/6s] 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 ... [21s/21s] NOTE
.parseOneCool: no visible binding for global variable start
.parseOneCool: no visible binding for global variable end
.parseOneCool: no visible binding for global variable chromosome
.parseOneCool: no visible binding for global variable index
.parseOneCool: no visible binding for global variable id1
.parseOneCool: no visible binding for global variable id2
.parseOneHiCPro: no visible binding for global variable chromosome
.parseOneHiCPro: no visible binding for global variable start
.parseOneHiCPro: no visible binding for global variable end
.parseOneHiCPro: no visible binding for global variable index
.parseOneHiCPro: no visible binding for global variable startIndex
.parseOneHiCPro: no visible binding for global variable stopIndex
.setFromTabular: no visible binding for global variable chromosome
.setFromTabular: no visible binding for global variable position 1
.setFromTabular: no visible binding for global variable position 2
.setFromTabular: no visible global function definition for .
.setFromTabular: no visible binding for global variable bin.1
.setFromTabular: no visible binding for global variable bin.2
.setFromTabular: no visible binding for global variable variable
.setFromTabular: no visible binding for global variable indexC
.setFromTabular: no visible binding for global variable index
.setFromTabular: no visible binding for global variable end
.setFromTabular: no visible binding for global variable start
Undefined global functions or variables:
. bin.1 bin.2 chromosome end id1 id2 index indexC position 1 position
2 start startIndex stopIndex variable
Consider adding
importFrom("stats", "end", "start")
to your NAMESPACE file.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in vignettes ... OK
* checking examples ... [12s/12s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [10s/10s]
[10s/10s] 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: 2 NOTEs
See
/media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3498/7bc27ccdf740804daf0555cf74602cbc5266ffef/HiCParser.Rcheck/00check.log
for details.
===============================
BiocCheck('HiCParser_0.99.3.tar.gz')
===============================
Installing HiCParser
Package installed successfully
HiCParser session metadata
sourceDir: /tmp/RtmpfOCeZB/file988443d11fc3f/HiCParser
BiocVersion: 3.20
Package: HiCParser
PackageVersion: 0.99.3
BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3498/7bc27ccdf740804daf0555cf74602cbc5266ffef/HiCParser.BiocCheck
BiocCheckVersion: 1.43.1
sourceDir: /tmp/RtmpfOCeZB/file988443d11fc3f/HiCParser
installDir: /tmp/RtmpfOCeZB/file988442b66b41d
isTarBall: TRUE
platform: unix
Running BiocCheck on HiCParser
* 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...
i NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with
'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (60%).
* Checking for pinned package versions in DESCRIPTION...
* 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 HiCParser...
* 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 2
functions greater than 50 lines.
The longest 5 functions are:
.setFromTabular() (R/tabularParsers.R): 139 lines
.parseOneCool() (R/coolParser.R): 59 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; 2 lines (0%) are > 80 characters long.
First few lines:
vignettes/HiCParser.Rmd#L40 `r BiocStyle::Biocpkg("HiCParser")` is b ...
vignettes/HiCParser.Rmd#L359 Lun ATL, Perry M and Ing-Simmons E (2016 ...
i NOTE: Consider multiples of 4 spaces for line indents; 1 lines (0%) are not.
First few lines:
vignettes/HiCParser.Rmd#L360 for Hi-C, ChIA-PET and related experim ...
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 v1.43.1 results
0 ERRORS | 0 WARNINGS | 4 NOTES
i See the HiCParser.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.