===============================
R CMD BUILD
===============================
* checking for file Pirat/DESCRIPTION ... OK
* preparing Pirat:
* 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
* looking to see if a data/datalist file should be added
* building Pirat_0.99.2.tar.gz
===============================
BiocCheckGitClone('Pirat')
===============================
BiocCheckVersion: 1.39.27
BiocVersion: 3.19
Package: Pirat
PackageVersion: 0.99.2
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3308/58bdb6f28301dd551f1438e58556f00f842ee0e5/Pirat
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...
* 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 results
0 ERRORS | 0 WARNINGS | 1 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory /home/pkgbuild/packagebuilder/workers/jobs/3308/58bdb6f28301dd551f1438e58556f00f842ee0e5/Pirat.Rcheck
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* using option --no-vignettes
* checking for file Pirat/DESCRIPTION ... OK
* checking extension type ... Package
* this is package Pirat 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 ... NOTE
Found the following hidden files and directories:
.github
These were most likely included in error. See section Package
structure in the Writing R Extensions manual.
* checking for portable file names ... WARNING
Found the following file with a non-portable file name:
.github/workflows/R CMD check Bioc.yml
These are not fully portable file names.
See section Package structure in the Writing R Extensions manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package Pirat can be installed ... NOTE
Found the following notes/warnings:
Non-staged installation was used
See /home/pkgbuild/packagebuilder/workers/jobs/3308/58bdb6f28301dd551f1438e58556f00f842ee0e5/Pirat.Rcheck/00install.out for details.
* 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 ... [6s/6s] 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 whether startup messages can be suppressed ... [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 ... [22s/22s] NOTE
estimate_gamma: no visible global function definition for lm
estimate_psi_df: no visible binding for global variable var
estimate_psi_df: no visible binding for global variable x
mod_Pirat_server : <anonymous>: no visible global function definition
for observe
plot_pep_correlations: no visible global function definition for cor
plot_pep_correlations: no visible binding for global variable group
remove_NA_pep_reset: no visible global function definition for
remove_pep_from_idx
Undefined global functions or variables:
cor group lm observe remove_pep_from_idx var x
Consider adding
importFrom("stats", "cor", "lm", "var")
to your NAMESPACE file.
Found the following calls to data() loading into the global environment:
File Pirat/R/mod_Pirat.R:
data(list(peptides_ab = t(assay(obj())), adj = metadata(obj())$adj,
mask_prot_diff = metadata(obj())$mask_prot_diff, mask_pep_diff = metadata(obj())$mask_pep_diff))
See section Good practice in ?data.
* 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 ... [1s/1s] OK
* checking data for ASCII and uncompressed saves ... WARNING
Note: significantly better compression could be obtained
by using R CMD build --resave-data
old_size new_size compress
ropers.RData 2.8Mb 2.2Mb xz
* checking line endings in shell scripts ... OK
* checking files in vignettes ... OK
* checking examples ... [28s/24s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
pipeline_llkimpute 11.744 0.451 8.745
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running test_pirat.R [0s/0s]
[0s/0s] 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 WARNINGs, 3 NOTEs
See
/home/pkgbuild/packagebuilder/workers/jobs/3308/58bdb6f28301dd551f1438e58556f00f842ee0e5/Pirat.Rcheck/00check.log
for details.
===============================
BiocCheck('Pirat_0.99.2.tar.gz')
===============================
BiocCheckVersion: 1.39.27
BiocVersion: 3.19
Package: Pirat
PackageVersion: 0.99.2
sourceDir: /tmp/RtmpC8TGbS/file3196df7329cfbe/Pirat
installDir: /tmp/RtmpC8TGbS/file3196df5e702079
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3308/58bdb6f28301dd551f1438e58556f00f842ee0e5/Pirat.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...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
Bioconductor dependencies found in Imports & Depends (25%).
* Checking for pinned package versions in DESCRIPTION...
* Checking DESCRIPTION/NAMESPACE consistency...
* 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 Pirat...
* Checking coding practice...
* NOTE: Avoid 1:...; use seq_len() or seq_along()
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* NOTE: Avoid using '=' for assignment and use '<-' instead
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2
times)
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 5 functions greater than 50 lines.
* Checking man page documentation...
* NOTE: Consider adding runnable examples to man pages that
document exported objects.
* NOTE: Usage of dontrun{} / donttest{} tags found in man page
examples. 5% of man pages use at least one of these tags.
* 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; 37 lines (2%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 618 lines
(31%) 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 is in the Support Site Watched Tags.
BiocCheck results
0 ERRORS | 0 WARNINGS | 9 NOTES
See the Pirat.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.