===============================
R CMD BUILD
===============================
* checking for file omXplore/DESCRIPTION ... OK
* preparing omXplore:
* 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 omXplore_0.99.3.tar.gz
===============================
BiocCheckGitClone('omXplore')
===============================
BiocCheckVersion: 1.39.27
BiocVersion: 3.19
Package: omXplore
PackageVersion: 0.99.3
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3347/053cd207de0758b2c5fce050415a701a47fe3356/omXplore
platform: unix
isTarBall: FALSE
* Checking valid files...
* ERROR: System files found that should not be Git tracked.
omXplore.Rproj
* 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...
* Checking that provided CITATION file is correctly formatted...
* WARNING: The 'doi' argument is missing or empty in the CITATION's
'bibentry()'. Only include a CITATION file if there is a preprint
or publication associated with this Bioconductor package.
BiocCheck results
1 ERRORS | 1 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory /home/pkgbuild/packagebuilder/workers/jobs/3347/053cd207de0758b2c5fce050415a701a47fe3356/omXplore.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 omXplore/DESCRIPTION ... OK
* checking extension type ... Package
* this is package omXplore 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 ... 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 ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package omXplore 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 ... [14s/14s] OK
* checking whether the package can be loaded with stated dependencies ... [13s/13s] OK
* checking whether the package can be unloaded cleanly ... [13s/13s] OK
* checking whether the namespace can be loaded with stated dependencies ... [13s/13s] OK
* checking whether the namespace can be unloaded cleanly ... [13s/13s] OK
* checking loading without being on the library search path ... [14s/14s] OK
* checking whether startup messages can be suppressed ... [14s/14s] 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 ... [47s/47s] NOTE
Build_X_CC: no visible global function definition for metadata
Build_X_CC: no visible global function definition for metadata<-
Check_MSnSet_Consistency : <anonymous>: no visible global function
definition for experimentData
MAE_Compatibility_with_Prostar_1x : <anonymous>: no visible binding for
global variable .colData
SE_Compatibility_with_Prostar_1.x: no visible global function
definition for experimentData
SE_Compatibility_with_Prostar_1.x: no visible global function
definition for metadata
SE_Compatibility_with_Prostar_1.x: no visible global function
definition for metadata<-
Undefined global functions or variables:
.colData experimentData metadata metadata<-
Found the following assignments to the global environment:
File omXplore/R/modules.R:
assign(f_dest_name, eval(parse(text = f_fullname)), envir = globalenv())
* 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 ... WARNING
Undocumented arguments in Rd file 'accessors.Rd'
slot.name
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter Writing R documentation files in the Writing R
Extensions manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of data directory ... OK
* checking data for non-ASCII characters ... [8s/8s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in vignettes ... OK
* checking examples ... [34s/34s] ERROR
Running examples in omXplore-Ex.R failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pkgs.require
> ### Title: Loads packages
> ### Aliases: pkgs.require
>
> ### ** Examples
>
> pkgs.require('DAPAR')
Error in FUN(X[[i]], ...) :
Please install DAPAR: BiocManager::install('DAPAR')
Calls: pkgs.require -> lapply -> FUN
Execution halted
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [13s/13s]
[13s/13s] 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: 1 ERROR, 1 WARNING, 2 NOTEs
See
/home/pkgbuild/packagebuilder/workers/jobs/3347/053cd207de0758b2c5fce050415a701a47fe3356/omXplore.Rcheck/00check.log
for details.
===============================
BiocCheck('omXplore_0.99.3.tar.gz')
===============================
BiocCheckVersion: 1.39.27
BiocVersion: 3.19
Package: omXplore
PackageVersion: 0.99.3
sourceDir: /tmp/RtmpCxoVso/file14d2cb6bf22142/omXplore
installDir: /tmp/RtmpCxoVso/file14d2cb2a66479d
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3347/053cd207de0758b2c5fce050415a701a47fe3356/omXplore.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 (15%).
* 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 omXplore...
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* NOTE: Avoid the use of 'paste' in condition signals
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 32 functions greater than 50 lines.
* Checking man page documentation...
Registered S3 method overwritten by 'quantmod':
method from
as.zoo.data.frame zoo
* NOTE: Consider adding runnable examples to man pages that
document exported objects.
* NOTE: Usage of dontrun{} / donttest{} tags found in man page
examples. 6% 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; 70 lines (1%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 2417 lines
(27%) 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 | 8 NOTES
See the omXplore.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.